psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.64.0_rc2 of psi-ms.obo

[Jones, A. <And...@li...>]

Hi Gerhard,


Sorry my previous email on this topic perhaps wasn't clear. I don't think we can obsolete the neutral loss terms because they are still needed for mzIdentML 1.1 - which will not be able to incorporate split terms, due to 1..1 cardinality on the relevant CvParam element.

Can we roll back this change for now, until we decide how to handle this issue.

Best wishes
Andy

-----Original Message-----
From: Gerhard Mayer [mailto:may...@ru...] 
Sent: 07 May 2014 12:18
To: psi...@li...; psi...@li...; psi...@li...
Subject: [Psidev-ms-vocab] Release candidate 3.64.0_rc2 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.64.0_rc2 of the psi-ms.obo file.

It contains new terms for mzTab, for specifying the neutral losses, for collision-induced dissociation and for PeptideShaker.

The neutral losses are now defined as terms independently from the ions in order to decouple the two concepts ion and neutral loss from each other.
The old neutral loss terms are now obsoleted.

Furthermore some terms from the purgatory branch are now obsolete.
In addition I corrected some spelling errors in definitions.


Changed CV terms in version 3.64.0_rc2 of psi-ms.obo:
=====================================================
************ The following terms from the purgatory branch are now
obsoleted:
MS:1000329 linked scan
MS:1000268 mass spectrometry
MS:1000013 resolution type
MS:1000020 scanning method
MS:1000459 spectrum instrument description

************ The following neutral loss terms are now obsoleted:
MS:1001148 a ion-H2O
MS:1001146 a ion-NH3
MS:1001150 b ion-H2O
MS:1002450 b ion-H3PO4
MS:1001149 b ion-NH3
MS:1001152 y ion-H2O
MS:1002451 y ion-H3PO4
MS:1001151 y ion-NH3


New CV terms in version 3.64.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002452
name: Maui
def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002453
name: No fixed modifications searched
def: "No fixed modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002454
name: No variable modifications searched
def: "No variable modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002455
name: H2O neutral loss
def: "Neutral loss of water." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "Neutral loss of ammonia." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "Neutral loss of phosphoric acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002458
name: PeptideShaker
def: "PeptideShaker is a software for the interpretation of proteomics identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002459
name: MS Amanda csv format
def: "MS Amanda csv output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002461
name: protein group-level confidence
def: "Estimation of the global confidence of protein groups." [PSI:PI]
is_a: MS:1002346 ! protein group-level result details

[Term]
id: MS:1002462
name: distinct peptide-level global FNR
def: "Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002463
name: distinct peptide-level global confidence
def: "Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002464
name: PSM-level global FNR
def: "Estimation of the global false negative rate of peptide spectrum matches." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002465
name: PSM-level global confidence
def: "Estimation of the global confidence of peptide spectrum matches." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002472
name: beam-type high-energy collision-induced dissociation
def: "A beam-type collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately
1000 eV." [PSI:PI]
is_a: MS:1000422 ! high-energy collision-induced dissociation

[Term]
id: MS:1002473
name: trap-type high-energy collision-induced dissociation
def: "A trap-type collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately
1000 eV." [PSI:PI]
is_a: MS:1000422 ! high-energy collision-induced dissociation

[Term]
id: MS:1002474
name: electron transfer dissociation followed by beam-type collision-induced dissociation
def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations by transferring electrons to them, after which the fragments are further dissociated using beam-type collisional excitation." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1002472 ! beam-type high-energy collision-induced dissociation

Best Regards,
Gerhard

--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.64.0_rc2 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.64.0_rc2 of the psi-ms.obo file.

It contains new terms for mzTab, for specifying the neutral losses, for
collision-induced dissociation and for PeptideShaker.

The neutral losses are now defined as terms independently from the ions in
order to decouple the two concepts ion and neutral loss from each other.
The old neutral loss terms are now obsoleted.

Furthermore some terms from the purgatory branch are now obsolete.
In addition I corrected some spelling errors in definitions.


Changed CV terms in version 3.64.0_rc2 of psi-ms.obo:
=====================================================
************ The following terms from the purgatory branch are now 
obsoleted:
MS:1000329 linked scan
MS:1000268 mass spectrometry
MS:1000013 resolution type
MS:1000020 scanning method
MS:1000459 spectrum instrument description

************ The following neutral loss terms are now obsoleted:
MS:1001148 a ion-H2O
MS:1001146 a ion-NH3
MS:1001150 b ion-H2O
MS:1002450 b ion-H3PO4
MS:1001149 b ion-NH3
MS:1001152 y ion-H2O
MS:1002451 y ion-H3PO4
MS:1001151 y ion-NH3


New CV terms in version 3.64.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002452
name: Maui
def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net]
is_a: MS:1001456 ! analysis software
is_a: MS:1001457 ! data processing software

[Term]
id: MS:1002453
name: No fixed modifications searched
def: "No fixed modifications are included as a parameter for the search, 
and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002454
name: No variable modifications searched
def: "No variable modifications are included as a parameter for the 
search, and therefore they are not reported." [PSI:PI]
is_a: MS:1002094 ! common search engine input parameter

[Term]
id: MS:1002455
name: H2O neutral loss
def: "Neutral loss of water." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002456
name: NH3 neutral loss
def: "Neutral loss of ammonia." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002457
name: H3PO4 neutral loss
def: "Neutral loss of phosphoric acid." [PSI:PI]
is_a: MS:1000336 ! neutral loss

[Term]
id: MS:1002458
name: PeptideShaker
def: "PeptideShaker is a software for the interpretation of proteomics 
identification results." [PSI:PI, http://peptide-shaker.googlecode.com]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002459
name: MS Amanda csv format
def: "MS Amanda csv output format." [PSI:PI]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1002460
name: protein group-level global FNR
def: "Estimation of the global false negative rate of protein groups." 
[PSI:PI]
is_a: MS:1002346 ! protein group-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002461
name: protein group-level confidence
def: "Estimation of the global confidence of protein groups." [PSI:PI]
is_a: MS:1002346 ! protein group-level result details

[Term]
id: MS:1002462
name: distinct peptide-level global FNR
def: "Estimation of the global false negative rate for distinct peptides 
once redundant identifications of the same peptide have been removed (id 
est multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002463
name: distinct peptide-level global confidence
def: "Estimation of the global confidence for distinct peptides once 
redundant identifications of the same peptide have been removed (id est 
multiple PSMs have been collapsed to one entry)." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1002464
name: PSM-level global FNR
def: "Estimation of the global false negative rate of peptide spectrum 
matches." [PSI:PI]
is_a: MS:1002345 ! PSM-level result details
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002465
name: PSM-level global confidence
def: "Estimation of the global confidence of peptide spectrum matches." 
[PSI:PI]
is_a: MS:1002345 ! PSM-level result details

[Term]
id: MS:1002466
name: PeptideShaker PSM score
def: "The probability based PeptideShaker PSM score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002467
name: PeptideShaker PSM confidence
def: "The probability based PeptideShaker PSM confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002468
name: PeptideShaker peptide score
def: "The probability based PeptideShaker peptide score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002469
name: PeptideShaker peptide confidence
def: "The probability based PeptideShaker peptide confidence." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002470
name: PeptideShaker protein group score
def: "The probability based PeptideShaker protein group score." [PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002471
name: PeptideShaker protein group confidence
def: "The probability based PeptideShaker protein group confidence." 
[PSI:PI]
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002472
name: beam-type high-energy collision-induced dissociation
def: "A beam-type collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:PI]
is_a: MS:1000422 ! high-energy collision-induced dissociation

[Term]
id: MS:1002473
name: trap-type high-energy collision-induced dissociation
def: "A trap-type collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:PI]
is_a: MS:1000422 ! high-energy collision-induced dissociation

[Term]
id: MS:1002474
name: electron transfer dissociation followed by beam-type 
collision-induced dissociation
def: "A process to fragment ions in a mass spectrometer by inducing 
fragmentation of cations by transferring electrons to them, after which 
the fragments are further dissociated using beam-type collisional 
excitation." [PSI:PI]
synonym: "EThcD" EXACT []
is_a: MS:1002472 ! beam-type high-energy collision-induced dissociation

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Fwd: RE: new terms describing beam-type dissociation?

[Gerhard M. <may...@ru...>]

Hi Henk, Matt and Pierre-Alain,

if I understood you correctly, you want to obsolete the term MS:1000422 and
replace it by two beam-type and trap-type specific terms, so that we can 
"HCD" as
RELATED synonym,

whereas an own term for the EThcD method isn't needed, because you can 
describe that
now by the combination of the two terms
MS:1000598 (electron transfer dissociation) and
MS:1002458 (beam-type high-energy collision-induced dissociation)

Would the following be ok for you?


[Term]
id: MS:1000422
name: high-energy collision-induced dissociation
def: "OBSOLETE A collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:MS]
synonym: "HCD" EXACT []
is_a: MS:1000044 ! dissociation method
comment: This term was made obsolete because it was replaced by 
beam-type high-energy collision-induced dissociation (MS:1002458) and 
trap-type high-energy collision-induced dissociation (MS:1002459).
is_obsolete: true

[Term]
id: MS:1002458
name: beam-type high-energy collision-induced dissociation
def: "A beam-type collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:MS]
synonym: "HCD" RELATED []
is_a: MS:1000044 ! dissociation method

[Term]
id: MS:1002459
name: trap-type high-energy collision-induced dissociation
def: "A trap-type collision-induced dissociation process wherein the 
projectile ion has the translational energy higher than approximately 
1000 eV." [PSI:MS]
synonym: "HCD" RELATED []
is_a: MS:1000044 ! dissociation method

