psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] New version 4.1.25 of psi-ms.obo

[Felipe da V. L. <lep...@gm...>]

Thanks Gerhard

On Tue, Apr 9, 2019, 9:09 AM mayerg97 via Psidev-ms-dev <
psi...@li...> wrote:

> Dear proteomics/metabolomics community,
>
> following are the new/changed terms for the version 4.1.25 of the
> psi-ms.obo file. It can be downloaded from
> https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
>
>
> @Felipe: I left out PTMProphet:PTM Score (see Eric's last email):
> "
> PTM Prophet has quite a substantial number of metrics.
>      At the PSM level, we have:
>          normalized information content
>          number of localized modifications
>      At the site level, we have:
>          modification localization probability
>          O-score
>          M-score
> "
>
> If you need such PTMProphet metrics, then please send me a list with
> proposal for their exact name and definitions.
>
>
>
> New CV terms in version 4.1.25 of psi-ms.obo:
> =============================================
> [Term]
> id: MS:1003011
> name: pFind
> def: "Sequence-tag-based search engine pFind." [PMID:30295672]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1003012
> name: KSDP score
> def: "Kernel mass spectral dot product scoring function." [PMID:15044235]
> is_a: MS:1001143 ! PSM-level search engine specific statistic
> relationship: has_order MS:1002108 ! higher score better
>
> [Term]
> id: MS:1003013
> name: i3tms
> def: "i3-tms search engine and data-analysis software." [PSI:PI]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1003014
> name: MSFragger
> def: "A database search-based peptide identification tool." [PMID:28394336]
> is_a: MS:1001456 ! analysis software
>
> [Term]
> id: MS:1003015
> name: razor peptide
> def: "A peptide which is shared between protein groups and assigned to
> the protein group with the largest number of identified peptides." [PSI:PI]
> is_a: MS:1000860 ! peptide
>
> [Term]
> id: MS:1003016
> name: ProteinProphet:peptide weight
> def: "Fraction of peptide evidence attributable to a protein or a set of
> indistinguishable proteins." [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002490 ! peptide-level scoring
> is_a: MS:1001153 ! search engine specific score
> relationship: has_order MS:1002108 ! higher score better
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> [Term]
> id: MS:1003017
> name: ProteinProphet:peptide group weight
> def: "Fraction of peptide evidence attributable to a group of proteins."
> [PSI:PI]
> xref: value-type:xsd\:float "The allowed value-type for this CV term."
> is_a: MS:1002490 ! peptide-level scoring
> is_a: MS:1001153 ! search engine specific score
> relationship: has_order MS:1002108 ! higher score better
> relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
>
> [Term]
> id: MS:1003018
> name: Philosopher
> def: "General proteomics processing toolkit for shotgun proteomics."
> [https://philosopher.nesvilab.org/]
> is_a: MS:1001456 ! analysis software
>
>
>
> Changed CV terms in version 4.1.25 of psi-ms.obo:
> =================================================
> ************ adde synonym 'InterProphet'
> [Term]
> id: MS:1002288
> name: iProphet
> def: "A program in the TPP that calculates distinct peptide
> probabilities based on several lines of corroborating evidence including
> search results from multiple search engines via the pepXML format."
> [PMID:21876204]
> synonym: "InterProphet" EXACT []
> is_a: MS:1002286 ! Trans-Proteomic Pipeline software
>
>
> Best Regards,
> Gerhard
>
> --
>
> ----------------------------------------------------------------------
>
> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
>
> Scientific assistant
>
> Medizinisches Proteom-Center
>
> DEPARTMENT Medical Bioinformatics
>
> Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum
>
> Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554
>
> E-mail ger...@ru...
>
> www.medizinisches-proteom-center.de
>
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

[Psidev-ms-dev] New version 4.1.25 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the version 4.1.25 of the
psi-ms.obo file. It can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


@Felipe: I left out PTMProphet:PTM Score (see Eric's last email):
"
PTM Prophet has quite a substantial number of metrics.
     At the PSM level, we have:
         normalized information content
         number of localized modifications
     At the site level, we have:
         modification localization probability
         O-score
         M-score
"

If you need such PTMProphet metrics, then please send me a list with
proposal for their exact name and definitions.



New CV terms in version 4.1.25 of psi-ms.obo:
=============================================
[Term]
id: MS:1003011
name: pFind
def: "Sequence-tag-based search engine pFind." [PMID:30295672]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003012
name: KSDP score
def: "Kernel mass spectral dot product scoring function." [PMID:15044235]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003013
name: i3tms
def: "i3-tms search engine and data-analysis software." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003014
name: MSFragger
def: "A database search-based peptide identification tool." [PMID:28394336]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003015
name: razor peptide
def: "A peptide which is shared between protein groups and assigned to 
the protein group with the largest number of identified peptides." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003016
name: ProteinProphet:peptide weight
def: "Fraction of peptide evidence attributable to a protein or a set of 
indistinguishable proteins." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1003017
name: ProteinProphet:peptide group weight
def: "Fraction of peptide evidence attributable to a group of proteins." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1003018
name: Philosopher
def: "General proteomics processing toolkit for shotgun proteomics." 
[https://philosopher.nesvilab.org/]
is_a: MS:1001456 ! analysis software



Changed CV terms in version 4.1.25 of psi-ms.obo:
=================================================
************ adde synonym 'InterProphet'
[Term]
id: MS:1002288
name: iProphet
def: "A program in the TPP that calculates distinct peptide 
probabilities based on several lines of corroborating evidence including 
search results from multiple search engines via the pepXML format." 
[PMID:21876204]
synonym: "InterProphet" EXACT []
is_a: MS:1002286 ! Trans-Proteomic Pipeline software


Best Regards,
Gerhard

-- 

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

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

Scientific assistant

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554

E-mail ger...@ru...

www.medizinisches-proteom-center.de

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

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

Hi Gerhard, Felipe, thanks for this proposal, I have a few suggested
amendments, below in red (and *** in case color doesn't come through):



-----Original Message-----
From: mayerg97 via Psidev-ms-vocab <psi...@li...>

Dear proteomics/metabolomics community,



following are the new/changed terms for the release candidate 4.1.25_rc1 of
the psi-ms.obo file.





