psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] New version 3.77.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new release 3.77.0 of the psi-ms.obo file.

Changed CV terms in version 3.77.0 of psi-ms.obo:
=================================================
************ Added string value type
[Term]
id: MS:1002487
name: MassIVE dataset identifier
def: "Dataset identifier issued by the MassIVE repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier


New CV terms in version 3.77.0 of psi-ms.obo:
=============================================
************ Term for Tide search engine
[Term]
id: MS:1002575
name: Tide
def: "Tide open-source sequence search program developed at the 
University of Washington." [PMID:21761931]
is_a: MS:1001456 ! analysis software

Best Regards,
Gerhard
-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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 3.77.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.77.0_rc1 of the psi-ms.obo file.


Changed CV terms in version 3.77.0_rc1 of psi-ms.obo:
=====================================================
************ Added string value type
[Term]
id: MS:1002487
name: MassIVE dataset identifier
def: "Dataset identifier issued by the MassIVE repository. A dataset can 
refer to either a single sample as part of a study, or all samples that 
are part of the study corresponding to a publication." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000878 ! external reference identifier



New CV terms in version 3.77.0_rc1 of psi-ms.obo:
=================================================
************ Term for Tide search engine
[Term]
id: MS:1002575
name: Tide
def: "Tide open-source sequence search program developed at the 
University of Washington." [PMID:21761931]
is_a: MS:1001456 ! analysis software

Best Regards,
Gerhard
-- 

*--*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-21006 | *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] PEFF poll

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

Hi everyone, for anyone interested in weighing in on some of the decisions
we’re trying to make with respect to the final design of PEFF, whether or
not you’ve been able to make the calls, please make your opinion known. The
votes are not necessarily binding, but will hopefully serve to determine
which issues have strong majority opinion and which are still divided and
may need some more thinking and debate.



http://doodle.com/e37uwaa83mzgshtn



Dilemma 1: To go along with \VariantComplex, the we name the simple form
\Variant or \VariantSimple?

D1A1 Variant

D1A2 VariantSimple



Dilemma 2: Do we allow tagging of Variants?

D2A1: No tagging explicitly (custom keywords still possible but not
mainstream)

D2A2: Support \VariantSimple_TAG=

D2A3: Allow optional extra tag for each: \VariantSimple=(100|A)(105|C|TAG)



Dilemma 3: Do we combine or separate the \ModRed terms?

D3A1: Separate \ModResPsi, \ModResUnimod, \ModRes

D3A2: Combine \ModResPsi & \ModResUnimod, but keep separate \ModRes

D3A3: Combine them all into \ModRes



Dilemma 4: Do we note deletion with empty or with a - ?

D4A1: Empty

D4A2: - (dash)



The poll allows you to put a Yes, IfNeedBe, and No for each option. Feel
free to use IfNeedBe to show half-hearted support.



Feel free to only answer some of the dilemmas and not others if you do not
have an opinion.



Let’s see if this works.



Ready. Set. Participate!



Regards,

Eric

[Psidev-ms-dev] Notes from today's PEFF call

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

Hi everyone, here are my notes from today’s PEFF call:



Present: Juanan, Pierre-Alain, Karl, Eric, Lydie, Harald, Simon,



Agenda:

- Dilemma 1: \Variant or \VariantSimple

+ No strong feeling. Try a Doodle vote



- Dilemma 2: Modify \Variant* keys with a further category

+ Opposing views on whether this should be here. Keep it simple, or allow
some added tags

+ Lydie says they would rather have two PEFF files, one for gold level
data, one for silver level, for example

+ Suggest that maybe each item could have an optional tag, e.g. instead of
(223|A), allow (223|A|dbSNP)

+ Something like this implicitly already exists: the ability to create
another key that allows, e.g., a free-text label

+ i.e. someone can create (using existing infrastructure)
\VariantSimpleTagged=(223|A|neXtProt_dbSNP)(225|T|Specimen1)…

+ Try a poll



- Dilemma 3:

+ Juanan advocates combining them

+ General agreement of combination

+ But then reconsidered later after discussing next



- What about \ModRes? Okay as implemented? Combine with the previous as
well?

+ Many opinions both ways and more

+ Also a suggestion of \ModRes for both PSI-MOD and Unimod and then
\ModResCustom for other things

+ Would we save space by putting the names in the header?

+ Eric advocates that keeping them all separate as currently done makes it
easier for readers. Explicit keys makes it easier for reader to know what
to expect, rather than expending code trying to determine what kind of
information is present

+ Easy consensus did not come. Try a vote and pick a way

+ For voting: yes, no, doesn’t matter



- Custom key definitions

+ Did not have time to discuss this

+ Request that Pierre-Alain (and anyone else) follow up on the email Eric
sent, and insert it into the spec doc

+ And then hold a slot for discussion on this on the next call



Eugene's comments:

1) Bigger picture and longevity - will the current format stand the test

of time - proteoforms come to mind and future advances in MS etc.