Regards,
Gerhard


Am 02.05.2014 12:08, schrieb Henk van den Toorn:
> Hi Matt and Pierre-Alain,
>
> Thanks for your response. Pierre-Alain, I think you're right in saying 
> it's not an exact synonym. As Matt pointed out, the "energy" part of 
> the terms is confusing in itself. Please note HCD is not "High 
> Energy", but, according to Thermo, "Higher energy" CID. The collision 
> energy is not higher than CID, but the energy to keep the ions in the 
> C-lens is higher:
>
> https://www.researchgate.net/post/What_does_higher_in_HCD_Higher-energy_collisional_dissociation_mean
>
> Although the list of activation methods is nice and flat now, maybe 
> it's worth the consideration to split the CID term in a beam-type and 
> a trap-type sub-terms?
>
> Combining the activation types within the activation element is an 
> apparent solution for the EThcD, thank you for the suggestion.
>
> Regards, Henk
>
>
> On 5/1/2014 9:03 PM, Chambers, Matthew wrote:
>
>     Hi Henk,
>
>     Combined activation techniques are covered by including CV terms
>     for both techniques in the activation element. Thus we don't need
>     combined terms. We already have a high-energy CID (HCD) term, but
>     it's true that referring to beam type CID as HCD is not
>     vendor-neutral. I'm fine with renaming the HCD term to "beam-type
>     collision induced dissociation" and making HCD a synonym. I don't
>     think a new term is necessary. The "high energy" part should IMO
>     have always been left to be specified by the collision voltage
>     parameter, since AFAIK the difference in fragmentation between LE
>     and HE CID is not that much different than changing the voltage
>     away from the "optimum" for either LE or HE. The beam vs. trap
>     part really does make a (orthogonal) difference though.
>
>     -Matt
>
>     On 5/1/2014 8:55 AM, Henk van den Toorn wrote:
>
>         Dear community
>
>
>         I'd like to propose two new terms that should be able to
>         describe some fragmentation techniques that are not in the
>         vocabulary yet:
>         Children (is_a) of "dissociation method" (MS:1000044
>         <https://www.ebi.ac.uk/ontology-lookup/?termId=MS%3A1000044>)
>
>         The terms would be needed to describe HCD and ETHCD but in
>         more neutral terms. The exact synonyms are in fact the
>         vendor-specific terms so maybe they should be omitted.
>
>         beam-type collision-induced dissociation
>         The dissociation of an ion after collisional excitation.
>         Exact synonym: HCD
>
>         and
>
>         electron transfer dissociation followed by beam-type
>         collision-induced dissociation
>         def: A process to fragment ions in a mass spectrometer by
>         inducing fragmentation of cations by transferring electrons to
>         them, after which the fragments are further dissociated using
>         beam-type collisional excitation.
>         Exact Synonym: EThcD
>
>         Thank you, Henk van den Toorn
>
>         Some references (taken from Wikipedia)
>
>          1. Frese, Christian K.; A. F. Maarten Altelaar, Henk van den
>             Toorn, Dirk Nolting, Jens Griep-Raming,Albert J. R. Heck,
>             and Shabaz Mohammed (November 20, 2012). "Toward full
>             peptide sequence coverage by dual fragmentation combining
>             electron-transfer and higher-energy collision dissociation
>             tandem mass spectrometry"
>             <http://www.ncbi.nlm.nih.gov/pubmed/23106539/>. /Anal Chem/.
>          2. Syka, John EP; Coon JJ, Schroeder MJ, Shabanowitz J, Hunt
>             DF (2004). "Peptide and protein sequence analysis by
>             electron transfer dissociation mass spectrometry"
>             <http://www.pnas.org/content/101/26/9528>. /PNAS/ *101*
>             (26): 9528--9533.
>          3. Olsen JV; Macek B, Lange O, Makarov A, Horning S, Mann M
>             (September 2007). "Higher-energy C-trap dissociation for
>             peptide modification analysis."
>             <http://www.ncbi.nlm.nih.gov/pubmed/17721543/>. /Nature
>             methods/ *4* (9): 709--712.
>          4. Frese, Christian K.; Houjiang Zhou,Thomas Taus, A. F.
>             Maarten Altelaar, Karl Mechtler,Albert J. R. Heck, and
>             Shabaz Mohammed (March 1, 2013). "Unambiguous Phosphosite
>             Localization using Electron-Transfer/Higher-Energy
>             Collision Dissociation (EThcD)"
>             <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588588/>.
>             /J Proteome Res/.
>
>         -- 
>
>         ________________________________________
>
>         *Henk van den Toorn*
>
>         Biomolecular Mass Spectrometry and Proteomics
>         Bijvoet Center for Biomolecular Research and Utrecht Institute
>         for Pharmaceutical Sciences
>
>         Padualaan 8, 3584 CH Utrecht, The Netherlands
>
>
>         E-mail: h.w...@uu...
>         <mailto:h.w...@uu...>, Tel: +31 30 253 6758, Fax:
>         +31 30 253 6919
>
>
>
>
>         ------------------------------------------------------------------------------
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>
>
>
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>
>         Psidev-ms-vocab mailing list
>
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>
>         https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab
>
> -- 
>
> ________________________________________
>
> *Henk van den Toorn*
>
> Biomolecular Mass Spectrometry and Proteomics
> Bijvoet Center for Biomolecular Research and Utrecht Institute for 
> Pharmaceutical Sciences
>
> Padualaan 8, 3584 CH Utrecht, The Netherlands
>
>
> E-mail: h.w...@uu... <mailto:h.w...@uu...>, Tel: 
> +31 30 253 6758, Fax: +31 30 253 6919
>
>
>
>
>
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-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.63.0 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the new version 3.63.0 of the psi-ms.obo file.

It contains a new term for a Paragon-specific search setting,
two new terms for PEAKS scores and two new terms for ion series.


Changed CV terms in version 3.63.0 of psi-ms.obo:
=================================================
************ Slightly changed the definitions of the following ions 
series terms:
[Term]
id: MS:1001146
name: param: a ion-NH3
def: "Ion a-NH3 parameter information, type of product: a ion with lost 
ammonia." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001148
name: param: a ion-H2O
def: "Ion a-H2O if a significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001149
name: param: b ion-NH3
def: "Ion b-NH3 parameter information, type of product: b ion with lost 
ammonia." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001150
name: param: b ion-H2O
def: "Ion b-H2O if b significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001151
name: param: y ion-NH3
def: "Ion y-NH3 parameter information, type of product: y ion with lost 
ammonia." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001152
name: param: y ion-H2O
def: "Ion y-H2O if y significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001232
name: frag: b ion - NH3
def: "Ion b-NH3 fragmentation information, type of product: b ion 
without ammonia." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1001233
name: frag: y ion - NH3
def: "Ion y-NH3 fragmentation information, type of product: y ion 
without ammonia." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type

[Term]
id: MS:1001235
name: frag: a ion - NH3
def: "Ion a-NH3 fragmentation information, type of product: a ion 
without ammonia." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type


New CV terms in version 3.63.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002447
name: Paragon:special factor
def: "The Paragon method setting indicating a list of one or more 
'special factors', which generally capture secondary effects (relative 
to other settings) as a set of probabilities of modification features 
that override the assumed levels. For example the 'gel-based ID' special 
factor causes an increase probability of oxidation on several resides 
because of the air exposure impact on a gel, in addition to other 
effects." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002448
name: PEAKS:inChorusPeptideScore
def: "The PEAKS inChorus peptide score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002449
name: PEAKS:inChorusProteinScore
def: "The PEAKS inChorus protein score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002450
name: param: b ion-H3PO4
def: "Ion b-H3PO4: b ion with lost phosphoric acid." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1002451
name: param: y ion-H3PO4
def: "Ion y-H3PO4: y ion with lost phosphoric acid." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.63.0_rc3 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.63.0_rc3 of the psi-ms.obo file.

It contains a new term for a Paragon-specific search setting,
two new terms for PEAKS scores and two new terms for ion series.


Changed CV terms in version 3.63.0_rc3 of psi-ms.obo:
=====================================================
************ Slightly changed the definitions of the following ions 
series terms:
[Term]
id: MS:1001146
name: param: a ion-NH3
def: "Ion a-NH3 parameter information, type of product: a ion with lost 
ammonium." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001148
name: param: a ion-H2O
def: "Ion a-H2O if a significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001149
name: param: b ion-NH3
def: "Ion b-NH3 parameter information, type of product: b ion with lost 
ammonium." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001150
name: param: b ion-H2O
def: "Ion b-H2O if b significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001151
name: param: y ion-NH3
def: "Ion y-NH3 parameter information, type of product: y ion with lost 
ammonium." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001152
name: param: y ion-H2O
def: "Ion y-H2O if y significant and fragment includes STED." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search


New CV terms in version 3.63.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002447
name: Paragon:special factor
def: "The Paragon method setting indicating a list of one or more 
'special factors', which generally capture secondary effects (relative 
to other settings) as a set of probabilities of modification features 
that override the assumed levels. For example the 'gel-based ID' special 
factor causes an increase probability of oxidation on several resides 
because of the air exposure impact on a gel, in addition to other 
effects." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002448
name: PEAKS:inChorusPeptideScore
def: "The PEAKS inChorus peptide score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002449
name: PEAKS:inChorusProteinScore
def: "The PEAKS inChorus protein score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002450
name: param: b ion-H3PO4
def: "Ion b-H3PO4: b ion with lost phosphoric acid." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1002451
name: param: y ion-H3PO4
def: "Ion y-H3PO4: y ion with lost phosphoric acid." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] PSI Meeting coming up soon

[Jones, A. <And...@li...>]

Hi all,

Further to Eric’s message. If you have had any problems booking the hotel room, please let me know. Certainly there should still be rooms reserved, yet we’ve tried to book a room recently online and we’re not able to do it. The hotel are investigating the problem.

Please don’t book rooms elsewhere, since if our room quota is not used up – we will be charged for unused rooms,
Best wishes
Andy

From: Eric Deutsch [mailto:ede...@sy...]
Sent: 29 March 2014 01:05
To: Mass spectrometry standard development; psi...@li...; Psi...@eb...
Cc: Eric Deutsch
Subject: [Psidev-ms-dev] PSI Meeting coming up soon

Hi everyone, the PSI meeting is almost upon us. If you are planning on participating in the meeting and have not yet registered for the meeting, please do so very soon.

The PSI meeting will take place at the Schloss Reinhartshausen Kempinski (Rudesheim, close to Frankfurt), Germany on April 13-16. Please don’t forget to register in the PSI web site, since we need to have the final numbers in the next few days:

http://www.psidev.info/psi2014

Like in previous years, we have decided to use the PSI web page, since for logistics it is actually much easier for us to have a joint registration for the PSI, ProteomeXchange and IMEX meetings. Please, remember the schedule for that week:

- HUPO Proteomics Standards Initiative (PSI) meeting (April 13-16 am, http://www.psidev.info/). This time there will be also formal participation from the metabolomics community (COSMOS project, http://www.cosmos-fp7.eu/).
- 4th ProteomeXchange meeting (April 16 pm-17). The idea is to finish shortly after lunch on April 17th.
- At the same time partners of the IMEX consortium (for protein interaction databases) will have their annual meeting on April 16 pm-17, in the same venue.

Regarding the accommodation, you need to do the reservation by yourself at the hotel (information is available at http://www.psidev.info/psi2014). You need to provide the keyword “PSI” to get the reduced rate. Please stay in that hotel because we have pre-booked a number of rooms that we will have to pay for anyway if they are not occupied.

We look forward to seeing you there!

Eric

[Psidev-ms-dev] Release candidate 3.63.0_rc2 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.63.0_rc2 of the psi-ms.obo file.

It contains a new term for a Paragon-specific search setting
and two new terms for PEAKS scores.


Changed CV terms in version 3.63.0_rc2 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.63.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002447
name: Paragon:special factor
def: "The Paragon method setting indicating a list of one or more 
'special factors', which generally capture secondary effects (relative 
to other settings) as a set of probabilities of modification features 
that override the assumed levels. For example the 'gel-based ID' special 
factor causes an increase probability of oxidation on several resides 
because of the air exposure impact on a gel, in addition to other 
effects." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter

[Term]
id: MS:1002448
name: PEAKS:inChorusPeptideScore
def: "The PEAKS inChorus peptide score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002449
name: PEAKS:inChorusProteinScore
def: "The PEAKS inChorus protein score." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] PSI Meeting coming up soon

[Eric D. <ede...@sy...>]

Hi everyone, the PSI meeting is almost upon us. If you are planning on
participating in the meeting and have not yet registered for the meeting,
please do so very soon.



The PSI meeting will take place at the *Schloss Reinhartshausen
Kempinski *(Rudesheim,
close to Frankfurt), Germany on *April 13-16*. *Please don't forget to
register* in the PSI web site, since we need to have the final numbers in
the next few days:



http://www.psidev.info/psi2014



Like in previous years, we have decided to use the PSI web page, since for
logistics it is actually much easier for us to have a joint registration
for the PSI, ProteomeXchange and IMEX meetings. Please, remember the
schedule for that week:



- HUPO Proteomics Standards Initiative (PSI) meeting (April 13-16 am,
http://www.psidev.info/). This time there will be also formal participation
from the metabolomics community (COSMOS project, http://www.cosmos-fp7.eu/).

- 4th *ProteomeXchange meeting* (April 16 pm-17). The idea is to finish
shortly after lunch on April 17th.