New CV terms in version 4.1.25_rc1 of psi-ms.obo:

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

[Term]

id: MS:1003011

name: pFind

def: "Sequence-tag-based search engine pFind." [PMID:30295672]

is_a: MS:1001456 ! analysis software



[Term]

id: MS:1003012

name: KSDP score

def: "Kernel mass spectral dot product scoring function." [PMID:15044235]

is_a: MS:1001143 ! PSM-level search engine specific statistic

relationship: has_order MS:1002108 ! higher score better



[Term]

id: MS:1003013

name: i3tms

def: "i3-tms search engine and data-analysis software." [PSI:PI]

is_a: MS:1001456 ! analysis software



[Term]

id: MS:1003014

name: MSFragger

def: "A database search-based peptide identification tool." [PMID:28394336]

is_a: MS:1002286 ! Trans-Proteomic Pipeline software



[Term]

id: MS:1003015

name: razor peptide

def: "A peptide which is shared between protein groups and assigned to

the protein group with the largest number of identified peptides." [PSI:PI]

is_a: MS:1000860 ! peptide



*** Begin

The following term should not be added as is. PTMProphet doesn’t have a
“PTM Score”.

x [Term]

x id: MS:1003016

x name: PTMProphet:PTM Score

x def: "The PTM score from PTMProphet software." [PSI:MS]

x xref: value-type:xsd\:string "The allowed value-type for this CV term."

X is_a: MS:1001968 ! PTM localization PSM-level statistic

X relationship: has_regexp MS:1002505 ! regular expression for modification
localization scoring

*** PTM Prophet has quite a substantial number of metrics.

At the PSM level, we have:

normalized information content

number of localized modifications

At the site level, we have:

               modification localization probability

               O-score

M-score

So I think we may actually want 5 terms, not a single term (and not called
PTM Score).

@Felipe, are you eager to write terms, or were you just thinking that we
will need something eventually?

The paper is currently under revision. I suggest we exclude 3016 from this
RC, and circle back in a few weeks to provide a more complete set of terms
and definitions. Does that sound okay?

*** End





[Term]

id: MS:1003017

name: ProteinProphet:peptide weight

def: "Peptide weight used for FDR filtering." [PSI:PI]

***def: "Fraction of peptide evidence attributable to a protein or a set of
indistinguishable proteins." [PSI:PI]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002490 ! peptide-level scoring

is_a: MS:1001153 ! search engine specific score

relationship: has_order MS:1002108 ! higher score better

relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

*** NOTE: Although some may use this for filtering, any score could
potentially be used for filtering, and I suggest that a potential use
should not be part of the definition, or else 100 other terms would also be
characterized as “for FDR filtering” (but I discourage that)



[Term]

id: MS:1003018

name: ProteinProphet:peptide group weight

def: "Peptide group weight used for FDR filtering." [PSI:PI]

***def: "Fraction of peptide evidence attributable to a group of proteins."
[PSI:PI]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1002490 ! peptide-level scoring

is_a: MS:1001153 ! search engine specific score

relationship: has_order MS:1002108 ! higher score better

relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive





Changed CV terms in version 4.1.25_rc1 of psi-ms.obo:

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

************ added synonym 'InterProphet'

[Term]

id: MS:1002288

name: iProphet

def: "A program in the TPP that calculates distinct peptide

probabilities based on several lines of corroborating evidence including

search results from multiple search engines via the pepXML format."

[PMID:21876204]

synonym: "InterProphet" EXACT []

is_a: MS:1002286 ! Trans-Proteomic Pipeline software



Best Regards,

Gerhard



-- 



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



Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER



Scientific assistant



Medizinisches Proteom-Center



DEPARTMENT Medical Bioinformatics



Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum



Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554



E-mail ger...@ru...



www.medizinisches-proteom-center.de







_______________________________________________

Psidev-ms-vocab mailing list

Psi...@li...

https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

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

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the release candidate 4.1.25_rc1 
of the
psi-ms.obo file.


New CV terms in version 4.1.25_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003011
name: pFind
def: "Sequence-tag-based search engine pFind." [PMID:30295672]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003012
name: KSDP score
def: "Kernel mass spectral dot product scoring function." [PMID:15044235]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1003013
name: i3tms
def: "i3-tms search engine and data-analysis software." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003014
name: MSFragger
def: "A database search-based peptide identification tool." [PMID:28394336]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

[Term]
id: MS:1003015
name: razor peptide
def: "A peptide which is shared between protein groups and assigned to 
the protein group with the largest number of identified peptides." [PSI:PI]
is_a: MS:1000860 ! peptide

[Term]
id: MS:1003016
name: PTMProphet:PTM Score
def: "The PTM score from PTMProphet software." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1003017
name: ProteinProphet:peptide weight
def: "Peptide weight used for FDR filtering." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1003018
name: ProteinProphet:peptide group weight
def: "Peptide group weight used for FDR filtering." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002490 ! peptide-level scoring
is_a: MS:1001153 ! search engine specific score
relationship: has_order MS:1002108 ! higher score better
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive


Changed CV terms in version 4.1.25_rc1 of psi-ms.obo:
=====================================================
************ added synonym 'InterProphet'
[Term]
id: MS:1002288
name: iProphet
def: "A program in the TPP that calculates distinct peptide 
probabilities based on several lines of corroborating evidence including 
search results from multiple search engines via the pepXML format." 
[PMID:21876204]
synonym: "InterProphet" EXACT []
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

Best Regards,
Gerhard

-- 

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

Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER

Scientific assistant

Medizinisches Proteom-Center

DEPARTMENT Medical Bioinformatics

Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554

E-mail ger...@ru...

www.medizinisches-proteom-center.de

[Psidev-ms-dev] New version 4.1.24 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the new release 4.1.24 of the
psi-ms.obo file. It contains a new term for the LPPtiger software.


New CV terms in version 4.1.24 of psi-ms.obo:
=============================================
[Term]
id: MS:1003010
name: LPPtiger
def: "Software for lipidome-specific prediction and identification of 
oxidized phospholipids from LC-MS datasets." [PMID:29123162]
is_a: MS:1002964 ! lipidomics analysis software
is_a: MS:1001457 ! data processing software


Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] New version 4.1.23 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new/changed terms for the new release 4.1.23 of the
psi-ms.obo file. The obsolete term 'database version' was reactivated.