+ Full proteoforms seems easily supported with the current structure with
separate entries. Variants would be the actual PTMs for a given proteoform.

+ May require a few additional terms, but the structure seems fine

+ If there are some specific use cases, this would be helpful



2) Do we have anyone representing NCBI/Refseq - if not what can we do

about it. What about Ensembl, Eupathdb etc. - these are all well utilised

resources especially EupathDB for those folks working with pathogens and

mass spec.

+ We should make an effort. If they don’t participate now, they will be
targeted as reviewers ;-)



3) Has anyone approached Juergen Cox or someone on his team to become

involved considering Maxquant usage in the proteomics community?

+ Emanuele has shown him the specification



+ Ended here.

+ Eric will send out a Doodle poll to try voting on some items

+ Eric will send a poll to pick a date for the next call





- Review examples of PEFF files

- Review PEFF-supporting software

- Central location for all supporting documentation

[Psidev-ms-dev] PEFF call in 1 hr

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

Hi everyone, this is just a reminder about the PEFF call in 1 hr. Dial in
details:



Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



access code: 297427 #

[Psidev-ms-dev] PEFF custom key-value definitions

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

Hi everyone, another intended feature that is not in the current
specification that Pierre-Alain mentions is the ability to define custom
key-value pairs. Maybe Pierre-Alain can flesh this out, but from what I
gather, the documentation should go something like the below. Please
consider this and let’s discuss at the call tomorrow.



In order to use a custom key-value pair (i.e. the key is not in the CV) in
the sequence header blocks, it MUST be predefined in the file header.



The definition MUST be of the form:



# SpecificKey=KEYNAME:”KEYDEFINITION”:VALUEREGEXP



For example, to define a SecondaryStructure term:



# SpecificKey=SecondaryStructure:"Secondary structure element and
position":\([0-9]+\|[0-9]+\|[\w:]*\|\S+?\)



And then use:



\SecondaryStructure=(617|673|ncithesaurus:C47937|Helix)



Pierre-Alain, did I capture this correctly?



The regexp part will be tricky..



Thanks,

Eric

Re: [Psidev-ms-dev] Next PEFF call?

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

Hi everyone, most responders indicated that they could attend this coming
Thursday, so please mark your calendars for this coming Thursday 8am
Pacific, 4pm UK. I will send out a reminder and dial-in details as we get
closer.



Regards,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, June 25, 2015 1:21 PM
*To:* Mass spectrometry standard development;
psi...@li...
*Cc:* Eric Deutsch
*Subject:* Next PEFF call?



Hi everyone, if you wish to participate in the next PEFF call, please mark
the slots when you can make it either next Thursday or the following, and
we’ll decide on the best slot:



http://doodle.com/but4z7ihv75byyp7



thanks,

Eric

[Psidev-ms-dev] Ideas for PEFF ModRes construct

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

Hi everyone, at the last call there was extended discussion on how to
implement the \ModRes* construct. The currently implemented state is this:



\ModResPsi=(100|100|MOD:00046|O-phospho-L-serine)            (where all 4
fields are required)

\ModResUnimod=(100|100|UNIMOD:21|Phospho)                       (where all
4 fields are required):

\ModRes=(100|100|CustomMod:2|Phosphoserine)                      (where
fields 1,2,4 are required):



Dilemma 3: Should we combine ModResPsi and ModResUnimod?

- In favor: a) the value format is exactly the same and since accession
number is required, and the desired key would be unique so two is
unnecessary

- Against: x) For anyone who keys by name only, there is potential
ambiguity where UniMod and PSI-MOD names collide (which may be very rare),
y) there are important implications depending on which CV is used, most
importantly that PSI-MOD encodes a specific residue, whereas UniMod
provides a list of possible residues, some of which are common and some of
which are very rare, and this motivates separation, z) ?



I had originally envisioned that \ModRes would be very rare, but there
seems quite a bit of interest in this. Both Karl and Robert described some
current software and workflows that involve a custom mods file and so this
seems important to support. They are mostly interested in keying off names
rather than accessions. So I think the proposal stands as written:



\ModRes=(100|100|CustomMod:2|Phosphoserine)



Where the accession is not required but the name is. There was a proposal
to add the deltamass, but this was not liked. The general assumption will
be that software will be free to try to interpret either the accession or
the name, and then look up the delta mass (either avg or monoisotopic) or
the molecular composition and/or any other information in a custom
modification file that the software knows about. In general, major
providers such as neXtProt and UniProt should not use this. This would be
reserved for local solutions.



So, in general, there seemed enthusiasm for keeping \ModRes mostly as is.



Please think about this some more, and let’s discuss on the call on
Thursday.