- At the same time partners of the IMEX consortium (for protein interaction
databases) will have their annual meeting on April 16 pm-17, in the same
venue.



Regarding the accommodation, *you need to do the reservation by yourself *at
the hotel (information is available at http://www.psidev.info/psi2014). You
need to provide the keyword *"PSI"* to get the reduced rate. Please *stay
in that hotel because we have pre-booked a number of rooms that we will
have to pay for anyway if they are not occupied. *



We look forward to seeing you there!



Eric

[Psidev-ms-dev] Release candidate 3.62.0_rc1 of psi-ms.obo

[Gerhard M. <may...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.63.0_rc1 of the psi-ms.obo file.

It contains a new term for a Paragon-specific search setting.


Changed CV terms in version 3.63.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.63.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002447
name: Paragon:special factor
def: "The Paragon method setting indicating a list of one or more 
'special factors', which generally capture secondary effects (relative 
to other settings) as a set of probabilities of modification features 
that override the assumed levels. For example the 'gel-based ID' special 
factor causes an increase probability of oxidation on several resides 
because of the air exposure impact on a gel, in addition to other 
effects." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002421 ! Paragon input parameter


Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum
  
Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 3.62.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached you find the new version 3.62.0 of the psi-ms.obo file.

It contains three new terms for Agilent instruments.


Changed CV terms in version 3.62.0 of psi-ms.obo:
=================================================
No changed CV terms


New CV terms in version 3.62.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002444
name: 6420 Triple Quadrupole LC/MS
def: "The 6420 Quadrupole LC/MS system is a Agilent liquid
chromatography instrument combined with a Agilent triple quadrupole mass
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002445
name: 6460 Triple Quadrupole LC/MS
def: "The 6460 Quadrupole LC/MS system is a Agilent liquid
chromatography instrument combined with a Agilent triple quadrupole mass
spectrometer. It is similar to the 6420 but adds Agilent Jet Stream
(AJS) technology to increase sensitivity." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002446
name: 6490 Triple Quadrupole LC/MS
def: "The 6490 Quadrupole LC/MS system is a Agilent liquid
chromatography instrument combined with a Agilent triple quadrupole mass
spectrometer. It is similar to the 6420 but adds the Agilent iFunnel
technology to increase sensitivity." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model


Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.62.0_rc1 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.62.0_rc1 of the psi-ms.obo file.

It contains three new terms for Agilent instruments.


Changed CV terms in version 3.62.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.62.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002444
name: 6420 Triple Quadrupole LC/MS
def: "The 6420 Quadrupole LC/MS system is a Agilent liquid
chromatography instrument combined with a Agilent triple quadrupole mass
spectrometer." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002445
name: 6460 Triple Quadrupole LC/MS
def: "The 6460 Quadrupole LC/MS system is a Agilent liquid
chromatography instrument combined with a Agilent triple quadrupole mass
spectrometer. It is similar to the 6420 but adds Agilent Jet Stream
(AJS) technology to increase sensitivity." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

[Term]
id: MS:1002446
name: 6490 Triple Quadrupole LC/MS
def: "The 6490 Quadrupole LC/MS system is a Agilent liquid
chromatography instrument combined with a Agilent triple quadrupole mass
spectrometer. It is similar to the 6420 but adds the Agilent iFunnel
technology to increase sensitivity." [PSI:MS]
is_a: MS:1000490 ! Agilent instrument model

Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] New Agilent instrument terms?

[Eric D. <ede...@sy...>]

Hi everyone, I would like to propose the following new terms for some
instruments that we seem to be missing in the CV:



[Term]

id: MS:100????

name: 6420 Triple Quadrupole LC/MS

def: "The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography
instrument combined with a Agilent triple quadrupole mass spectrometer."
[PSI:MS]

is_a: MS:1000490 ! Agilent instrument model

[Term]

id: MS:100????

name: 6460 Triple Quadrupole LC/MS

def: "The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography
instrument combined with a Agilent triple quadrupole mass spectrometer. It
is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to
increase sensitivity." [PSI:MS]

is_a: MS:1000490 ! Agilent instrument model



[Term]

id: MS:100????

name: 6490 Triple Quadrupole LC/MS

def: "The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography
instrument combined with a Agilent triple quadrupole mass spectrometer. It
is similar to the 6420 but adds the Agilent iFunnel technology to increase
sensitivity." [PSI:MS]

is_a: MS:1000490 ! Agilent instrument model



I modeled these entries after MS:1000477.



Any comments, corrections, or additions? I left out the resolution and
range information present in MS:1000477 since I don't know it for these
instruments.



Thanks,

Eric

[Psidev-ms-dev] New version 3.61.0 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached you find the new version 3.61.0 of the psi-ms.obo file.

It contains new CV terms for flagging the SpectrumIdentificationLists in
mzIdentML version 1.2 and terms for the netCDF ANDI file formats.


Changed CV terms in version 3.61.0 of psi-ms.obo:
=================================================
No changed CV terms


New CV terms in version 3.61.0 of psi-ms.obo:
=============================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is the final set of identifications to be interpreted by
consuming software. Amongst the set of SpectrumIdentificationList(s)
that are flagged with the term, each spectrum must not be referenced
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is not the final set of identifications to be interpreted by
consuming software. This term should be used when results are provided
from multiple search engines for the results from each search engine
before they are combined to give consensus identifications. Amongst the
set of SpectrumIdentificationList(s) that are flagged with the term,
each spectrum may be referenced from more than one
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002441
name: Andi-MS format
def: "AIA Analytical Data Interchange file format for mass spectrometry
data." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002442
name: chromatograph file format
def: "The format of the chromatography file being used. This could be a
instrument or vendor specific proprietary file format or a converted
open file format." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002443
name: Andi-CHROM format
def: "AIA Analytical Data Interchange file format for chromatography
data." [PSI:PI]
is_a: MS:1002442 ! chromatograph file format

Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

[Karl C. <cl...@br...>]

Andy,

 

I can’t think of a good reason for separately counting modified and
unmodified peptides when doing a peptide-level FDR analysis. When you
mention that the spectra might be quite different, my thought is: so why
does that really matter? And even if they are the differences will be on the
order of the differences between 2 different precursor charge states of an
unmodified peptide. So why treat precursor charges and mods differently?
Instead I think the more important question comes back to what one is trying
to capture with a peptide-level metric. I believe that a peptide-level
metric is usually oriented toward measuring extent of protein identification
and depth of peptide coverage of a sample. In that sense, counting modified
forms separately is going to skew the metric by inappropriately inflating
your peptide count in a whole proteome experiment with  sampling handling
effects (i.e. oxidized Met, deamidated Asn, etc). If one is working with a
dataset from a PTM enrichment experiment (phospho, acetyl, ubiquitin), then
the core metric is more suited to a site-level collapsing than a
peptide-level collapsing. Furthermore, when I said site-level, I mean driven
by the primary site type of interest i.e. in a phospho-enriched PTM dataset,
sample handling artifacts like oxidized/unoxidized Met for the same
phosphosite would be collapsed together, while PTM’s like  2 differently
localized  phosphosites in the same peptide would be kept separate.

 

The best reason I can think of for counting modified and unmodified peptides
separately when doing a peptide-level analysis, is when one would prefer to
have a site-level analysis for an enriched PTM dataset, but the particular
software platform being used isn’t sophisticated enough to have implemented
site-level collapsing  (requires a site-localization metric on each
identification).  So instead a crude mod vs unmod separation has been
implemented by collapsing base on precursor MH+ and sequence, or case
insensitive sequence comparison (when mods are indicated by lower case).

 

--Karl 

 

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, February 27, 2014 9:51 AM
To: 'Mass spectrometry standard development';
'psi...@li...';
'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

I’m interested to hear this discussion. We’re currently implementing
peptide-level FDR analysis in our mzidLibrary software, and were working on
the basis of “peptide+modification site” being the distinct unit for our
calculation, but Karl’s email indicates to me that there isn’t consensus on
how this is done. For the purposes of global stats, I understood that one of
the reasons for doing peptide-level stats was that there could be a
consistent incorrect assignment occurring across all spectra reporting on
the same peptide. The spectra for a modified peptide would be rather
different from the unmodified peptide, so I don’t understand the logic for
collapsing these down into one entry (except for protein inference by a
peptide sequence centric approach).

 

Best wishes

Andy 

 

 

 

From: Karl Clauser [mailto:cl...@br...] 
Sent: 27 February 2014 14:30
To: 'Mass spectrometry standard development';
psi...@li...; psi...@li...
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Hi folks,

 

I just wanted to chime in here that I think Eric's definition of distinct
peptide is pretty close to that which is the most widely-implemented
interpretation.

                >distinct peptide - a distinct sequence of amino acids
irrespective of mass modifications or charge.

It is most applicable when one is doing protein parsimony and reporting a
peptide-level FDR. It is also consistent with the MCP publication
guidelines.

 

I'm not sure I see much practical use for 

                > modified peptide - one species of distinct peptide with a
specific mass-modification configuration, but irrespective of charge.

 

Instead I'd like to toss into the discussion a related concept (modification
site), which is often used in papers that enrich for a particular PTM
(phospho, acetyl, ubiquitin). While the concept is often used there isn't
really a generic name. For example it is used when reporting the total
number of phosphosites observed, since the count of unique peptides isn't
usually relevant.

 

Modification site – a particular modification localized to a specific
position in the protein sequence, irrespective of precursor charge, missed
cleavage state, or precursor mass. When collapsing a set of PSM's to the
site level, allowing for different missed cleavage states is challenging
because one typically needs to know the AA position in the intact protein
sequence, thus protein parsimony issues arise.

 

Note that when counting the total number of phosphosites
identified/quantified, if a particular site is located in peptide that has
another nearby site then the singly and doubly phosphorylated observations
of those are often reported separately because they may be regulated
differently and have dissimilar quantitative behavior.

 

--Karl

 

-----Original Message-----
From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, February 27, 2014 8:46 AM
To: 'psi...@li...'; 'Mass spectrometry standard
development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Hi all,

 

Wow - I didn't realise my request for a new CV term would open such a can of
worms :-)

 

Probably it makes sense to defer this update (support for peptide-level
stats) and discuss as an agenda item at the PSI meeting in April, then do as
a minor update to mzid 1.2 at a later stage?

 

I want to get mzid 1.2 in process ASAP, and I don't think we'll get this
resolved very easily, since as you mention there are lots of different ways
of doing "peptide-level stats", and we should try get it right.

Cheers

Andy

 

 

-----Original Message-----

From: Seymour, Sean L [ <mailto:Sea...@ab...>
mailto:Sea...@ab...]

Sent: 26 February 2014 17:55

To: Eric Deutsch; Mass spectrometry standard development;
<mailto:psi...@li...>
psi...@li...;
<mailto:psi...@li...>
psi...@li...

Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Hi Eric,

 

I like your breakdown of the concepts, but not all the names. Your 'distinct
peptide' is really a 'sequence' to me. And I'm not too crazy about using
'modified peptide' as the term for what I described as my view of what a
'peptide' is, particularly because this would have to apply to unmodified
peptides as well. 

 

While I find myself using them, I find the modifiers 'distinct' and 'unique'
to be ambiguous as well, since these are used by some framings of protein
inference to refer to a peptide or sequence's degree of specificity to just
one protein. I guess this is where I come back to 'peptide' and 'sequence'
having the most straightforward meaning if we insist on clear definitions
most consistent with what those words really mean and would be understood to
mean outside of our little domain. I'm fine with 'PSM' and 'Peptide ion' for
your first two, but would prefer just 'Peptide' and 'Sequence' for the last
two. A peptide is an actual compound that has a structural formula and a
sequence has...well, a sequence.