New CV terms in version 4.1.23 of psi-ms.obo:
=============================================
No new terms


Changed CV terms in version 4.1.23 of psi-ms.obo:
=================================================
************ reactivated an obsolete term (for usage e.g. in mzTab)
[Term]
id: MS:1001016
name: database version
def: "Version of the search database. In mzIdentML use the attribute 
instead." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001011 ! search database details


Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru... <mailto:ger...@ru...>

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

Re: [Psidev-ms-dev] [Psidev-pi-dev] Training materials

[Horvatovich, P.L. <p.l...@ru...>]

Dear Andy and All,

Unfortunately, I will be not attending the meeting but would be interested
both for any tutorial materials and/or or materials (slides documents etc)
summarising the outcome of the meeting.

With best regards,

Peter Horvatovich

On Tue, Mar 12, 2019 at 12:30 PM Jones, Andy <And...@li...>
wrote:

> Hi all,
>
>
>
> Apologies for the cross-posting. The PSI meeting kicks off next Monday in
> Cape Town and hoping to see lots of you there. We are going to have lots of
> local participation from individuals new to PSI processes and standards,
> and as such, we have decided to give various tutorials in different slots
> to bring people up to speed.
>
>
>
> If you have any slides introducing one of the core PSI standards, data
> submission to a public repository or some other relevant aspect of data
> sharing, please send them over to me (off the mailing list), and I will add
> them to a shared drive that various people can access when we’re in Cape
> Town, so that we can be flexible at who gives a tutorial dependent on
> availability during the meeting.
>
>
>
> Best wishes
>
> Andy
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>


-- 

Peter Horvatovich
Associate Professor

University of Groningen
Faculty of Sciences and Engineering
Groningen Research Institute of Pharmacy
Analytical Biochemistry

Building 3226, Room 6.9
Antonius Deusinglaan 1
9713 AV Groningen
Internal Zip Code XB20
P.O. Box 196
9700 AD Groningen
The Netherlands

Telephone: +31-(0)50-363 3341
Fax: +31 (0)50 363 7582
Mobile: +31 (0)6 2459 7203
Email: p.l...@ru...
Homepage: www.biomac.nl

[Psidev-ms-dev] Training materials

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

Hi all,

Apologies for the cross-posting. The PSI meeting kicks off next Monday in Cape Town and hoping to see lots of you there. We are going to have lots of local participation from individuals new to PSI processes and standards, and as such, we have decided to give various tutorials in different slots to bring people up to speed.

If you have any slides introducing one of the core PSI standards, data submission to a public repository or some other relevant aspect of data sharing, please send them over to me (off the mailing list), and I will add them to a shared drive that various people can access when we're in Cape Town, so that we can be flexible at who gives a tutorial dependent on availability during the meeting.

Best wishes
Andy

[Psidev-ms-dev] New version 4.1.22 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.22 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

New CV terms in version 4.1.22 of psi-ms.obo:
=============================================
[Term]
id: MS:1003004
name: maXis II
def: "Bruker Daltonics' maXis II." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1003005
name: timsTOF Pro
def: "Bruker Daltonics' timsTOF Pro." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1003006
name: mean inverse reduced ion mobility array
def: "Array of inverse reduced ion mobilities, averaged from a matrix of 
binned m/z and ion mobility values, corresponding to a spectrum of 
individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003007
name: raw ion mobility array
def: "Array of raw drift times." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

[Term]
id: MS:1003008
name: raw inverse reduced ion mobility array
def: "Array of raw inverse reduced ion mobilities." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003009
name: Shimadzu Biotech LCD format
def: "Shimadzu Biotech LCD file format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: PEFF:0001035
name: initiator methionine
def: "N-terminal methionine residue of a protein that can be 
co-translationally cleaved." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for each 
VariantSimple item



Changed CV terms in version 4.1.22 of psi-ms.obo:
=================================================
************    "volt-second per square centimeter"
************ --> volt-second per square centimeter
[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
relationship: has_units MS:1002814 ! volt-second per square centimeter

************    Removed relationship: has_units MS:1002814 ! volt-second 
per square centimeter
[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times, averaged from a matrix of binned m/z and ion 
mobility values, corresponding to a spectrum of individual peaks encoded 
with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

************     MS:1002901 ! search engine specific score for proteoforms
************ --> MS:1002906 ! search engine specific score for proteoforms
[Term]
id: MS:1002930
name: TopPIC:proteoform-level FDR
def: "TopPIC proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002906 ! search engine specific score for proteoforms

[Term]
id: MS:1002952
name: TopMG:proteoform-level FDR
def: "TopMG proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002906 ! search engine specific score for proteoforms

Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] HUPO PSI recommendation document, PSI Extended FASTA Format (PEFF) 60-days public review

[Sylvie Ricard-B. <syl...@un...>]

Dear colleague, dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Mass Spectrometry Standards Working Group has submitted to the 
PSI document process a proposal for a PSI standard, the PSI Extended 
FASTA Format (PEFF). With the growing interest in proteogenomics, PEFF 
neatly addresses in a standardized manner the growing problem challenge 
of how to encode and use not just the protein sequences, but also the 
many known annotations on those protein sequences.
After having passed a 30-day review of the PSI steering group with minor 
changes, the proposed document version 1.0.0 DRAFT now goes through 
*60-days public comments and external review phase until* *March 25th, 
2019*).

The specification document and three example files 
(PEFF_Tiny_Valid.peff, SmallTestDB-PEFF1.0.peff and 
PEFF_AnnotID_Insulin_Valid.peff) are attached to this e-mail and are 
available in the PEFF GitHub repository https://github.com/HUPO-PSI/PEFF
Athough not included in this submission bundle, PEFF 1.0 files 
(according to the current draft specification) can already be downloaded 
from the neXtProt knowledge base, 
e.g.ftp://ftp.nextprot.org/pub/current_release/peff/
or through the web interface
https://www.nextprot.org/entry/NX_P00738/ (then select download link in 
upper right and choose PEFF)
https://api.nextprot.org/export/entry/NX_P00738.peff

Furthermore, software supporting PEFF is already being developed. The 
widely used Comet search engine supports the current draft of PEFF as 
described here http://comet-ms.sourceforge.net/release/release_201701/ 
(search on page for PEFF)

We invite both positive and negative comments on the relevance, 
correctness and clarity of the proposal (e.g. is the standard 
comprehensively described and are the examples in agreement with the 
specification?) as a whole or of specific parts of it.