Thanks,

Eric

[Psidev-ms-dev] Ideas for PEFF \Variant* construct

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

Hi everyone, here is a summary of the proposed PEFF \Variant* construct.
There has been quite a bit of discussion. I think we still need some more
discussion on this to come to a conclusion.



The current perhaps minimum safe level is this:



\VariantSimple=(223|A)               (allows just single amino acid
substitutions. *=nonsense allowed)

\VariantComplex=(100|100|AP)               (everything else including
indels and more)



Dilemma 1 is whether the keyword should be just \Variant or \VariantSimple

- In favor \VariantSimple if a) starker contrast to VariantComplex, b)
value will be different from current \Variant already in the wild

- In favor of \Variant is x) it is shorter, y) very few files exist in the
wild so reusing keyword with different format not an issue



Dilemma 2 is whether we should support some form of tagging of variant
lists (either suffixes or an alternate implementation).

This topic is beyond the scope of the original PEFF, and so one possible
decision is not to get fancy and stand with the current state.

However, a very reasonable suggestion was made about considering the use
cases. There is a very strong use case where a user will want to search a
dataset with a PEFF file, finding variants, and then examine the variants
to determine which are interesting. A basic categorization system would
allow each set of variants to be tagged with their category, which may or
may not be used. Consider the case where someone has an RNA-seq experiment
that finds several SNPs for the sample at hand. Suppose the person begins
with a PEFF file from neXtProt that already has SNPs in it, and the user
wishes to add some unique to the sample. The PEFF format could potentially
support a “_suffix” tag that could be interpreted by software. Suppose the
PEFF file from neXtProt came with some of these:

\VariantSimple_dbSNP=

\VariantSimple_COSMIC=

\VariantSimple_UniProtKB=

\VarantSimple_Germline=

\VariantSimple_Somatic=

Then the user could potentially add:

\VariantSimple_RNAseq=

via a script that would edit the PEFF file.



It would then be relatively simple to write software where perhaps the
search engine would look for them all (or could allow a user to only search
a subset), but then analysis software could easily differentiate between
classes, showing the user that the search turned up 683 SNPs corresponding
to UniProtKB, 125 SNPs corresponding to COSMIC, and 256 SNPs corresponding
to RNAseq.



- In favor of this approach: a) it allows selective searching against
subsets of varants, b) it allows easy filtering of PEFF files for subsets
of variants, c) It is quite flexible in terms of future use, d) It allow
easy categorization of discovered variants; e) ?

- Against this approach: x) it is beyond the scope of what we set out to
do; y) it is clunky and requires parsing of partial keywords; z) ?



- First, can anyone think of a more elegant way to do it?

- Second, do we even want to do something like this?



Please consider this for the next call on Thursday.



Thanks,

Eric

[Psidev-ms-dev] Next PEFF call?

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

Hi everyone, if you wish to participate in the next PEFF call, please mark
the slots when you can make it either next Thursday or the following, and
we’ll decide on the best slot:



http://doodle.com/but4z7ihv75byyp7



thanks,

Eric

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, I am moving this thread to the psidev pi and ms lists both so
it is easier for everyone to follow and participate.



Notes from today’s call:



Present: Juanan, Simon, Robert, Karl, Harald, Emanuele, Eric, ?



Discuss in-line comments:

- pg 5: Add version number?

+ Should this be on the PEFF line or a key-value pair? No strong opinion.
Having on the first line make sense. "# PEFF 1.0"

- pg 5: user-defined key-value pairs

+ Let's define this properly in the doc and provide an example

- pg 5: empty lines

+ no opinions

- pg 6: spaces between parens?

+ specify clearly NO SPACE

- pg 6: length field

+ Use the word SHOULD. Validators must check it if present and generate and
error if not matching

- pg 6: switching SimpleVariant to VariantSimple?

+ OK, yes change

+ Karl suggests just "Variant". Instead of VariantSimple. No other opinions.

+ We had changed Variant to VariantSimple to explicitly contrast it with
VariantComplex and to have a different name than PEFFs already in the wild
because the exact concept is a bit different than before

+ Let us NOT add a third field in VariantSimple to encode frequency or
category

- pg 6: VariantSomatic, VariantCOSMIC

+ This was generally viewed positively. Needs to be expanded for
VariantSimple and VariantComplex

+ Conversation moves toward VariantSimple_Somatic and VariantSimple_Germline

+ Karl points out that at search time, maybe all of these categories would
be searched, BUT when you want to view the results, then use these
different categories after the underscore.

+ Conversation ends up at \VariantSimple_xxxxxxx, where parsers would find
VariantSimple_xxxxxxx, not find it in the CV, split the VariantSimple from
the xxxxxxx, find VariantSimple in the CV and treat it appropriately with
the xxxxxxx as a software-specific tag on those variants that could be used
for results filtering, etc.

+ This is getting a bit hairy

+ Eric will try to summarize and make a proposal in a separate thread.