 

It's also not completely clear to me from the definition of the third if you
count different arrangements of the same mods on the same sequence as
different peptides. From the chemist's perspective, they are different. They
would come in different vials from a different number in a catalog and have
different structural formulae. I think that's what you mean, but it could be
spelled out a little more.

 

I definitely think we can agree on terms but allow room for slightly varied
concepts for things deeply interior to our domain. We were should really try
to agree and use things consistently is where our domain interfaces with
other who don't understand all the fine points of mass spec and proteomics.
This is where I think the terms 'peptide' and 'sequence' are particularly
important. No biologist should ever have to know or care about a PSM or how
many charge states a peptide ionizes to in a mass spec.

 

Sean

 

-----Original Message-----

From: Eric Deutsch [ <mailto:ede...@sy...>
mailto:ede...@sy...]

Sent: Wednesday, February 26, 2014 9:29 AM

To: Mass spectrometry standard development; Seymour, Sean L;
<mailto:psi...@li...>
psi...@li...;
<mailto:psi...@li...>
psi...@li...

Cc: Eric Deutsch

Subject: RE: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

FWIW, these are the terms we try to use (PeptideAtlas/TPP):

 

PSM - peptide-spectrum match - one instance of a spectrum matched to a
specific peptide ion.

 

peptide ion - one species of distinct peptide with a specific charge state
and mass-modification configuration.

 

modified peptide - one species of distinct peptide with a specific
mass-modification configuration, but irrespective of charge.

 

 

distinct peptide - a distinct sequence of amino acids irrespective of mass
modifications or charge.

 

 

We try not to use peptide by itself because it is so ambiguous.

 

Do you think it's possible to all agree on a set of terms and definitions?

 

E

 

 

 

-----Original Message-----

From: Jones, Andy [ <mailto:And...@li...>
mailto:And...@li...]

Sent: Wednesday, February 26, 2014 8:57 AM

To: 'Seymour, Sean L'; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Totally agree with what you're saying here - I think my concept of peptide I
intended here was the same as yours, but much less well elaborated. I agree
these terms have not been clearly defined by us ever, and perhaps we should
add a reference guide somewhere on the PSI site or in the mzid 1.2 spec doc
we can refer to when we say "distinct peptide", "PSM" etc.

 

-----Original Message-----

From: Seymour, Sean L [ <mailto:Sea...@ab...>
mailto:Sea...@ab...]

Sent: 26 February 2014 16:50

To: Jones, Andy; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo

 

Hi all,

 

If we're going to go down the very useful road of capturing attributes at
the level of the peptide, I think we need to very clearly define what we
mean by a peptide. To anyone with a chemistry background like myself, a
peptide would mean a structurally unique molecule. Different charges states
of this molecule are not different peptides, they are derivative states that
arise from the analytical process in the mass spec. Different modification
states of a sequence are different peptides. Different arrangements of the
same modifications on the same sequence are different peptides. The same
exact match to two different spectra is one peptide, not two peptides. While
this view may seem obvious to some of you, there is a great range of how
this term is used in my experience, including violation of all of the
previous specific statements.

 

Perhaps we've already clearly defined 'peptide' somewhere, and I don't need
to say this, but I think this is very important so I want to be sure.

I'm very much in favor of including concepts at this level since it is more
aligned with the physical analyte, sheds redundancy complications, and is
more useful when moving to targeted analyses via MRM or DIA. It might be
useful to develop/collect all our terms at this level to be sure we've
defined them right. Many concepts at the spectrum level have an analog at
the peptide level so it may be useful to map this out as well - ex RT of MS2
trigger vs. RT of the peptide apex of elution.

 

Sean

 

 

 

-----Original Message-----

From: Jones, Andy [ <mailto:And...@li...>
mailto:And...@li...]

Sent: Wednesday, February 26, 2014 8:24 AM

To: 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo

 

Thanks for this Gerhard. Apologies, I discovered a further term which we
would like added (discussed here:

 <http://code.google.com/p/psi-pi/issues/detail?id=80>
http://code.google.com/p/psi-pi/issues/detail?id=80):

 

Term: "best PSM per peptide"

No value slot

Def: "To support peptide-level statistical approaches or scores, this term
SHOULD be used to annotate the best scoring PSM reporting on a given
distinct peptide (sequence and modifications distinct)"

 

 

 

-----Original Message-----

From: Gerhard Mayer [ <mailto:Ger...@ru...>
mailto:Ger...@ru...]

Sent: 26 February 2014 14:45

To:  <mailto:psi...@li...>
psi...@li...;

 <mailto:psi...@li...>
psi...@li...; Mass spectrometry standard development

Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

 

Dear proteomics community,

 

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

 

It contains two new CV terms for flagging the SpectrumIdentificationLists in
mzIdentML version 1.2.

 

 

Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:

=====================================================

No changed CV terms

 

 

New CV terms in version 3.61.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002438

name: spectrum identification list result details

def: "Information about the list of PSMs (SpectrumIdentificationList)."

[PSI:PI]

relationship: part_of MS:1001000 ! spectrum interpretation

 

[Term]

id: MS:1002439

name: final PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that
this is the final set of identifications to be interpreted by consuming
software. Amongst the set of SpectrumIdentificationList(s) that are flagged
with the term, each spectrum must not be referenced from more than one
SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details

 

[Term]

id: MS:1002440

name: intermediate PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that
this is not the final set of identifications to be interpreted by consuming
software. This term should be used when results are provided from multiple
search engines for the results from each search engine before they are
combined to give consensus identifications. Amongst the set of
SpectrumIdentificationList(s) that are flagged with the term, each spectrum
may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details

 

Best Regards,

Gerhard

--

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics /
Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150

D-44801 Bochum

 

Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:     <mailto:ger...@ru...> ger...@ru...

Web:      <http://www.medizinisches-proteom-center.de>
http://www.medizinisches-proteom-center.de

 

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agreement; provided that the foregoing does not invalidate the binding
effect of any digital or other electronic reproduction of a manual signature
that is included in any attachment.

 

 

 

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Customize your own dashboards, set traffic alerts and generate reports.

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[Psidev-ms-dev] Release candidate 3.61.0_rc2 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.61.0_rc2 of the psi-ms.obo file.

It contains new CV terms for flagging the SpectrumIdentificationLists in
mzIdentML version 1.2 and for netCDF ANDI file formats.


Changed CV terms in version 3.61.0_rc2 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc2 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is the final set of identifications to be interpreted by
consuming software. Amongst the set of SpectrumIdentificationList(s)
that are flagged with the term, each spectrum must not be referenced
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is not the final set of identifications to be interpreted by
consuming software. This term should be used when results are provided
from multiple search engines for the results from each search engine
before they are combined to give consensus identifications. Amongst the
set of SpectrumIdentificationList(s) that are flagged with the term,
each spectrum may be referenced from more than one
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002441
name: Andi-MS format
def: "AIA Analytical Data Interchange file format for mass spectrometry
data." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002442
name: chromatograph file format
def: "The format of the chromatography file being used. This could be a
instrument or vendor specific proprietary file format or a converted
open file format." [PSI:PI]
is_a: MS:1001459 ! file format

[Term]
id: MS:1002443
name: Andi-CHROM format
def: "AIA Analytical Data Interchange file format for chromatography
data." [PSI:PI]
is_a: MS:1002442 ! chromatograph file format

Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

[Eric D. <ede...@sy...>]

Great, thanks, this is a good discussion. It will be difficult to achieve
consensus, I suspect, but it's worth trying and doing the best we can. I'm
not sure what to make of Matt's suggestions of acronyms. On the one hand,
they're very specific and allow a long string of precise wording to be
condensed into a short object, but on the other hand, having a flotilla of
similar acronyms will probably seem ridiculous to all but a few of us who
think ontologies are a really neat idea.



In response to Sean's specific question: we view a "modified peptide" to
have a very specific mass modification configuration, e.g. phososerine on
the 8th residue. We do not have a term for a specific peptide sequence with
two phospho mods at unspecified locations.. maybe we should define that
concept as well.



Perhaps it makes sense to define all (most of) the possible concepts
clearly and assign them a specific acronym, and then assign terse common
names the most relevant ones. Tricky.



Thanks for chiming in, Karl. I think including PTM localization terms as
part of the definition set would be great. I've occasionally struggled to
find the right terms to describe a location/site where I think I know the
PTM is (or for which I have very strong evidence) versus a location/site
where the PTM might possibly be, among many. If we can achieve consistent
terminology for that, that might well be helpful.



Thanks,

Eric







*From:* Jones, Andy [mailto:And...@li...]
*Sent:* Thursday, February 27, 2014 6:51 AM
*To:* 'Mass spectrometry standard development'; '
psi...@li...'; 'psi...@li...
'
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo



I'm interested to hear this discussion. We're currently implementing
peptide-level FDR analysis in our mzidLibrary software, and were working on
the basis of "peptide+modification site" being the distinct unit for our
calculation, but Karl's email indicates to me that there isn't consensus on
how this is done. For the purposes of global stats, I understood that one
of the reasons for doing peptide-level stats was that there could be a
consistent incorrect assignment occurring across all spectra reporting on
the same peptide. The spectra for a modified peptide would be rather
different from the unmodified peptide, so I don't understand the logic for
collapsing these down into one entry (except for protein inference by a
peptide sequence centric approach).



Best wishes

Andy







*From:* Karl Clauser
[mailto:cl...@br...<cl...@br...>]

*Sent:* 27 February 2014 14:30
*To:* 'Mass spectrometry standard development';
psi...@li...; psi...@li...
*Subject:* Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo



Hi folks,



I just wanted to chime in here that I think Eric's definition of distinct
peptide is pretty close to that which is the most widely-implemented
interpretation.

                >distinct peptide - a distinct sequence of amino acids
irrespective of mass modifications or charge.

It is most applicable when one is doing protein parsimony and reporting a
peptide-level FDR. It is also consistent with the MCP publication
guidelines.



I'm not sure I see much practical use for

                > modified peptide - one species of distinct peptide with a
specific mass-modification configuration, but irrespective of charge.



Instead I'd like to toss into the discussion a related concept
(modification site), which is often used in papers that enrich for a
particular PTM (phospho, acetyl, ubiquitin). While the concept is often
used there isn't really a generic name. For example it is used when
reporting the total number of phosphosites observed, since the count of
unique peptides isn't usually relevant.



Modification site - a particular modification localized to a specific
position in the protein sequence, irrespective of precursor charge, missed
cleavage state, or precursor mass. When collapsing a set of PSM's to the
site level, allowing for different missed cleavage states is challenging
because one typically needs to know the AA position in the intact protein
sequence, thus protein parsimony issues arise.



Note that when counting the total number of phosphosites
identified/quantified, if a particular site is located in peptide that has
another nearby site then the singly and doubly phosphorylated observations
of those are often reported separately because they may be regulated
differently and have dissimilar quantitative behavior.



--Karl



-----Original Message-----
From: Jones, Andy
[mailto:And...@li...<And...@li...>]

Sent: Thursday, February 27, 2014 8:46 AM
To: 'psi...@li...'; 'Mass spectrometry standard
development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo



Hi all,



Wow - I didn't realise my request for a new CV term would open such a can
of worms :-)



Probably it makes sense to defer this update (support for peptide-level
stats) and discuss as an agenda item at the PSI meeting in April, then do
as a minor update to mzid 1.2 at a later stage?



I want to get mzid 1.2 in process ASAP, and I don't think we'll get this
resolved very easily, since as you mention there are lots of different ways
of doing "peptide-level stats", and we should try get it right.