Please feel free to forward this message to potentially interested 
colleagues. There is no requirement that people commenting should have 
had any prior contact with the PSI.

Please send comments by e-mail to syl...@un....

I thank you very much in advance for your valuable time and contribution.

Best regards.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...
http://www.icbms.fr
The French Society for Matrix Biology http://www.sfbmec.fr
The International Society for Matrix Biology http://ismb.org

[Psidev-ms-dev] PSI2019

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

Hi all,
A polite reminder to register for the PSI 2019 meeting, which will take place in Cape Town, SA, March 18-20 : http://psidev.info/hupo-psi-meeting-2019 if you are interested in data sharing for proteomics. We are also planning to run some training activities as part of the meeting, so that new participants can learn about existing standards and related software.

There is no cost to register for the meeting, although participants must pay their own travel and hotel costs. Please forward this on to anyone who you think might be interested in attending – we are always keen to attract new participants.

Best wishes
Andy

[Psidev-ms-dev] Release candidate 4.1.22_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release candidate 4.1.22_rc1 of the
psi-ms.obo file. It contains some added terms for Bruker instruments, for
a Shimadzu format, some error corrections and the updated terms for the
ion mobility arrays.


New CV terms in version 4.1.22_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1003004
name: maXis II
def: "Bruker Daltonics' maXis II." [PSI:MS]
is_a: MS:1001547 ! Bruker Daltonics maXis series

[Term]
id: MS:1003005
name: timsTOF Pro
def: "Bruker Daltonics' timsTOF Pro." [PSI:MS]
is_a: MS:1000122 ! Bruker Daltonics instrument model

[Term]
id: MS:1003006
name: mean inverse reduced ion mobility array
def: "Array of inverse reduced ion mobilities, averaged from a matrix of 
binned m/z and ion mobility values, corresponding to a spectrum of 
individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003007
name: raw ion mobility array
def: "Array of raw drift times." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

[Term]
id: MS:1003008
name: raw inverse reduced ion mobility array
def: "Array of raw inverse reduced ion mobilities." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units MS:1002814 ! volt-second per square centimeter

[Term]
id: MS:1003009
name: Shimadzu Biotech LCD format
def: "Shimadzu Biotech LCD file format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: PEFF:0001035
name: initiator methionine
def: "N-terminal methionine residue of a protein that can be 
co-translationally cleaved." [PSI:PEFF]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for each 
VariantSimple item



Changed CV terms in version 4.1.22_rc1 of psi-ms.obo:
=====================================================
************    "volt-second per square centimeter"
************ --> volt-second per square centimeter
[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1002892 ! ion mobility attribute
relationship: has_units MS:1002814 ! volt-second per square centimeter

************    Removed relationship: has_units MS:1002814 ! volt-second 
per square centimeter
[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times, averaged from a matrix of binned m/z and ion 
mobility values, corresponding to a spectrum of individual peaks encoded 
with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002893 ! ion mobility array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second

************     MS:1002901 ! search engine specific score for proteoforms
************ --> MS:1002906 ! search engine specific score for proteoforms
[Term]
id: MS:1002930
name: TopPIC:proteoform-level FDR
def: "TopPIC proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002906 ! search engine specific score for proteoforms

[Term]
id: MS:1002952
name: TopMG:proteoform-level FDR
def: "TopMG proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002906 ! search engine specific score for proteoforms


Best Regards,
Gerhard

-- 

*----------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*Scientific assistant*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail *ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] 答复: mzML base64binary conversion

[戚达(Da Q. <qi...@ge...>]

Hi Jim, Eric, Hannes

Thanks for all your replies. Python is exactly what I am looking for.

Best,
Da

发件人: Eric Deutsch <ede...@sy...>
发送时间: 2019年1月9日 8:40
收件人: Mass spectrometry standard development <psi...@li...>
抄送: Eric Deutsch <ede...@sy...>
主题: Re: [Psidev-ms-dev] mzML base64binary conversion

Hi Da Qi, there are many libraries out there for many languages that read mzML, so you may not need to re-implement it yourself. If Python is a language of choice, you might look at this recent paper:

http://www.mcponline.org/content/early/2018/12/18/mcp.RP118.001070?papetoc=



From: Shofstahl, Jim <jim...@th...<mailto:jim...@th...>>
Sent: Tuesday, January 8, 2019 6:50 AM
To: Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>
Subject: Re: [Psidev-ms-dev] mzML base64binary conversion

The spectral data (and chromatogram data) is stored as a Base64 encoded string.  Most of the programming languages will contain methods/functions to convert to and from the
Base64 format.  In C# those methods are part of the Convert class.

https://docs.microsoft.com/en-us/dotnet/api/system.convert?view=netframework-4.7.2

The FromBase64String method takes a string value and converts it to a byte[] array which can then be converted to another data type.  We tend to convert it using
as a MemoryStream object but there are other ways to do the conversion:

        protected static float[] ConvertToFloat(byte[] array, int points)
        {
            var arrayValues = new float[points];

            using (var memStream = new MemoryStream(array))
            {
                using (var binReader = new BinaryReader(memStream))
                {
                    for (var i = 0; i < points; i++)
                    {
                        arrayValues[i] = binReader.ReadSingle();
                    }
                }
            }

            // Return the value(s)
            return arrayValues;
        }

From: 戚达(Da Qi) <qi...@ge...<mailto:qi...@ge...>>
Sent: Monday, January 7, 2019 5:43 PM
To: psi...@li...<mailto:psi...@li...>
Subject: [Psidev-ms-dev] mzML base64binary conversion

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi,

Does anyone know how to decode the binary string to real data in mzML?