Discussion of PTMs

- pg 8: Why have separate terms for ModResPSi and MosResUnimod?

+ General agreement on merging ModResPSi and MosResUnimod

- pg 8: Add a deltaMass to ModRes

+ Karl suggests elemental composition instead of deltamass

+ Karl has a use case where his search engine keys on the name and ignores
the accession field

+ Robert concurs. They have a local modifications file as well and keys on
the name

+ Karl suggests having name before the accession although not strongly

- pg 8: Should we really support ModRes at all? Force UniMod submission?

+ Forcing UniMod submission maybe not mandatory, but perhaps force users to
inject their pet modification into their local CV

+ We run out of time before we can conclude what to do here

+ Eric will send out some proposals for everyone to review



+ Ran out of time here

+ Eric will send around a Doodle poll on whether to continue in 1 week or 2





Eugene's comments:

1) Bigger picture and longevity - will the current format stand the test

of time - proteoforms come to mind and future advances in MS etc.

2) Do we have anyone representing NCBI/Refseq - if not what can we do

about it. What about Ensembl, Eupathdb etc. - these are all well utilised

resources especially EupathDB for those folks working with pathogens and

mass spec.

3) Has anyone approached Juergen Cox or someone on his team to become

involved considering Maxquant usage in the proteomics community?



- Review examples of PEFF files

- Review PEFF-supporting software

- Central location for all supporting documentation







-----Original Message-----
From: Eric Deutsch [mailto:ede...@sy...]
Sent: Wednesday, June 24, 2015 10:57 PM
To: Robert Chalkley; Harald Barsnes; Karl Clauser
Cc: Juan Antonio Vizcaino; Eugene Kapp; Emanuele Alpi; Pierre-Alain Binz;
Yasset Perez-Riverol; Patrick Pedrioli; Lydie Lane; Gerben Menschaert;
en...@uw...; Matt Chambers; David Creasy; xiaojing wang; Emanuele Alpi;
Andy Jones; jim shofstahl; Eric Deutsch
Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, thank you for the comments and ideas. Let's discuss them at

the call in 9 hours. Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



access code: 297427 #



Agenda:



Discuss in-line comments:

- pg 5: Add version number?

- pg 5: user-defined key-value pairs

- pg 5: empty lines

- pg 6: spaces between parens?

- pg 6: length field

- pg 6: switching SimpleVariant to VariantSimple?

- pg 6: VariantSomatic, VariantCOSMIC

- pg 8: Why have separate terms for ModResPSi and MosResUnimod?

- pg 8: Add a deltaMass to ModRes

- pg 8: Should we really support ModRes at all? Force UniMod submission?



Eugene's comments:

1) Bigger picture and longevity - will the current format stand the test

of time - proteoforms come to mind and future advances in MS etc.

2) Do we have anyone representing NCBI/Refseq - if not what can we do

about it. What about Ensembl, Eupathdb etc. - these are all well utilised

resources especially EupathDB for those folks working with pathogens and

mass spec.

3) Has anyone approached Juergen Cox or someone on his team to become

involved considering Maxquant usage in the proteomics community?



- Review examples of PEFF files

- Review PEFF-supporting software

- Central location for all supporting documentation







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

From: Robert Chalkley [mailto:cha...@cg... <cha...@cg...>]

Sent: Wednesday, June 24, 2015 11:58 AM

To: Harald Barsnes; Karl Clauser

Cc: 'Juan Antonio Vizcaino'; 'Eugene Kapp'; 'Eric Deutsch'; 'Emanuele

Alpi'; 'Pierre-Alain Binz'; 'Yasset Perez-Riverol'; 'Patrick Pedrioli';

'Lydie Lane'; 'Gerben Menschaert'; en...@uw...; 'Matt Chambers'; 'David

Creasy'; 'xiaojing wang'; 'Emanuele Alpi'; 'Andy Jones'; 'jim shofstahl'

Subject: Re: PEFF call Thursday 8am Seattle, 4pm UK time



I have added a few edits and comments to the attached.



Robert



On 6/24/2015 4:38 AM, Harald Barsnes wrote:

>

> Hi all,

>

> Attached are my comments on the current PEFF draft. The most important

> being the need for examples on how to use user-defined key-value pairs.

>

> Best regards,

> Harald

>

>

>

>

> Den 2015-06-23 15:41, skrev Karl Clauser:

>> Hi folks,

>>

>> To Juan's version I add some edits to names of keys for variants and

>> added comments related to forseeable extensions/options related to

>> variant quality/importance.