Cheers

Andy





-----Original Message-----

From: Seymour, Sean L [mailto:Sea...@ab...<Sea...@ab...>
]

Sent: 26 February 2014 17:55

To: Eric Deutsch; Mass spectrometry standard development;
psi...@li...; psi...@li...

Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo



Hi Eric,



I like your breakdown of the concepts, but not all the names. Your
'distinct peptide' is really a 'sequence' to me. And I'm not too crazy
about using 'modified peptide' as the term for what I described as my view
of what a 'peptide' is, particularly because this would have to apply to
unmodified peptides as well.



While I find myself using them, I find the modifiers 'distinct' and
'unique' to be ambiguous as well, since these are used by some framings of
protein inference to refer to a peptide or sequence's degree of specificity
to just one protein. I guess this is where I come back to 'peptide' and
'sequence' having the most straightforward meaning if we insist on clear
definitions most consistent with what those words really mean and would be
understood to mean outside of our little domain. I'm fine with 'PSM' and
'Peptide ion' for your first two, but would prefer just 'Peptide' and
'Sequence' for the last two. A peptide is an actual compound that has a
structural formula and a sequence has...well, a sequence.



It's also not completely clear to me from the definition of the third if
you count different arrangements of the same mods on the same sequence as
different peptides. From the chemist's perspective, they are different.
They would come in different vials from a different number in a catalog and
have different structural formulae. I think that's what you mean, but it
could be spelled out a little more.



I definitely think we can agree on terms but allow room for slightly varied
concepts for things deeply interior to our domain. We were should really
try to agree and use things consistently is where our domain interfaces
with other who don't understand all the fine points of mass spec and
proteomics. This is where I think the terms 'peptide' and 'sequence' are
particularly important. No biologist should ever have to know or care about
a PSM or how many charge states a peptide ionizes to in a mass spec.



Sean



-----Original Message-----

From: Eric Deutsch
[mailto:ede...@sy...<ede...@sy...>
]

Sent: Wednesday, February 26, 2014 9:29 AM

To: Mass spectrometry standard development; Seymour, Sean L;
psi...@li...; psi...@li...

Cc: Eric Deutsch

Subject: RE: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo



FWIW, these are the terms we try to use (PeptideAtlas/TPP):



PSM - peptide-spectrum match - one instance of a spectrum matched to a
specific peptide ion.



peptide ion - one species of distinct peptide with a specific charge state
and mass-modification configuration.



modified peptide - one species of distinct peptide with a specific
mass-modification configuration, but irrespective of charge.





distinct peptide - a distinct sequence of amino acids irrespective of mass
modifications or charge.





We try not to use peptide by itself because it is so ambiguous.



Do you think it's possible to all agree on a set of terms and definitions?



E







-----Original Message-----

From: Jones, Andy
[mailto:And...@li...<And...@li...>
]

Sent: Wednesday, February 26, 2014 8:57 AM

To: 'Seymour, Sean L'; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo



Totally agree with what you're saying here - I think my concept of peptide
I intended here was the same as yours, but much less well elaborated. I
agree these terms have not been clearly defined by us ever, and perhaps we
should add a reference guide somewhere on the PSI site or in the mzid 1.2
spec doc we can refer to when we say "distinct peptide", "PSM" etc.



-----Original Message-----

From: Seymour, Sean L [mailto:Sea...@ab...<Sea...@ab...>
]

Sent: 26 February 2014 16:50

To: Jones, Andy; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo



Hi all,



If we're going to go down the very useful road of capturing attributes at
the level of the peptide, I think we need to very clearly define what we
mean by a peptide. To anyone with a chemistry background like myself, a
peptide would mean a structurally unique molecule. Different charges states
of this molecule are not different peptides, they are derivative states
that arise from the analytical process in the mass spec. Different
modification states of a sequence are different peptides. Different
arrangements of the same modifications on the same sequence are different
peptides. The same exact match to two different spectra is one peptide, not
two peptides. While this view may seem obvious to some of you, there is a
great range of how this term is used in my experience, including violation
of all of the previous specific statements.



Perhaps we've already clearly defined 'peptide' somewhere, and I don't need
to say this, but I think this is very important so I want to be sure.

I'm very much in favor of including concepts at this level since it is more
aligned with the physical analyte, sheds redundancy complications, and is
more useful when moving to targeted analyses via MRM or DIA. It might be
useful to develop/collect all our terms at this level to be sure we've
defined them right. Many concepts at the spectrum level have an analog at
the peptide level so it may be useful to map this out as well - ex RT of
MS2 trigger vs. RT of the peptide apex of elution.



Sean







-----Original Message-----

From: Jones, Andy
[mailto:And...@li...<And...@li...>
]

Sent: Wednesday, February 26, 2014 8:24 AM

To: 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo



Thanks for this Gerhard. Apologies, I discovered a further term which we
would like added (discussed here:

http://code.google.com/p/psi-pi/issues/detail?id=80):



Term: "best PSM per peptide"

No value slot

Def: "To support peptide-level statistical approaches or scores, this term
SHOULD be used to annotate the best scoring PSM reporting on a given
distinct peptide (sequence and modifications distinct)"







-----Original Message-----

From: Gerhard Mayer
[mailto:Ger...@ru...<Ger...@ru...>
]

Sent: 26 February 2014 14:45

To: psi...@li...;

psi...@li...; Mass spectrometry standard development

Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo



Dear proteomics community,



attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.



It contains two new CV terms for flagging the SpectrumIdentificationLists
in mzIdentML version 1.2.





Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:

=====================================================

No changed CV terms





New CV terms in version 3.61.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002438

name: spectrum identification list result details

def: "Information about the list of PSMs (SpectrumIdentificationList)."

[PSI:PI]

relationship: part_of MS:1001000 ! spectrum interpretation



[Term]

id: MS:1002439

name: final PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is the final set of identifications to be interpreted by
consuming software. Amongst the set of SpectrumIdentificationList(s) that
are flagged with the term, each spectrum must not be referenced from more
than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



[Term]

id: MS:1002440

name: intermediate PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is not the final set of identifications to be interpreted by
consuming software. This term should be used when results are provided from
multiple search engines for the results from each search engine before they
are combined to give consensus identifications. Amongst the set of
SpectrumIdentificationList(s) that are flagged with the term, each spectrum
may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



Best Regards,

Gerhard

--

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics /
Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    ger...@ru...

Web:     http://www.medizinisches-proteom-center.de



--------------------------------------------------------------------------

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binding effect of any digital or other electronic reproduction of a manual
signature that is included in any attachment.







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Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

I’m interested to hear this discussion. We’re currently implementing peptide-level FDR analysis in our mzidLibrary software, and were working on the basis of “peptide+modification site” being the distinct unit for our calculation, but Karl’s email indicates to me that there isn’t consensus on how this is done. For the purposes of global stats, I understood that one of the reasons for doing peptide-level stats was that there could be a consistent incorrect assignment occurring across all spectra reporting on the same peptide. The spectra for a modified peptide would be rather different from the unmodified peptide, so I don’t understand the logic for collapsing these down into one entry (except for protein inference by a peptide sequence centric approach).

Best wishes
Andy



From: Karl Clauser [mailto:cl...@br...]
Sent: 27 February 2014 14:30
To: 'Mass spectrometry standard development'; psi...@li...; psi...@li...
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo


Hi folks,



I just wanted to chime in here that I think Eric's definition of distinct peptide is pretty close to that which is the most widely-implemented interpretation.

                >distinct peptide - a distinct sequence of amino acids irrespective of mass modifications or charge.

It is most applicable when one is doing protein parsimony and reporting a peptide-level FDR. It is also consistent with the MCP publication guidelines.



I'm not sure I see much practical use for

                > modified peptide - one species of distinct peptide with a specific mass-modification configuration, but irrespective of charge.



Instead I'd like to toss into the discussion a related concept (modification site), which is often used in papers that enrich for a particular PTM (phospho, acetyl, ubiquitin). While the concept is often used there isn't really a generic name. For example it is used when reporting the total number of phosphosites observed, since the count of unique peptides isn't usually relevant.



Modification site – a particular modification localized to a specific position in the protein sequence, irrespective of precursor charge, missed cleavage state, or precursor mass. When collapsing a set of PSM's to the site level, allowing for different missed cleavage states is challenging because one typically needs to know the AA position in the intact protein sequence, thus protein parsimony issues arise.



Note that when counting the total number of phosphosites identified/quantified, if a particular site is located in peptide that has another nearby site then the singly and doubly phosphorylated observations of those are often reported separately because they may be regulated differently and have dissimilar quantitative behavior.



--Karl



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Thursday, February 27, 2014 8:46 AM
To: 'psi...@li...'; 'Mass spectrometry standard development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo



Hi all,



Wow - I didn't realise my request for a new CV term would open such a can of worms :-)



Probably it makes sense to defer this update (support for peptide-level stats) and discuss as an agenda item at the PSI meeting in April, then do as a minor update to mzid 1.2 at a later stage?



I want to get mzid 1.2 in process ASAP, and I don't think we'll get this resolved very easily, since as you mention there are lots of different ways of doing "peptide-level stats", and we should try get it right.

Cheers

Andy





-----Original Message-----

From: Seymour, Sean L [mailto:Sea...@ab...]

Sent: 26 February 2014 17:55

To: Eric Deutsch; Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>

Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo



Hi Eric,



I like your breakdown of the concepts, but not all the names. Your 'distinct peptide' is really a 'sequence' to me. And I'm not too crazy about using 'modified peptide' as the term for what I described as my view of what a 'peptide' is, particularly because this would have to apply to unmodified peptides as well.



While I find myself using them, I find the modifiers 'distinct' and 'unique' to be ambiguous as well, since these are used by some framings of protein inference to refer to a peptide or sequence's degree of specificity to just one protein. I guess this is where I come back to 'peptide' and 'sequence' having the most straightforward meaning if we insist on clear definitions most consistent with what those words really mean and would be understood to mean outside of our little domain. I'm fine with 'PSM' and 'Peptide ion' for your first two, but would prefer just 'Peptide' and 'Sequence' for the last two. A peptide is an actual compound that has a structural formula and a sequence has...well, a sequence.



It's also not completely clear to me from the definition of the third if you count different arrangements of the same mods on the same sequence as different peptides. From the chemist's perspective, they are different. They would come in different vials from a different number in a catalog and have different structural formulae. I think that's what you mean, but it could be spelled out a little more.



I definitely think we can agree on terms but allow room for slightly varied concepts for things deeply interior to our domain. We were should really try to agree and use things consistently is where our domain interfaces with other who don't understand all the fine points of mass spec and proteomics. This is where I think the terms 'peptide' and 'sequence' are particularly important. No biologist should ever have to know or care about a PSM or how many charge states a peptide ionizes to in a mass spec.



Sean



-----Original Message-----

From: Eric Deutsch [mailto:ede...@sy...]

Sent: Wednesday, February 26, 2014 9:29 AM

To: Mass spectrometry standard development; Seymour, Sean L; psi...@li...<mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>

Cc: Eric Deutsch

Subject: RE: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo



FWIW, these are the terms we try to use (PeptideAtlas/TPP):



PSM - peptide-spectrum match - one instance of a spectrum matched to a specific peptide ion.



peptide ion - one species of distinct peptide with a specific charge state and mass-modification configuration.



modified peptide - one species of distinct peptide with a specific mass-modification configuration, but irrespective of charge.





distinct peptide - a distinct sequence of amino acids irrespective of mass modifications or charge.





We try not to use peptide by itself because it is so ambiguous.