<binaryDataArrayList count="2">
                                                            <binaryDataArray encodedLength="268">
                                                                        <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
                                                            <binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>
                                                            </binaryDataArray>
                                                            <binaryDataArray encodedLength="268">
                                                                        <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
                                                            <binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>
                                                            </binaryDataArray>
                                                </binaryDataArrayList>

Best,
Da Qi

Re: [Psidev-ms-dev] mzML base64binary conversion

[Joshua K. <mob...@gm...>]

Hello,

I'm the author of the psims, and unfortunately it doesn't actually do any
reading itself, just writing. Internally, it uses Pyteomics (
https://pypi.org/project/pyteomics/) to read mzML files, which does decode
the array data for you. Pyteomics is great in that it gets you the data
into memory in a structure you can see through and then gets out of the
way. There's also pymzML (https://pypi.org/project/pymzML/), which provides
several additional tools to then manipulate the spectrum. And of course,
pyOpenMS.

While we're assuming Python is the target language, Hannes provided great
self-contained examples, but here's a function that lets you indicate your
data were compressed, and unpacks the data into a numpy array:
```python
import base64
import zlib

import numpy as np

def decode_array(bytestring, compressed=False, dtype=np.float32):
    # make sure we're dealing with bytes
    try:
        decoded_string = bytestring.encode("ascii")
    except AttributeError:
        decoded_string = bytestring
    decoded_string = base64.decodestring(decoded_string)
    if compressed:
        decoded_string = zlib.decompress(decoded_string)
    array = np.fromstring(decoded_string, dtype=dtype)
    return array
```

On Tue, Jan 8, 2019 at 8:10 PM Eric Deutsch <ede...@sy...>
wrote:

> Hi Da Qi, there are many libraries out there for many languages that read
> mzML, so you may not need to re-implement it yourself. If Python is a
> language of choice, you might look at this recent paper:
>
>
>
> http://www.mcponline.org/content/early/2018/12/18/mcp.RP118.001070?papetoc
> =
>
>
>
>
>
>
>
> *From:* Shofstahl, Jim <jim...@th...>
> *Sent:* Tuesday, January 8, 2019 6:50 AM
> *To:* Mass spectrometry standard development <
> psi...@li...>
> *Subject:* Re: [Psidev-ms-dev] mzML base64binary conversion
>
>
>
> The spectral data (and chromatogram data) is stored as a Base64 encoded
> string.  Most of the programming languages will contain methods/functions
> to convert to and from the
>
> Base64 format.  In C# those methods are part of the Convert class.
>
>
>
>
> https://docs.microsoft.com/en-us/dotnet/api/system.convert?view=netframework-4.7.2
>
>
>
> The FromBase64String method takes a string value and converts it to a
> byte[] array which can then be converted to another data type.  We tend to
> convert it using
>
> as a MemoryStream object but there are other ways to do the conversion:
>
>
>
>         protected static float[] ConvertToFloat(byte[] array, int points)
>
>         {
>
>             var arrayValues = new float[points];
>
>
>
>             using (var memStream = new MemoryStream(array))
>
>             {
>
>                 using (var binReader = new BinaryReader(memStream))
>
>                 {
>
>                     for (var i = 0; i < points; i++)
>
>                     {
>
>                         arrayValues[i] = binReader.ReadSingle();
>
>                     }
>
>                 }
>
>             }
>
>
>
>             // Return the value(s)
>
>             return arrayValues;
>
>         }
>
>
>
> *From:* 戚达(Da Qi) <qi...@ge...>
> *Sent:* Monday, January 7, 2019 5:43 PM
> *To:* psi...@li...
> *Subject:* [Psidev-ms-dev] mzML base64binary conversion
>
>
>
> *CAUTION:* This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe.
>
>
>
> Hi,
>
>
>
> Does anyone know how to decode the binary string to real data in mzML?
>
>
>
> <binaryDataArrayList count="2">
>
>
> <binaryDataArray encodedLength="268">
>
>
> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS"
> unitAccession="MS:1000040" unitName="m/z"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
>
>
> <binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>
>
>
> </binaryDataArray>
>
>
> <binaryDataArray encodedLength="268">
>
>
> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array"
> unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
>
>
> <binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>
>
>
> </binaryDataArray>
>
>                                                 </binaryDataArrayList>
>
>
>
> Best,
>
> Da Qi
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

Re: [Psidev-ms-dev] mzML base64binary conversion

[Hannes R. <han...@gm...>]

Hi Da Qi

As others pointed out, there are multiple libraries that do this. However,
a complete (and simple) solution in Python 2 would look like this:

import struct
coded="O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ="
struct.unpack('<%sf' % (len( coded.decode('base64') ) // 4),
coded.decode('base64'))

or in Python 3:

import struct, base64
coded=b"O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ="
struct.unpack('<%sf' % (len( base64.decodebytes(coded) ) // 4),
base64.decodebytes(coded))

Best regards

Hannes


On Mon, Jan 7, 2019 at 8:43 PM 戚达(Da Qi) <qi...@ge...> wrote:

> Hi,
>
>
>
> Does anyone know how to decode the binary string to real data in mzML?
>
>
>
> <binaryDataArrayList count="2">
>
>
> <binaryDataArray encodedLength="268">
>
>
> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS"
> unitAccession="MS:1000040" unitName="m/z"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
>
>
> <binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>
>
>
> </binaryDataArray>
>
>
> <binaryDataArray encodedLength="268">
>
>
> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array"
> unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
>
>
> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
>
>
> <binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>
>
>
> </binaryDataArray>
>
>                                                 </binaryDataArrayList>
>
>
>
> Best,
>
> Da Qi
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

Re: [Psidev-ms-dev] mzML base64binary conversion

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

Hi Da Qi, there are many libraries out there for many languages that read
mzML, so you may not need to re-implement it yourself. If Python is a
language of choice, you might look at this recent paper:



http://www.mcponline.org/content/early/2018/12/18/mcp.RP118.001070?papetoc=







*From:* Shofstahl, Jim <jim...@th...>
*Sent:* Tuesday, January 8, 2019 6:50 AM
*To:* Mass spectrometry standard development <
psi...@li...>
*Subject:* Re: [Psidev-ms-dev] mzML base64binary conversion



The spectral data (and chromatogram data) is stored as a Base64 encoded
string.  Most of the programming languages will contain methods/functions
to convert to and from the

Base64 format.  In C# those methods are part of the Convert class.