>>

>> --Karl

>>

>> FROM: Juan Antonio Vizcaino [mailto:ju...@eb... <ju...@eb...>]

>> SENT: Tuesday, June 23, 2015 6:59 AM

>> TO: Eugene Kapp

>> CC: Eric Deutsch; Emanuele Alpi; Pierre-Alain Binz; Yasset

>> Perez-Riverol; Patrick Pedrioli; Harald Barsnes; Lydie Lane; Gerben

>> Menschaert; en...@uw...; Matt Chambers; David Creasy; Chalkley; Karl

>> Clauser; xiaojing wang; Emanuele Alpi; Andy Jones; jim shofstahl

>> SUBJECT: Re: PEFF call Thursday 8am Seattle, 4pm UK time

>>

>> Hi all,

>>

>> I am attaching the specification document with some comments, mostly

>> details.

>>

>> About Eugene's comments:

>>

>> - About longevity, of course, the current version could of course be

>> extended in the future. In this context, it is maybe a good idea to

>> write at the beginning of the file the version of the PEFF format

>> that is used in the file.

>>

>> - We can get here someone from Ensembl involved here, but my

>> experience is that they are not interested much in proteomics related

>> things. What may work is that we approach them in the future once the

>> format is finalised. I think it is more practical that Uniprot

>> supports it here, and then maybe Ensembl would be interested in

>> supporting it as well. In this context, there are no examples of

>> nucleotide sequence database in the spec document.

>>

>> - About Jurgen, Emanuele is going next week to the MaxQuant summer

>> school, and maybe he could talk to him in person (more practical than

>> by e-mail). As far as Emanuele told me, they are developing an

>> analogous format, so it may be definitely useful to speak to him.

>>

>> Cheers,

>>

>> Juan



--

Robert Chalkley PhD

Adjunct Associate Professor

Genentech Hall, N474A

Tel: 415 476 5189

Fax: 415 502 1655



NIGMS Mass Spectrometry Facility

University of California San Francisco

600 16th Street,

Genentech Hall, suite N472A

San Francisco, CA 94158-2517

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

[Emanuele A. <alp...@al...>]

Hello to all,

Thanks for your welcome Pierre-Alain and thank you Juan for having 
introduced me here.

As far as I'm concerned, I just grabbed two PEFF doc files which I found 
as attached files in one of the previous mails from these lists but I 
haven't gone through them yet; so I currently am not able to comment any 
further.
Generically speaking, as far as UniProt is concerned, we are happy to 
try accommodating the final PEFF format which this group will come up with.