Do you think it's possible to all agree on a set of terms and definitions?



E







-----Original Message-----

From: Jones, Andy [mailto:And...@li...]

Sent: Wednesday, February 26, 2014 8:57 AM

To: 'Seymour, Sean L'; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard development'

Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo



Totally agree with what you're saying here - I think my concept of peptide I intended here was the same as yours, but much less well elaborated. I agree these terms have not been clearly defined by us ever, and perhaps we should add a reference guide somewhere on the PSI site or in the mzid 1.2 spec doc we can refer to when we say "distinct peptide", "PSM" etc.



-----Original Message-----

From: Seymour, Sean L [mailto:Sea...@ab...]

Sent: 26 February 2014 16:50

To: Jones, Andy; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard development'

Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo



Hi all,



If we're going to go down the very useful road of capturing attributes at the level of the peptide, I think we need to very clearly define what we mean by a peptide. To anyone with a chemistry background like myself, a peptide would mean a structurally unique molecule. Different charges states of this molecule are not different peptides, they are derivative states that arise from the analytical process in the mass spec. Different modification states of a sequence are different peptides. Different arrangements of the same modifications on the same sequence are different peptides. The same exact match to two different spectra is one peptide, not two peptides. While this view may seem obvious to some of you, there is a great range of how this term is used in my experience, including violation of all of the previous specific statements.



Perhaps we've already clearly defined 'peptide' somewhere, and I don't need to say this, but I think this is very important so I want to be sure.

I'm very much in favor of including concepts at this level since it is more aligned with the physical analyte, sheds redundancy complications, and is more useful when moving to targeted analyses via MRM or DIA. It might be useful to develop/collect all our terms at this level to be sure we've defined them right. Many concepts at the spectrum level have an analog at the peptide level so it may be useful to map this out as well - ex RT of MS2 trigger vs. RT of the peptide apex of elution.



Sean







-----Original Message-----

From: Jones, Andy [mailto:And...@li...]

Sent: Wednesday, February 26, 2014 8:24 AM

To: 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard development'

Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo



Thanks for this Gerhard. Apologies, I discovered a further term which we would like added (discussed here:

http://code.google.com/p/psi-pi/issues/detail?id=80):



Term: "best PSM per peptide"

No value slot

Def: "To support peptide-level statistical approaches or scores, this term SHOULD be used to annotate the best scoring PSM reporting on a given distinct peptide (sequence and modifications distinct)"







-----Original Message-----

From: Gerhard Mayer [mailto:Ger...@ru...]

Sent: 26 February 2014 14:45

To: psi...@li...<mailto:psi...@li...>;

psi...@li...<mailto:psi...@li...>; Mass spectrometry standard development

Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo



Dear proteomics community,



attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.



It contains two new CV terms for flagging the SpectrumIdentificationLists in mzIdentML version 1.2.





Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:

=====================================================

No changed CV terms





New CV terms in version 3.61.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002438

name: spectrum identification list result details

def: "Information about the list of PSMs (SpectrumIdentificationList)."

[PSI:PI]

relationship: part_of MS:1001000 ! spectrum interpretation



[Term]

id: MS:1002439

name: final PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



[Term]

id: MS:1002440

name: intermediate PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details



Best Regards,

Gerhard

--

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150

D-44801 Bochum



Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:    ger...@ru...<mailto:ger...@ru...>

Web:     http://www.medizinisches-proteom-center.de



--------------------------------------------------------------------------

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Network behavioral analysis & security monitoring. All-in-one tool.

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Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

[Karl C. <cl...@br...>]

Hi folks,

 

I just wanted to chime in here that I think Eric's definition of distinct
peptide is pretty close to that which is the most widely-implemented
interpretation.

                >distinct peptide - a distinct sequence of amino acids
irrespective of mass modifications or charge.

It is most applicable when one is doing protein parsimony and reporting a
peptide-level FDR. It is also consistent with the MCP publication
guidelines.

 

I'm not sure I see much practical use for 

                > modified peptide - one species of distinct peptide with a
specific mass-modification configuration, but irrespective of charge.

 

Instead I'd like to toss into the discussion a related concept (modification
site), which is often used in papers that enrich for a particular PTM
(phospho, acetyl, ubiquitin). While the concept is often used there isn't
really a generic name. For example it is used when reporting the total
number of phosphosites observed, since the count of unique peptides isn't
usually relevant.

 

Modification site – a particular modification localized to a specific
position in the protein sequence, irrespective of precursor charge, missed
cleavage state, or precursor mass. When collapsing a set of PSM's to the
site level, allowing for different missed cleavage states is challenging
because one typically needs to know the AA position in the intact protein
sequence, thus protein parsimony issues arise.

 

Note that when counting the total number of phosphosites
identified/quantified, if a particular site is located in peptide that has
another nearby site then the singly and doubly phosphorylated observations
of those are often reported separately because they may be regulated
differently and have dissimilar quantitative behavior.

 

--Karl

 

-----Original Message-----
From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, February 27, 2014 8:46 AM
To: 'psi...@li...'; 'Mass spectrometry standard
development'; 'psi...@li...'
Subject: Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Hi all,

 

Wow - I didn't realise my request for a new CV term would open such a can of
worms :-)

 

Probably it makes sense to defer this update (support for peptide-level
stats) and discuss as an agenda item at the PSI meeting in April, then do as
a minor update to mzid 1.2 at a later stage?

 

I want to get mzid 1.2 in process ASAP, and I don't think we'll get this
resolved very easily, since as you mention there are lots of different ways
of doing "peptide-level stats", and we should try get it right.

Cheers

Andy

 

 

-----Original Message-----

From: Seymour, Sean L [ <mailto:Sea...@ab...>
mailto:Sea...@ab...]

Sent: 26 February 2014 17:55

To: Eric Deutsch; Mass spectrometry standard development;
<mailto:psi...@li...>
psi...@li...;
<mailto:psi...@li...>
psi...@li...

Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] [Psidev-pi-dev] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Hi Eric,

 

I like your breakdown of the concepts, but not all the names. Your 'distinct
peptide' is really a 'sequence' to me. And I'm not too crazy about using
'modified peptide' as the term for what I described as my view of what a
'peptide' is, particularly because this would have to apply to unmodified
peptides as well. 

 

While I find myself using them, I find the modifiers 'distinct' and 'unique'
to be ambiguous as well, since these are used by some framings of protein
inference to refer to a peptide or sequence's degree of specificity to just
one protein. I guess this is where I come back to 'peptide' and 'sequence'
having the most straightforward meaning if we insist on clear definitions
most consistent with what those words really mean and would be understood to
mean outside of our little domain. I'm fine with 'PSM' and 'Peptide ion' for
your first two, but would prefer just 'Peptide' and 'Sequence' for the last
two. A peptide is an actual compound that has a structural formula and a
sequence has...well, a sequence.

 

It's also not completely clear to me from the definition of the third if you
count different arrangements of the same mods on the same sequence as
different peptides. From the chemist's perspective, they are different. They
would come in different vials from a different number in a catalog and have
different structural formulae. I think that's what you mean, but it could be
spelled out a little more.

 

I definitely think we can agree on terms but allow room for slightly varied
concepts for things deeply interior to our domain. We were should really try
to agree and use things consistently is where our domain interfaces with
other who don't understand all the fine points of mass spec and proteomics.
This is where I think the terms 'peptide' and 'sequence' are particularly
important. No biologist should ever have to know or care about a PSM or how
many charge states a peptide ionizes to in a mass spec.

 

Sean

 

-----Original Message-----

From: Eric Deutsch [ <mailto:ede...@sy...>
mailto:ede...@sy...]

Sent: Wednesday, February 26, 2014 9:29 AM

To: Mass spectrometry standard development; Seymour, Sean L;
<mailto:psi...@li...>
psi...@li...;
<mailto:psi...@li...>
psi...@li...

Cc: Eric Deutsch

Subject: RE: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

FWIW, these are the terms we try to use (PeptideAtlas/TPP):

 

PSM - peptide-spectrum match - one instance of a spectrum matched to a
specific peptide ion.

 

peptide ion - one species of distinct peptide with a specific charge state
and mass-modification configuration.

 

modified peptide - one species of distinct peptide with a specific
mass-modification configuration, but irrespective of charge.

 

 

distinct peptide - a distinct sequence of amino acids irrespective of mass
modifications or charge.

 

 

We try not to use peptide by itself because it is so ambiguous.

 

Do you think it's possible to all agree on a set of terms and definitions?

 

E

 

 

 

-----Original Message-----

From: Jones, Andy [ <mailto:And...@li...>
mailto:And...@li...]

Sent: Wednesday, February 26, 2014 8:57 AM

To: 'Seymour, Sean L'; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo

 

Totally agree with what you're saying here - I think my concept of peptide I
intended here was the same as yours, but much less well elaborated. I agree
these terms have not been clearly defined by us ever, and perhaps we should
add a reference guide somewhere on the PSI site or in the mzid 1.2 spec doc
we can refer to when we say "distinct peptide", "PSM" etc.

 

-----Original Message-----

From: Seymour, Sean L [ <mailto:Sea...@ab...>
mailto:Sea...@ab...]

Sent: 26 February 2014 16:50

To: Jones, Andy; 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo

 

Hi all,

 

If we're going to go down the very useful road of capturing attributes at
the level of the peptide, I think we need to very clearly define what we
mean by a peptide. To anyone with a chemistry background like myself, a
peptide would mean a structurally unique molecule. Different charges states
of this molecule are not different peptides, they are derivative states that
arise from the analytical process in the mass spec. Different modification
states of a sequence are different peptides. Different arrangements of the
same modifications on the same sequence are different peptides. The same
exact match to two different spectra is one peptide, not two peptides. While
this view may seem obvious to some of you, there is a great range of how
this term is used in my experience, including violation of all of the
previous specific statements.

 

Perhaps we've already clearly defined 'peptide' somewhere, and I don't need
to say this, but I think this is very important so I want to be sure.

I'm very much in favor of including concepts at this level since it is more
aligned with the physical analyte, sheds redundancy complications, and is
more useful when moving to targeted analyses via MRM or DIA. It might be
useful to develop/collect all our terms at this level to be sure we've
defined them right. Many concepts at the spectrum level have an analog at
the peptide level so it may be useful to map this out as well - ex RT of MS2
trigger vs. RT of the peptide apex of elution.

 

Sean

 

 

 

-----Original Message-----

From: Jones, Andy [ <mailto:And...@li...>
mailto:And...@li...]

Sent: Wednesday, February 26, 2014 8:24 AM

To: 'psi...@li...';

'psi...@li...'; 'Mass spectrometry standard
development'

Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate

3.61.0_rc1 of psi-ms.obo

 

Thanks for this Gerhard. Apologies, I discovered a further term which we
would like added (discussed here:

 <http://code.google.com/p/psi-pi/issues/detail?id=80>
http://code.google.com/p/psi-pi/issues/detail?id=80):

 

Term: "best PSM per peptide"

No value slot

Def: "To support peptide-level statistical approaches or scores, this term
SHOULD be used to annotate the best scoring PSM reporting on a given
distinct peptide (sequence and modifications distinct)"

 

 

 

-----Original Message-----

From: Gerhard Mayer [ <mailto:Ger...@ru...>
mailto:Ger...@ru...]

Sent: 26 February 2014 14:45

To:  <mailto:psi...@li...>
psi...@li...;

 <mailto:psi...@li...>
psi...@li...; Mass spectrometry standard development

Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

 

Dear proteomics community,

 

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

 

It contains two new CV terms for flagging the SpectrumIdentificationLists in
mzIdentML version 1.2.