https://docs.microsoft.com/en-us/dotnet/api/system.convert?view=netframework-4.7.2



The FromBase64String method takes a string value and converts it to a
byte[] array which can then be converted to another data type.  We tend to
convert it using

as a MemoryStream object but there are other ways to do the conversion:



        protected static float[] ConvertToFloat(byte[] array, int points)

        {

            var arrayValues = new float[points];



            using (var memStream = new MemoryStream(array))

            {

                using (var binReader = new BinaryReader(memStream))

                {

                    for (var i = 0; i < points; i++)

                    {

                        arrayValues[i] = binReader.ReadSingle();

                    }

                }

            }



            // Return the value(s)

            return arrayValues;

        }



*From:* 戚达(Da Qi) <qi...@ge...>
*Sent:* Monday, January 7, 2019 5:43 PM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] mzML base64binary conversion



*CAUTION:* This email originated from outside of the organization. Do not
click links or open attachments unless you recognize the sender and know
the content is safe.



Hi,



Does anyone know how to decode the binary string to real data in mzML?



<binaryDataArrayList count="2">


<binaryDataArray encodedLength="268">


<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS"
unitAccession="MS:1000040" unitName="m/z"/>


<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>


<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>


<binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>


</binaryDataArray>


<binaryDataArray encodedLength="268">


<cvParam cvRef="MS" accession="MS:1000515" name="intensity array"
unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>


<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>


<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>


<binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>


</binaryDataArray>

                                                </binaryDataArrayList>



Best,

Da Qi

Re: [Psidev-ms-dev] mzML base64binary conversion

[Shofstahl, J. <jim...@th...>]

The spectral data (and chromatogram data) is stored as a Base64 encoded string.  Most of the programming languages will contain methods/functions to convert to and from the
Base64 format.  In C# those methods are part of the Convert class.

https://docs.microsoft.com/en-us/dotnet/api/system.convert?view=netframework-4.7.2

The FromBase64String method takes a string value and converts it to a byte[] array which can then be converted to another data type.  We tend to convert it using
as a MemoryStream object but there are other ways to do the conversion:

        protected static float[] ConvertToFloat(byte[] array, int points)
        {
            var arrayValues = new float[points];

            using (var memStream = new MemoryStream(array))
            {
                using (var binReader = new BinaryReader(memStream))
                {
                    for (var i = 0; i < points; i++)
                    {
                        arrayValues[i] = binReader.ReadSingle();
                    }
                }
            }

            // Return the value(s)
            return arrayValues;
        }

From: 戚达(Da Qi) <qi...@ge...>
Sent: Monday, January 7, 2019 5:43 PM
To: psi...@li...
Subject: [Psidev-ms-dev] mzML base64binary conversion

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi,

Does anyone know how to decode the binary string to real data in mzML?

<binaryDataArrayList count="2">
                                                            <binaryDataArray encodedLength="268">
                                                                        <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
                                                            <binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>
                                                            </binaryDataArray>
                                                            <binaryDataArray encodedLength="268">
                                                                        <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
                                                            <binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>
                                                            </binaryDataArray>
                                                </binaryDataArrayList>

Best,
Da Qi

[Psidev-ms-dev] mzML base64binary conversion

[戚达(Da Q. <qi...@ge...>]

Hi,

Does anyone know how to decode the binary string to real data in mzML?

<binaryDataArrayList count="2">
                                                            <binaryDataArray encodedLength="268">
                                                                        <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
                                                            <binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>
                                                            </binaryDataArray>
                                                            <binaryDataArray encodedLength="268">
                                                                        <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
                                                                        <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
                                                            <binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>
                                                            </binaryDataArray>
                                                </binaryDataArrayList>

Best,
Da Qi

Re: [Psidev-ms-dev] Ion Mobility units and representation of ion mobility in mzML

[mayerg97 <ger...@ru...>]

Hi Matt, hi all,

Am 14.12.2018 um 01:20 schrieb Chambers, Matthew:
> Why is having 3 units for one generic ion mobility array term a 
> problem? The definition of the term can simply defer to the unit as to 
> which kind of mobility is represented.
Of course you can conclude from the unit how to interpret the data in 
the array, but I think it's a good practice not to mix two different 
physical variables.
>
> The raw array thing is a different matter. If the mzML working group 
> decides to allow the combined spectrum representation with repeated 
> m/z, then raw terms could be useful for clarity, but 'mean' is 
> technically acceptable even if each value has only 1 input.
we should always strive for as much clarity as possible
> The combined spectrum representation has another issue on top of the 
> unique m/z values: what is the nativeID? How do you unambiguously 
> identify which spectrum was used for some analysis? Separate mobility 
> scans make that easy. With TIMS PASEF data, we merge it on a 
> per-precursor basis and use a single mobility value per merged scan. 
> Each merged scan uses a 'merged=xxx' nativeID and the original 
> nativeIDs are kept in the <scanList> element. But for non-PASEF data 
> (and MS1s from PASEF data) where there are usually hundreds or 
> thousands of mobility scans as part of the combined spectrum, the 
> <scanList> gets very bulky indeed. I discovered that mz5 performs very 
> poorly with large scan lists, and it drops auxiliary binary data 
> arrays entirely. It bloats mzML too. So it seems there would have to 
> be two nativeID formats for each vendor's ion mobility data.

I don't have experience with such ion mobility data. Can someone else 
comment or give hints about how to proceed here?