Kind Regards

Emanuele

Il 19/06/2015 07:40, Binz Pierre-Alain ha scritto:
>
> Hi Juan,
>
> Great to have Emanuele on board, welcome !
>
> It would be nice to confirm that our latest proposal to separate 
> simple variants (single amino acid replacement) from complex variants 
> (everything else) is not blocking. I wouldn’t believe it is, but it is 
> good to have an idea from the various users of UniProt, who are not 
> only proteomics users (same can be true for neXtProt btw).
>
> Cheers
>
> Pierre-Alain
>
> *De :*Juan Antonio Vizcaino [mailto:ju...@eb...]
> *Envoyé :* jeudi 18 juin 2015 18:25
> *À :* Eric Deutsch
> *Cc :* Binz Pierre-Alain; jim...@th...; Patrick 
> Pedrioli; en...@uw...; Robert Chalkley; xia...@va...; 
> Lydie Lane; Matt Chambers; Harald Barsnes; David Creasy; Eugene Kapp; 
> Ger...@gm...; Andy Jones; Yasset Perez-Riverol; Karl 
> Clauser; Emanuele Alpi; Mass spectrometry standard development; 
> psi...@li...
> *Objet :* Re: PEFF call Thursday 8am Seattle, 4pm UK time
>
> Hi all,
>
> I am now including also Emanuele Alpi in the loop. He is representing 
> the UniProt team in the EBI and will join the calls. They are very 
> interested in supporting PEFF in the future, since there is increasing 
> demand from UniProt users for them to provide a better support for 
> variation information and they were already thinking about ways to do 
> this.
>
> He will also coordinate efforts with the UniProt development team here 
> to produce additional example files (in addition to the human ones 
> provided by neXtProt).
>
> Cheers,
>
> Juan
>
>     On 18 Jun 2015, at 15:29, Eric Deutsch
>     <ede...@sy... <mailto:ede...@sy...>>
>     wrote:
>
>     Hi everyone, I know we had planned to call again today to discuss
>     PEFF, but I am behind on the preparations I wanted to get done
>     before the call. And I didn’t send a reminder or anything. So
>     let’s plan on meeting next Thursday at the regular time. In the
>     next week I will send out the revised documents and repository
>     where all the materials are, so that everyone has a chance to
>     review the documents before the call.
>
>     Thanks,
>
>     Eric
>
>     *From:*Eric Deutsch [mailto:ede...@sy...
>     <mailto:ede...@sy...>]
>     *Sent:*Thursday, May 28, 2015 3:32 PM
>     *To:*Pierre-Alain Binz;jim...@th...
>     <mailto:jim...@th...>; Patrick
>     Pedrioli;en...@uw... <mailto:en...@uw...>;cha...@cg...
>     <mailto:cha...@cg...>;xia...@va...
>     <mailto:xia...@va...>; Lydie Lane; Matt
>     Chambers;Har...@bi...
>     <mailto:Har...@bi...>; David Creasy; Eugene
>     Kapp;ju...@eb...
>     <mailto:ju...@eb...>;Ger...@gm...
>     <mailto:Ger...@gm...>; Jones, Andy; Yasset
>     Perez-Riverol; Karl Clauser
>     *Cc:*Mass spectrometry standard
>     development;psi...@li...
>     <mailto:psi...@li...>; Eric Deutsch
>     *Subject:*RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
>     Hi everyone, here are my notes from the second PEFF call today.
>     Please let me know if I captured anything incorrectly.
>
>     Present:Eric,Pierre-Alain,Jim,Robert,Xiaojing,Harald,Karl,Juan
>     Antonio, Simon, Julian, Gerhard,
>
>     Did I miss anyone?
>
>     Agenda:
>
>     - Review conclusions from last time
>
>     + Explicitly do not support the (CTRL+A) multi-header delimiter
>
>     + For variants, deprecate existing term and create two new terms,
>     one for simple single amino acid substitutions, and another for
>     more complex indels and extended replacements, etc.
>
>     + nonsense mutation supported via * character
>
>     + No regular expressions for the simple SAAV term, but do allow
>     regexp for the more complex
>
>     - Discuss degree of PTM complexity to support
>
>     + Proposed format for PTMs is
>     (startPosition|endPosition|accession|name)
>
>     + Two reasons for start and end: 1) there can be modifications
>     that span multiple residues, 2) only one way to encode for all
>
>     + Would we encode not just the position, but also the residue that
>     can be modified?
>
>     + PSI-MOD has implicit reference of which amino acid is being modified
>
>     + tricky issue
>
>     + Consensus: do not encode the amino acid being modified. Let it
>     be implicit from the CV or inferred by the reading software
>
>     + Describe explicitly how different start and stop positions would
>     be used with examples in the spec doc
>
>     - Support for UniMod vs. PSI-MOD
>
>     + Existing two terms ModRes and ModResPSI
>
>     + ModResPSI requires PSI-MOD identifier
>
>     + Proposal to just support UniMod instead
>
>     + Karl suggests that we should have explicit names in addition to
>     a modification so that it is human readable
>
>     + Pierre-Alain says that the reason for the two terms is that some
>     resources already use PSI-MOD and some use UniMod. Conversion
>     between the two is difficult.
>
>     + Do neXtProt/UniProt already support PSI-MOD and RESID? So
>     conversion to UniMod might be difficult?
>
>     + It is not possible to have a one-to-one mapping between PSI-MOD
>     and UniMod. Many-to-may mapping is possible.
>
>     + One problem with readability is that PSI-MOD names are very long
>
>     + Is it true that in the UniMod.obo that all term names are