 

 

Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:

=====================================================

No changed CV terms

 

 

New CV terms in version 3.61.0_rc1 of psi-ms.obo:

=================================================

[Term]

id: MS:1002438

name: spectrum identification list result details

def: "Information about the list of PSMs (SpectrumIdentificationList)."

[PSI:PI]

relationship: part_of MS:1001000 ! spectrum interpretation

 

[Term]

id: MS:1002439

name: final PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that
this is the final set of identifications to be interpreted by consuming
software. Amongst the set of SpectrumIdentificationList(s) that are flagged
with the term, each spectrum must not be referenced from more than one
SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details

 

[Term]

id: MS:1002440

name: intermediate PSM list

def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that
this is not the final set of identifications to be interpreted by consuming
software. This term should be used when results are provided from multiple
search engines for the results from each search engine before they are
combined to give consensus identifications. Amongst the set of
SpectrumIdentificationList(s) that are flagged with the term, each spectrum
may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]

is_a: MS:1002438 ! spectrum identification list result details

 

Best Regards,

Gerhard

--

---

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics /
Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150

D-44801 Bochum

 

Phone: +49(0)234/32-21006

Fax:        +49(0)234/32-14554

Email:     <mailto:ger...@ru...> ger...@ru...

Web:      <http://www.medizinisches-proteom-center.de>
http://www.medizinisches-proteom-center.de

 

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of, any agreement; provided that the foregoing does not invalidate the
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the sender and delete this message.  The sender disclaims that the content
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agreement; provided that the foregoing does not invalidate the binding
effect of any digital or other electronic reproduction of a manual signature
that is included in any attachment.

 

 

 

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Re: [Psidev-ms-dev] [Psidev-ms-vocab] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

Hi all,

Wow - I didn't realise my request for a new CV term would open such a can of worms :-)

Probably it makes sense to defer this update (support for peptide-level stats) and discuss as an agenda item at the PSI meeting in April, then do as a minor update to mzid 1.2 at a later stage?

I want to get mzid 1.2 in process ASAP, and I don't think we'll get this resolved very easily, since as you mention there are lots of different ways of doing "peptide-level stats", and we should try get it right.
Cheers
Andy


-----Original Message-----
From: Seymour, Sean L [mailto:Sea...@ab...] 
Sent: 26 February 2014 17:55
To: Eric Deutsch; Mass spectrometry standard development; psi...@li...; psi...@li...
Subject: Re: [Psidev-ms-vocab] [Psidev-ms-dev] [Psidev-pi-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

Hi Eric,

I like your breakdown of the concepts, but not all the names. Your 'distinct peptide' is really a 'sequence' to me. And I'm not too crazy about using 'modified peptide' as the term for what I described as my view of what a 'peptide' is, particularly because this would have to apply to unmodified peptides as well. 

While I find myself using them, I find the modifiers 'distinct' and 'unique' to be ambiguous as well, since these are used by some framings of protein inference to refer to a peptide or sequence's degree of specificity to just one protein. I guess this is where I come back to 'peptide' and 'sequence' having the most straightforward meaning if we insist on clear definitions most consistent with what those words really mean and would be understood to mean outside of our little domain. I'm fine with 'PSM' and 'Peptide ion' for your first two, but would prefer just 'Peptide' and 'Sequence' for the last two. A peptide is an actual compound that has a structural formula and a sequence has...well, a sequence.

It's also not completely clear to me from the definition of the third if you count different arrangements of the same mods on the same sequence as different peptides. From the chemist's perspective, they are different. They would come in different vials from a different number in a catalog and have different structural formulae. I think that's what you mean, but it could be spelled out a little more.

I definitely think we can agree on terms but allow room for slightly varied concepts for things deeply interior to our domain. We were should really try to agree and use things consistently is where our domain interfaces with other who don't understand all the fine points of mass spec and proteomics. This is where I think the terms 'peptide' and 'sequence' are particularly important. No biologist should ever have to know or care about a PSM or how many charge states a peptide ionizes to in a mass spec.

Sean

-----Original Message-----
From: Eric Deutsch [mailto:ede...@sy...]
Sent: Wednesday, February 26, 2014 9:29 AM
To: Mass spectrometry standard development; Seymour, Sean L; psi...@li...; psi...@li...
Cc: Eric Deutsch
Subject: RE: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

FWIW, these are the terms we try to use (PeptideAtlas/TPP):

PSM - peptide-spectrum match - one instance of a spectrum matched to a specific peptide ion.

peptide ion - one species of distinct peptide with a specific charge state and mass-modification configuration.

modified peptide - one species of distinct peptide with a specific mass-modification configuration, but irrespective of charge.

distinct peptide - a distinct sequence of amino acids irrespective of mass modifications or charge.


We try not to use peptide by itself because it is so ambiguous.

Do you think it's possible to all agree on a set of terms and definitions?

E



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:57 AM
To: 'Seymour, Sean L'; 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard development'
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Totally agree with what you're saying here - I think my concept of peptide I intended here was the same as yours, but much less well elaborated. I agree these terms have not been clearly defined by us ever, and perhaps we should add a reference guide somewhere on the PSI site or in the mzid 1.2 spec doc we can refer to when we say "distinct peptide", "PSM" etc.

-----Original Message-----
From: Seymour, Sean L [mailto:Sea...@ab...]
Sent: 26 February 2014 16:50
To: Jones, Andy; 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard development'
Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
3.61.0_rc1 of psi-ms.obo

Hi all,

If we're going to go down the very useful road of capturing attributes at the level of the peptide, I think we need to very clearly define what we mean by a peptide. To anyone with a chemistry background like myself, a peptide would mean a structurally unique molecule. Different charges states of this molecule are not different peptides, they are derivative states that arise from the analytical process in the mass spec. Different modification states of a sequence are different peptides. Different arrangements of the same modifications on the same sequence are different peptides. The same exact match to two different spectra is one peptide, not two peptides. While this view may seem obvious to some of you, there is a great range of how this term is used in my experience, including violation of all of the previous specific statements.

Perhaps we've already clearly defined 'peptide' somewhere, and I don't need to say this, but I think this is very important so I want to be sure.
I'm very much in favor of including concepts at this level since it is more aligned with the physical analyte, sheds redundancy complications, and is more useful when moving to targeted analyses via MRM or DIA. It might be useful to develop/collect all our terms at this level to be sure we've defined them right. Many concepts at the spectrum level have an analog at the peptide level so it may be useful to map this out as well - ex RT of MS2 trigger vs. RT of the peptide apex of elution.

Sean



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:24 AM
To: 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard development'
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
3.61.0_rc1 of psi-ms.obo

Thanks for this Gerhard. Apologies, I discovered a further term which we would like added (discussed here:
http://code.google.com/p/psi-pi/issues/detail?id=80):

Term: "best PSM per peptide"
No value slot
Def: "To support peptide-level statistical approaches or scores, this term SHOULD be used to annotate the best scoring PSM reporting on a given distinct peptide (sequence and modifications distinct)"



-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: 26 February 2014 14:45
To: psi...@li...;
psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the SpectrumIdentificationLists in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

--------------------------------------------------------------------------
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Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
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Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

[Seymour, S. L <Sea...@ab...>]

Hi Eric,

I like your breakdown of the concepts, but not all the names. Your 'distinct peptide' is really a 'sequence' to me. And I'm not too crazy about using 'modified peptide' as the term for what I described as my view of what a 'peptide' is, particularly because this would have to apply to unmodified peptides as well. 

While I find myself using them, I find the modifiers 'distinct' and 'unique' to be ambiguous as well, since these are used by some framings of protein inference to refer to a peptide or sequence's degree of specificity to just one protein. I guess this is where I come back to 'peptide' and 'sequence' having the most straightforward meaning if we insist on clear definitions most consistent with what those words really mean and would be understood to mean outside of our little domain. I'm fine with 'PSM' and 'Peptide ion' for your first two, but would prefer just 'Peptide' and 'Sequence' for the last two. A peptide is an actual compound that has a structural formula and a sequence has...well, a sequence.

It's also not completely clear to me from the definition of the third if you count different arrangements of the same mods on the same sequence as different peptides. From the chemist's perspective, they are different. They would come in different vials from a different number in a catalog and have different structural formulae. I think that's what you mean, but it could be spelled out a little more.

I definitely think we can agree on terms but allow room for slightly varied concepts for things deeply interior to our domain. We were should really try to agree and use things consistently is where our domain interfaces with other who don't understand all the fine points of mass spec and proteomics. This is where I think the terms 'peptide' and 'sequence' are particularly important. No biologist should ever have to know or care about a PSM or how many charge states a peptide ionizes to in a mass spec.

Sean

-----Original Message-----
From: Eric Deutsch [mailto:ede...@sy...] 
Sent: Wednesday, February 26, 2014 9:29 AM
To: Mass spectrometry standard development; Seymour, Sean L; psi...@li...; psi...@li...
Cc: Eric Deutsch
Subject: RE: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

FWIW, these are the terms we try to use (PeptideAtlas/TPP):

PSM - peptide-spectrum match - one instance of a spectrum matched to a specific peptide ion.

peptide ion - one species of distinct peptide with a specific charge state and mass-modification configuration.

modified peptide - one species of distinct peptide with a specific mass-modification configuration, but irrespective of charge.

distinct peptide - a distinct sequence of amino acids irrespective of mass modifications or charge.


We try not to use peptide by itself because it is so ambiguous.

Do you think it's possible to all agree on a set of terms and definitions?

E



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:57 AM
To: 'Seymour, Sean L'; 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard development'
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Totally agree with what you're saying here - I think my concept of peptide I intended here was the same as yours, but much less well elaborated. I agree these terms have not been clearly defined by us ever, and perhaps we should add a reference guide somewhere on the PSI site or in the mzid 1.2 spec doc we can refer to when we say "distinct peptide", "PSM" etc.

-----Original Message-----
From: Seymour, Sean L [mailto:Sea...@ab...]
Sent: 26 February 2014 16:50
To: Jones, Andy; 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard development'
Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
3.61.0_rc1 of psi-ms.obo

Hi all,

If we're going to go down the very useful road of capturing attributes at the level of the peptide, I think we need to very clearly define what we mean by a peptide. To anyone with a chemistry background like myself, a peptide would mean a structurally unique molecule. Different charges states of this molecule are not different peptides, they are derivative states that arise from the analytical process in the mass spec. Different modification states of a sequence are different peptides. Different arrangements of the same modifications on the same sequence are different peptides. The same exact match to two different spectra is one peptide, not two peptides. While this view may seem obvious to some of you, there is a great range of how this term is used in my experience, including violation of all of the previous specific statements.

Perhaps we've already clearly defined 'peptide' somewhere, and I don't need to say this, but I think this is very important so I want to be sure.
I'm very much in favor of including concepts at this level since it is more aligned with the physical analyte, sheds redundancy complications, and is more useful when moving to targeted analyses via MRM or DIA. It might be useful to develop/collect all our terms at this level to be sure we've defined them right. Many concepts at the spectrum level have an analog at the peptide level so it may be useful to map this out as well - ex RT of MS2 trigger vs. RT of the peptide apex of elution.

Sean



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:24 AM
To: 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard development'
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
3.61.0_rc1 of psi-ms.obo

Thanks for this Gerhard. Apologies, I discovered a further term which we would like added (discussed here:
http://code.google.com/p/psi-pi/issues/detail?id=80):

Term: "best PSM per peptide"
No value slot
Def: "To support peptide-level statistical approaches or scores, this term SHOULD be used to annotate the best scoring PSM reporting on a given distinct peptide (sequence and modifications distinct)"



-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: 26 February 2014 14:45
To: psi...@li...;
psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the SpectrumIdentificationLists in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

--------------------------------------------------------------------------
----
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Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clkt
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If you are not the intended recipient, please notify us by email by replying to the sender and delete this message.  The sender disclaims that the content of this email constitutes an offer to enter into, or the acceptance of, any agreement; provided that the foregoing does not invalidate the binding effect of any digital or other electronic reproduction of a manual signature that is included in any attachment.