Best regards
Gerhard


On 12/13/2018 5:30 PM, Hannes Röst wrote:
>> Dear Gerhard
>>
>> Yes, I think that would solve the problem. I also would like to hear
>> what Matt has to say about this as we were discussing this before. One
>> of the issues he raised is the constraint that all m/z need to be
>> unique in mzML.
>>
>> Best
>>
>> Hannes
>> On Thu, Dec 13, 2018 at 5:03 AM mayerg97 <ger...@ru...> wrote:
>>> Dear Hannes, hi all,
>>>
>>> thanks for your hints pointing out these problems.
>>>
>>> I think the problem results from the intermixing of two concepts:
>>> A real drift time measured in milliseconds resp. seconds
>>> and a "inversed reduced ion mobility" as e.g. provided by the Bruker 
>>> TIMS instruments,
>>> measured as volt-second per square centimeter (cm^2 / Vs).
>>>
>>> Would it solve the problem, if we split the current MS:1002816 term 
>>> into
>>>
>>> [Term]
>>> id: MS:1002816
>>> name: mean ion mobility array
>>> def: "Array of drift times, averaged from a matrix of binned m/z and 
>>> ion mobility values, corresponding to a spectrum of individual peaks 
>>> encoded with an m/z array." [PSI:MS]
>>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>>> is_a: MS:1002893 ! ion mobility array
>>> relationship: has_units UO:0000028 ! millisecond
>>> relationship: has_units UO:0000010 ! second
>>>
>>> and
>>>
>>> [Term]
>>> id: MS:1003006
>>> name: mean inverse reduced ion mobility array
>>> def: "Array of inverse reduced ion mobilities, averaged from a 
>>> matrix of binned m/z and ion mobility values, corresponding to a 
>>> spectrum of individual peaks encoded with an m/z array." [PSI:MS]
>>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>>> is_a: MS:1002893 ! ion mobility array
>>> relationship: has_units MS:1002814 ! volt-second per square centimeter
>>>
>>> and then adding two new terms for the raw arrays?
>>>
>>> [Term]
>>> id: MS:1003007
>>> name: raw ion mobility array
>>> def: "Array of raw drift times." [PSI:MS]
>>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>>> is_a: MS:1002893 ! ion mobility array
>>> relationship: has_units UO:0000028 ! millisecond
>>> relationship: has_units UO:0000010 ! second
>>>
>>> [Term]
>>> id: MS:1003008
>>> name: raw inverse reduced ion mobility array
>>> def: "Array of raw inverse reduced ion mobilities." [PSI:MS]
>>> xref: value-type:xsd\:float "The allowed value-type for this CV term."
>>> is_a: MS:1002893 ! ion mobility array
>>> relationship: has_units MS:1002814 ! volt-second per square centimeter
>>>
>>> Best regards
>>> Gerhard Mayer
>>>
>>>
>>> Am 11.12.2018 um 20:42 schrieb Hannes Röst:
>>>
>>> Hi all
>>>
>>> I have a question regarding the representation of ion mobility and its
>>> units which has raised a few questions here over at OpenMS. Currently
>>> (and I think we have discussed this elsewhere) there are 2 ways to
>>> represent ion mobility, either using single spectra or by collapsing
>>> them into long arrays, e.g.
>>>
>>>
>>> <spectrum>
>>>    <scanList ...>
>>>      <scan>
>>>        <cvParam cvRef="MS" accession="MS:1002476" value="1">
>>> ...
>>> </spectrum>
>>> <spectrum>
>>>    <scanList ...>
>>>      <scan>
>>>        <cvParam cvRef="MS" accession="MS:1002476" value="2">
>>> ...
>>> </spectrum>
>>>
>>> etc
>>>
>>> or one can represent them as binary data arrays in a single spectrum:
>>>
>>> <spectrum>
>>>    <binaryDataArrayList count="3">
>>>    <binaryDataArray/>    <!-- mz -->
>>>    <binaryDataArray/>    <!-- intensity -->
>>>    <binaryDataArray>
>>>      <!-- ion mobility -->
>>>      <cvParam cvRef="MS" accession="MS:1002893">
>>>      <binary>...</binary>
>>>    </binaryDataArray>
>>> </spectrum>
>>>
>>>
>>> where CV param 1002893 can be either 1002893 or one of its children
>>> 1002816 or 1002477. Now the first issue I have is that if I use
>>> 1002816 the unit could be either in (milli)seconds or in volt-second
>>> per square centimeter but if I use 1002477 then the unit is guaranteed
>>> to be (milli)seconds. So to me it would make sense if
>>>
>>> = 1002477 is measured in (milli)second and
>>> = 1002816 is measured in volt-second per square centimeter
>>>
>>> Why do we currently the have the 1002816 which allows all three units?
>>> Is this supposed to be a catch-all? Should this be used for all ion
>>> mobility data in the future?
>>>
>>> The second issue I have is that storing the raw data in the first
>>> format with many spectra per "frame" (e.g. per ion mobility scan) is
>>> very inefficient and I would like to use the second format. This would
>>> mean that we duplicate m/z values but we are currently not very
>>> worried about that. However, there isnt really an appropriate CV term
>>> for this because
>>>
>>> MS:1002476 ion mobility drift time
>>> MS:1002815 inverse reduced ion mobility
>>> MS:1001581 FAIMS compensation voltage
>>>
>>> are not allowed inside binaryDataArray and the terms
>>>
>>> MS:1002477 mean drift time array
>>> MS:1002816 mean ion mobility array
>>>
>>> relate to *mean* drift times, implying that the data has been
>>> pre-processed. However, I would like to store the raw m/z, raw
>>> intensity and raw ion mobility as three arrays in a single spectrum.
>>> So I would like to have
>>>
>>> (i) the possibility to store MS:1002476 ion mobility drift time,
>>> MS:1002815 inverse reduced ion mobility and MS:1001581 FAIMS
>>> compensation voltage directly in binaryDataArray or
>>> (ii) a new CV term like MS:1002816 but that does not refer to the
>>> *mean* but to the *raw* data
>>>
>>> This currently does not seem to be possible but highly desireable from
>>> a disk-space usage perspective. It further helps that numpress
>>> compression is much more efficient on three long arrays than on
>>> hundreds of very short arrays each in their own <spectrum> tag. Access
>>> to the raw data in a somewhat reasonable format will be essential for
>>> feature finders and quantitatve software that use ion mobility for
>>> Waters and Bruker data, so it would be great to have a standardized
>>> way of storing the data. Also, of course, it would be great to have a
>>> way to convert the mzML files into each other using either
>>> proteowizard or OpenMS.
>>>
>>> Best
>>>
>>> Hannes
>>>
>>>
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>> -- 
>>>
>>> --------------------------------------------------------------------
>>>
>>> Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER
>>>
>>> PhD student
>>>
>>> Medizinisches Proteom-Center
>>>
>>> DEPARTMENT Medical Bioinformatics
>>>
>>> Building ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum
>>>
>>> Fon +49 (0)234 32-29272 | Fax +49 (0)234 32-14554
>>>
>>> E-mail ger...@ru...
>>>
>>> www.medizinisches-proteom-center.de
>
-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

Re: [Psidev-ms-dev] PSI2019

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

Hi all,

I am pleased to announce that registration is now open for the PSI 2019 meeting, which will take place in Cape Town, SA, March 18-20 : http://psidev.info/hupo-psi-meeting-2019. As a reminder, there is no cost to register for the meeting, although participants must pay their own travel and hotel costs. Please forward this on to anyone who you think might be interested in attending – we are always keen to attract new participants.