>     unique? We hope so. Is required by OBO format?
>
>     + Continue to use ModResPSI and use a four-part entry
>     (startposition|endposition|accession|name)
>
>     + Add ModResUnimod term and support that
>
>     + But also keep the original ModRes. Discourage use of this except
>     when UniMod and PSI-MOD not feasible
>
>     + Suggest for a single PEFF file, only one of these terms should
>     be used. Don’t mix terms.
>
>     + Settle on (startPosition|endPosition|accession|name)
>
>     + This allows for significant complexity, and we should explicitly
>     allow readers to determine the level of complexity they will support
>
>     We ran out of time again here.
>
>     Major action items:
>
>     + Capture all these sentiments in the spec doc as well as the
>     example files and circulate in advance of the next telecall in 3
>     weeks time
>
>     - Review examples of PEFF
>
>     - Review PEFF-supporting software
>
>     - Central location for all supporting documentation
>
>     - Another call in 2-3 weeks to review progress on the action items?
>
>     + Yes, same time in 3 weeks
>
>     *From:*Eric Deutsch [mailto:ede...@sy...
>     <mailto:ede...@sy...>]
>     *Sent:*Wednesday, May 27, 2015 4:15 PM
>     *To:*Pierre-Alain Binz;jim...@th...
>     <mailto:jim...@th...>; Patrick
>     Pedrioli;en...@uw... <mailto:en...@uw...>;cha...@cg...
>     <mailto:cha...@cg...>;xia...@va...
>     <mailto:xia...@va...>; Lydie Lane; Matt
>     Chambers;Har...@bi...
>     <mailto:Har...@bi...>; David Creasy; Eugene
>     Kapp;ju...@eb...
>     <mailto:ju...@eb...>;Ger...@gm...
>     <mailto:Ger...@gm...>; Jones, Andy; Yasset
>     Perez-Riverol; Karl Clauser
>     *Cc:*Mass spectrometry standard
>     development;psi...@li...
>     <mailto:psi...@li...>; Eric Deutsch
>     *Subject:*RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
>     Hi everyone, this is a reminder that we planned a call Thursday
>     8am Seattle, 4pm UK time to continue our discussion on PEFF. I
>     hope we can get through the rest of the agenda this time. I have
>     another hard stop at 55 minutes past the hour, so we’ll try to
>     finish efficiently.
>
>     Dial in numbers:
>
>     + Germany: 08001012079
>
>     + Switzerland: 0800000860
>
>     + UK: 08081095644
>
>     + Generic international: +44 2083222500 (UK number)
>
>     + US: 877-420-0272
>
>     *access code: 297427 #*
>
>     Agenda:
>
>     - Review conclusions from last time
>
>     - Discuss degree of PTM complexity to support
>
>     - Support for UniMod vs. PSI-MOD
>
>     - Review examples of PEFF
>
>     - Review PEFF-supporting software
>
>     - Central location for all supporting documentation
>
>     - Listing of action items
>
>     Thanks,
>
>     Eric
>
>     *From:*Eric Deutsch [mailto:ede...@sy...
>     <mailto:ede...@sy...>]
>     *Sent:*Thursday, May 21, 2015 11:26 AM
>     *To:*Pierre-Alain Binz;jim...@th...
>     <mailto:jim...@th...>; Patrick
>     Pedrioli;en...@uw... <mailto:en...@uw...>;cha...@cg...
>     <mailto:cha...@cg...>;xia...@va...
>     <mailto:xia...@va...>; Lydie Lane; Matt
>     Chambers;Har...@bi...
>     <mailto:Har...@bi...>; David Creasy; Eugene
>     Kapp;ju...@eb...
>     <mailto:ju...@eb...>;Ger...@gm...
>     <mailto:Ger...@gm...>; Jones, Andy; Yasset
>     Perez-Riverol; Karl Clauser
>     *Cc:*Mass spectrometry standard
>     development;psi...@li...
>     <mailto:psi...@li...>; Eric Deutsch
>     *Subject:*RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
>     Hi everyone, here are my notes from the PEFF call today. Please
>     let me know if I captured anything incorrectly.
>
>     Note that we agreed to continue to the second part of the posted
>     agenda, which we did not finish today, next Thursday at the same
>     timeslot.
>
>     Present:Eric,Pierre-Alain,Jim,Robert,Xiaojing,Lydie,Harald,Gerben,Yasset,Karl,Juan
>     Antonio
>
>     Did I miss anyone?
>
>     Agenda:
>
>     - Review what remains to be done
>
>     + We need to finish spec doc, the extant single hand-crafted
>     example (~dozen entries), and the OBO file
>
>     + neXtProt has been generating PEFF files regularly (not quite
>     compliant the spec as previously written, but are now actively
>     fixing the neXtProt exporter so this discussion is timely)
>
>     + Writer from Alain Gateau? This is the neXtProt exporter?
>
>     + Reader from Harald
>
>     + Settle the open issues below and then update all these elements
>
>     + Full manuscript?
>
>     + General tool to work with PEFF files? Add/subtract elements,
>     adjust annotations? Would be great but not required.
>
>     - Discuss (CTRL+A) header delimiter
>
>     + Not new perhaps, this already exists in FASTA!
>
>     + Or maybe not in the FASTA specification is there is one, but
>     seen in the wild
>
>     + Original NCBI nr already has these (CTRL+A)
>
>     + This PEFF feature was mainly motivated by the fact that this
>     feature is already existing out there in the field, by NCBI nr at
>     least
>
>     + For software implementations, there are several things that
>     could happen when faced with this, which is not good.
>
>     + Some on the call feel this is a problematic feature that should
>     be avoided