--------------------------------------------------------------------------
----
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clkt
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Please be advised that this email may contain confidential 
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in any attachment.

Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

[Eric D. <ede...@sy...>]

FWIW, these are the terms we try to use (PeptideAtlas/TPP):

PSM - peptide-spectrum match - one instance of a spectrum matched to a
specific peptide ion.

peptide ion - one species of distinct peptide with a specific charge state
and mass-modification configuration.

modified peptide - one species of distinct peptide with a specific
mass-modification configuration, but irrespective of charge.

distinct peptide - a distinct sequence of amino acids irrespective of mass
modifications or charge.


We try not to use peptide by itself because it is so ambiguous.

Do you think it's possible to all agree on a set of terms and definitions?

E



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:57 AM
To: 'Seymour, Sean L'; 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard
development'
Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release
candidate 3.61.0_rc1 of psi-ms.obo

Totally agree with what you're saying here - I think my concept of peptide
I intended here was the same as yours, but much less well elaborated. I
agree these terms have not been clearly defined by us ever, and perhaps we
should add a reference guide somewhere on the PSI site or in the mzid 1.2
spec doc we can refer to when we say "distinct peptide", "PSM" etc.

-----Original Message-----
From: Seymour, Sean L [mailto:Sea...@ab...]
Sent: 26 February 2014 16:50
To: Jones, Andy; 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard
development'
Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
3.61.0_rc1 of psi-ms.obo

Hi all,

If we're going to go down the very useful road of capturing attributes at
the level of the peptide, I think we need to very clearly define what we
mean by a peptide. To anyone with a chemistry background like myself, a
peptide would mean a structurally unique molecule. Different charges
states of this molecule are not different peptides, they are derivative
states that arise from the analytical process in the mass spec. Different
modification states of a sequence are different peptides. Different
arrangements of the same modifications on the same sequence are different
peptides. The same exact match to two different spectra is one peptide,
not two peptides. While this view may seem obvious to some of you, there
is a great range of how this term is used in my experience, including
violation of all of the previous specific statements.

Perhaps we've already clearly defined 'peptide' somewhere, and I don't
need to say this, but I think this is very important so I want to be sure.
I'm very much in favor of including concepts at this level since it is
more aligned with the physical analyte, sheds redundancy complications,
and is more useful when moving to targeted analyses via MRM or DIA. It
might be useful to develop/collect all our terms at this level to be sure
we've defined them right. Many concepts at the spectrum level have an
analog at the peptide level so it may be useful to map this out as well -
ex RT of MS2 trigger vs. RT of the peptide apex of elution.

Sean



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:24 AM
To: 'psi...@li...';
'psi...@li...'; 'Mass spectrometry standard
development'
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate
3.61.0_rc1 of psi-ms.obo

Thanks for this Gerhard. Apologies, I discovered a further term which we
would like added (discussed here:
http://code.google.com/p/psi-pi/issues/detail?id=80):

Term: "best PSM per peptide"
No value slot
Def: "To support peptide-level statistical approaches or scores, this term
SHOULD be used to annotate the best scoring PSM reporting on a given
distinct peptide (sequence and modifications distinct)"



-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: 26 February 2014 14:45
To: psi...@li...;
psi...@li...; Mass spectrometry standard
development
Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the SpectrumIdentificationLists
in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is the final set of identifications to be interpreted by
consuming software. Amongst the set of SpectrumIdentificationList(s) that
are flagged with the term, each spectrum must not be referenced from more
than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is not the final set of identifications to be interpreted by
consuming software. This term should be used when results are provided
from multiple search engines for the results from each search engine
before they are combined to give consensus identifications. Amongst the
set of SpectrumIdentificationList(s) that are flagged with the term, each
spectrum may be referenced from more than one
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics /
Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

--------------------------------------------------------------------------
----
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clkt
rk
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev


Please be advised that this email may contain confidential information.
If you are not the intended recipient, please notify us by email by
replying to the sender and delete this message.  The sender disclaims that
the content of this email constitutes an offer to enter into, or the
acceptance of, any agreement; provided that the foregoing does not
invalidate the binding effect of any digital or other electronic
reproduction of a manual signature that is included in any attachment.



--------------------------------------------------------------------------
----
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clkt
rk
_______________________________________________
Psidev-ms-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

Totally agree with what you're saying here - I think my concept of peptide I intended here was the same as yours, but much less well elaborated. I agree these terms have not been clearly defined by us ever, and perhaps we should add a reference guide somewhere on the PSI site or in the mzid 1.2 spec doc we can refer to when we say "distinct peptide", "PSM" etc.

-----Original Message-----
From: Seymour, Sean L [mailto:Sea...@ab...] 
Sent: 26 February 2014 16:50
To: Jones, Andy; 'psi...@li...'; 'psi...@li...'; 'Mass spectrometry standard development'
Subject: RE: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Hi all,

If we're going to go down the very useful road of capturing attributes at the level of the peptide, I think we need to very clearly define what we mean by a peptide. To anyone with a chemistry background like myself, a peptide would mean a structurally unique molecule. Different charges states of this molecule are not different peptides, they are derivative states that arise from the analytical process in the mass spec. Different modification states of a sequence are different peptides. Different arrangements of the same modifications on the same sequence are different peptides. The same exact match to two different spectra is one peptide, not two peptides. While this view may seem obvious to some of you, there is a great range of how this term is used in my experience, including violation of all of the previous specific statements.

Perhaps we've already clearly defined 'peptide' somewhere, and I don't need to say this, but I think this is very important so I want to be sure. I'm very much in favor of including concepts at this level since it is more aligned with the physical analyte, sheds redundancy complications, and is more useful when moving to targeted analyses via MRM or DIA. It might be useful to develop/collect all our terms at this level to be sure we've defined them right. Many concepts at the spectrum level have an analog at the peptide level so it may be useful to map this out as well - ex RT of MS2 trigger vs. RT of the peptide apex of elution. 

Sean



-----Original Message-----
From: Jones, Andy [mailto:And...@li...]
Sent: Wednesday, February 26, 2014 8:24 AM
To: 'psi...@li...'; 'psi...@li...'; 'Mass spectrometry standard development'
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Thanks for this Gerhard. Apologies, I discovered a further term which we would like added (discussed here: http://code.google.com/p/psi-pi/issues/detail?id=80):

Term: "best PSM per peptide"
No value slot
Def: "To support peptide-level statistical approaches or scores, this term SHOULD be used to annotate the best scoring PSM reporting on a given distinct peptide (sequence and modifications distinct)"



-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: 26 February 2014 14:45
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the SpectrumIdentificationLists in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev


Please be advised that this email may contain confidential information.  If you are not the intended recipient, please notify us by email by replying to the sender and delete this message.  The sender disclaims that the content of this email constitutes an offer to enter into, or the acceptance of, any agreement; provided that the foregoing does not invalidate the binding effect of any digital or other electronic reproduction of a manual signature that is included in any attachment.

Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

[Seymour, S. L <Sea...@ab...>]

Hi all,

If we're going to go down the very useful road of capturing attributes at the level of the peptide, I think we need to very clearly define what we mean by a peptide. To anyone with a chemistry background like myself, a peptide would mean a structurally unique molecule. Different charges states of this molecule are not different peptides, they are derivative states that arise from the analytical process in the mass spec. Different modification states of a sequence are different peptides. Different arrangements of the same modifications on the same sequence are different peptides. The same exact match to two different spectra is one peptide, not two peptides. While this view may seem obvious to some of you, there is a great range of how this term is used in my experience, including violation of all of the previous specific statements.

Perhaps we've already clearly defined 'peptide' somewhere, and I don't need to say this, but I think this is very important so I want to be sure. I'm very much in favor of including concepts at this level since it is more aligned with the physical analyte, sheds redundancy complications, and is more useful when moving to targeted analyses via MRM or DIA. It might be useful to develop/collect all our terms at this level to be sure we've defined them right. Many concepts at the spectrum level have an analog at the peptide level so it may be useful to map this out as well - ex RT of MS2 trigger vs. RT of the peptide apex of elution. 

Sean



-----Original Message-----
From: Jones, Andy [mailto:And...@li...] 
Sent: Wednesday, February 26, 2014 8:24 AM
To: 'psi...@li...'; 'psi...@li...'; 'Mass spectrometry standard development'
Subject: Re: [Psidev-pi-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Thanks for this Gerhard. Apologies, I discovered a further term which we would like added (discussed here: http://code.google.com/p/psi-pi/issues/detail?id=80):

Term: "best PSM per peptide"
No value slot
Def: "To support peptide-level statistical approaches or scores, this term SHOULD be used to annotate the best scoring PSM reporting on a given distinct peptide (sequence and modifications distinct)"



-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...]
Sent: 26 February 2014 14:45
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the SpectrumIdentificationLists in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev


Please be advised that this email may contain confidential 
information.  If you are not the intended recipient, please notify us 
by email by replying to the sender and delete this message.  The 
sender disclaims that the content of this email constitutes an offer 
to enter into, or the acceptance of, any agreement; provided that the 
foregoing does not invalidate the binding effect of any digital or 
other electronic reproduction of a manual signature that is included 
in any attachment.

Re: [Psidev-ms-dev] [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

[Jones, A. <And...@li...>]

Thanks for this Gerhard. Apologies, I discovered a further term which we would like added (discussed here: http://code.google.com/p/psi-pi/issues/detail?id=80):

Term: "best PSM per peptide"
No value slot
Def: "To support peptide-level statistical approaches or scores, this term SHOULD be used to annotate the best scoring PSM reporting on a given distinct peptide (sequence and modifications distinct)"



-----Original Message-----
From: Gerhard Mayer [mailto:Ger...@ru...] 
Sent: 26 February 2014 14:45
To: psi...@li...; psi...@li...; Mass spectrometry standard development
Subject: [Psidev-ms-vocab] Release candidate 3.61.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the SpectrumIdentificationLists in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
--
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Bioinformatics / Biostatistics Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I), E.049a Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de

[Psidev-ms-dev] Release candidate 3.61.0_rc1 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached you find the release candidate 3.61.0_rc1 of the psi-ms.obo file.

It contains two new CV terms for flagging the
SpectrumIdentificationLists in mzIdentML version 1.2.


Changed CV terms in version 3.61.0_rc1 of psi-ms.obo:
=====================================================
No changed CV terms


New CV terms in version 3.61.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002438
name: spectrum identification list result details
def: "Information about the list of PSMs (SpectrumIdentificationList)."
[PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1002439
name: final PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is the final set of identifications to be interpreted by
consuming software. Amongst the set of SpectrumIdentificationList(s)
that are flagged with the term, each spectrum must not be referenced
from more than one SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

[Term]
id: MS:1002440
name: intermediate PSM list
def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate
that this is not the final set of identifications to be interpreted by
consuming software. This term should be used when results are provided
from multiple search engines for the results from each search engine
before they are combined to give consensus identifications. Amongst the
set of SpectrumIdentificationList(s) that are flagged with the term,
each spectrum may be referenced from more than one
SpectrumIdentificationResult." [PSI:PI]
is_a: MS:1002438 ! spectrum identification list result details

Best Regards,
Gerhard
-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de