We hope to see you there!
Best wishes
Andy

[Psidev-ms-dev] Ion Mobility units and representation of ion mobility in mzML

[Hannes R. <han...@gm...>]

Hi all

I have a question regarding the representation of ion mobility and its
units which has raised a few questions here over at OpenMS. Currently
(and I think we have discussed this elsewhere) there are 2 ways to
represent ion mobility, either using single spectra or by collapsing
them into long arrays, e.g.


<spectrum>
  <scanList ...>
    <scan>
      <cvParam cvRef="MS" accession="MS:1002476" value="1">
...
</spectrum>
<spectrum>
  <scanList ...>
    <scan>
      <cvParam cvRef="MS" accession="MS:1002476" value="2">
...
</spectrum>

etc

or one can represent them as binary data arrays in a single spectrum:

<spectrum>
  <binaryDataArrayList count="3">
  <binaryDataArray/>    <!-- mz -->
  <binaryDataArray/>    <!-- intensity -->
  <binaryDataArray>
    <!-- ion mobility -->
    <cvParam cvRef="MS" accession="MS:1002893">
    <binary>...</binary>
  </binaryDataArray>
</spectrum>


where CV param 1002893 can be either 1002893 or one of its children
1002816 or 1002477. Now the first issue I have is that if I use
1002816 the unit could be either in (milli)seconds or in volt-second
per square centimeter but if I use 1002477 then the unit is guaranteed
to be (milli)seconds. So to me it would make sense if

= 1002477 is measured in (milli)second and
= 1002816 is measured in volt-second per square centimeter

Why do we currently the have the 1002816 which allows all three units?
Is this supposed to be a catch-all? Should this be used for all ion
mobility data in the future?

The second issue I have is that storing the raw data in the first
format with many spectra per "frame" (e.g. per ion mobility scan) is
very inefficient and I would like to use the second format. This would
mean that we duplicate m/z values but we are currently not very
worried about that. However, there isnt really an appropriate CV term
for this because

MS:1002476 ion mobility drift time
MS:1002815 inverse reduced ion mobility
MS:1001581 FAIMS compensation voltage

are not allowed inside binaryDataArray and the terms

MS:1002477 mean drift time array
MS:1002816 mean ion mobility array

relate to *mean* drift times, implying that the data has been
pre-processed. However, I would like to store the raw m/z, raw
intensity and raw ion mobility as three arrays in a single spectrum.
So I would like to have

(i) the possibility to store MS:1002476 ion mobility drift time,
MS:1002815 inverse reduced ion mobility and MS:1001581 FAIMS
compensation voltage directly in binaryDataArray or
(ii) a new CV term like MS:1002816 but that does not refer to the
*mean* but to the *raw* data

This currently does not seem to be possible but highly desireable from
a disk-space usage perspective. It further helps that numpress
compression is much more efficient on three long arrays than on
hundreds of very short arrays each in their own <spectrum> tag. Access
to the raw data in a somewhat reasonable format will be essential for
feature finders and quantitatve software that use ion mobility for
Waters and Bruker data, so it would be great to have a standardized
way of storing the data. Also, of course, it would be great to have a
way to convert the mzML files into each other using either
proteowizard or OpenMS.

Best

Hannes

[Psidev-ms-dev] New version 4.1.21 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.21 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.21 of psi-ms.obo:
=============================================
[Term]
id: MS:1002998
name: LCMS-9030
def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1002999
name: LCMS-8060
def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003000
name: LCMS-8050
def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003001
name: LCMS-8045
def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003002
name: LCMS-8040
def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003003
name: LCMS-2020
def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] Release candidate 4.1.21_rc1 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

following are the new terms for the release candidate 4.1.21_rc1 of the
psi-ms.obo file. It contains some added terms for Shimadzu instruments.


New CV terms in version 4.1.21_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002998
name: LCMS-9030
def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1002999
name: LCMS-8060
def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003000
name: LCMS-8050
def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003001
name: LCMS-8045
def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003002
name: LCMS-8040
def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

[Term]
id: MS:1003003
name: LCMS-2020
def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS]
is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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

[Psidev-ms-dev] PSI2019

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

Dear all,

We have now finalised the location and date of the PSI2019 meeting, which will take place in Cape Town, South Africa on 18th-20th March, 2019. Please make a note in your diaries, if you are interested in joining the meeting.

We will be updating the PSI website in the coming weeks with details of the talks, work group tracks and the venue/logistics. We look forward to seeing many of you there!

Best wishes
Andy







From: Jones, Andy
Sent: 24 October 2018 17:07
To: 'psi...@eb...' <psi...@eb...>; 'psi...@li...' <psi...@li...>; 'psi...@li...' <psi...@li...>
Subject: PSI2019 plans

Hi all,

Apologies for the cross-posting. The PSI steering committee will shortly be finalising the venue for the PSI2019 meeting. If you have been to a previous meeting or might be interested in participating in 2019, please can you complete this very short google form to indicate your preferred venue: https://goo.gl/forms/8t4CogZu3xVzRVJQ2, before end Oct i.e. within one week. We would like to take on board community considerations for overseas travel before selecting the final location in early November. We expect to announce the final, selected location by mid November.

Best wishes
Andy Jones

[Psidev-ms-dev] New version 4.1.20 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.20 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


New CV terms in version 4.1.20 of psi-ms.obo:
=============================================
[Term]
id: MS:1002997
name: ProteomeXchange dataset identifier reanalysis number
def: "Index number of a reanalysis within a ProteomeXchange reprocessed 
dataset identifier container (RPXD)." [PSI:PI]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1000878 ! external reference identifier


Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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