>
>     + General consensus is that this should be an explicitly
>     disallowed feature. Keep it simple. Repeat the sequence.
>
>     + Could add a header keyvalue that could point to other redundant
>     entries?
>
>     - Discuss degree of sequence variant complexity to support
>
>     + Explicit examples of usage should be written into the
>     specification. This is not there yet.
>
>     + Discussion at PSI workshop last month moved strongly toward
>     excluding advanced variations completely
>
>     + Karl proposed having two different tags, one for simple
>     substitutions, and one for indels and other complex things
>
>     + Gerben in favor of including indels in separate tags
>
>     + Pierre-Alain okay to splitting into two tags as Karl suggested
>
>     + Karl stands by his suggestion. And also suggests deprecating
>     existing term to avoid confusion
>
>     + Explicitly require that SAAV changes be in the simple SAAV term,
>     and NOT in the more complex term
>
>     + Xiaojing asks what about nonsense mutation?
>
>     + In the simple SAAV, could allow a change to an asterisk: (223:*)
>     General agreement on this.
>
>     + (223|225|KPA) goes in the more complex term
>
>     + There were rumblings that regular expressions should not be
>     supported anywhere? i.e. no (223|[KR]) for simple, no
>     (223|225|[KR]PA) in complex. Eric is not sure if there was a
>     consensus on this.
>
>     Ran out of time here. Skipped to last agenda item. Will continue
>     here next week.
>
>     - Discuss degree of PTM complexity to support
>
>     - Support for UniMod vs. PSI-MOD
>
>     - Review examples of PEFF
>
>     - Review PEFF-supporting software
>
>     - Central location for all supporting documentation
>
>     - Time slot for future calls
>
>     + Broad agreement that Thursday at this time is good. We will meet
>     again at this time next week and continue with the agenda.
>
>     *From:*Eric Deutsch [mailto:ede...@sy...
>     <mailto:ede...@sy...>]
>     *Sent:*Wednesday, May 20, 2015 4:18 PM
>     *To:*Pierre-Alain Binz;jim...@th...
>     <mailto:jim...@th...>; Patrick
>     Pedrioli;en...@uw... <mailto:en...@uw...>;cha...@cg...
>     <mailto:cha...@cg...>;xia...@va...
>     <mailto:xia...@va...>; Lydie Lane; Matt
>     Chambers;Har...@bi...
>     <mailto:Har...@bi...>; David Creasy; Eugene
>     Kapp;ju...@eb...
>     <mailto:ju...@eb...>;Ger...@gm...
>     <mailto:Ger...@gm...>; Jones, Andy; Yasset
>     Perez-Riverol
>     *Cc:*Mass spectrometry standard
>     development;psi...@li...
>     <mailto:psi...@li...>; Eric Deutsch
>     *Subject:*RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
>     Hi everyone, just a reminder about the PEFF call tomorrow, see
>     below for details. Dial-in information:
>
>     Dial in numbers:
>
>     + Germany: 08001012079
>
>     + Switzerland: 0800000860
>
>     + UK: 08081095644
>
>     + Generic international: +44 2083222500 (UK number)
>
>     + US: 877-420-0272
>
>     *access code: 297427 #*
>
>     *From:*Eric Deutsch [mailto:ede...@sy...
>     <mailto:ede...@sy...>]
>     *Sent:*Monday, May 18, 2015 2:36 PM
>     *To:*Pierre-Alain Binz;jim...@th...
>     <mailto:jim...@th...>; Patrick
>     Pedrioli;en...@uw... <mailto:en...@uw...>;cha...@cg...
>     <mailto:cha...@cg...>;xia...@va...
>     <mailto:xia...@va...>; Lydie Lane; Matt
>     Chambers;Har...@bi...
>     <mailto:Har...@bi...>; David Creasy; Eugene
>     Kapp;ju...@eb...
>     <mailto:ju...@eb...>;Ger...@gm...
>     <mailto:Ger...@gm...>; Jones, Andy; Yasset
>     Perez-Riverol
>     *Cc:*Mass spectrometry standard
>     development;psi...@li...
>     <mailto:psi...@li...>; Eric Deutsch
>     *Subject:*PEFF call Thursday 8am Seattle, 4pm UK time
>
>     Hi everyone, it appears that we have near consensus for Thursday
>     at the earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.
>
>     Agenda:
>
>     - Review what remains to be done
>
>     - Discuss (CTRL+A) header delimiter
>
>     - Discuss degree of sequence variant complexity to support
>
>     - Discuss degree of PTM complexity to support
>
>     - Support for UniMod vs. PSI-MOD
>
>     - Review examples of PEFF
>
>     - Review PEFF-supporting software
>
>     - Central location for all supporting documentation
>
>     - Time slot for future calls
>
>     We may not get through this all, but let’s tackle as much as we
>     can and continue at the next call. I’m presenting at the top of
>     the next hour, so I’d like to limit this call to 55 mins.
>
>     I will send out dial-in information and reminder as we get closer.
>
>     Thanks,
>
>     Eric
>
>     *From:*Eric Deutsch [mailto:ede...@sy...
>     <mailto:ede...@sy...>]
>     *Sent:*Friday, May 15, 2015 10:05 AM
>     *To:*Pierre-Alain Binz;jim...@th...
>     <mailto:jim...@th...>; Patrick
>     Pedrioli;en...@uw... <mailto:en...@uw...>;cha...@cg...
>     <mailto:cha...@cg...>;xia...@va...
>     <mailto:xia...@va...>; Lydie Lane; Matt
>     Chambers;Har...@bi...
>     <mailto:Har...@bi...>; David Creasy; Eugene Kapp;
>     Eric Deutsch;ju...@eb...
>     <mailto:ju...@eb...>;Ger...@gm...
>     <mailto:Ger...@gm...>
>     *Cc:*Mass spectrometry standard
>     development;psi...@li...
>     <mailto:psi...@li...>
>     *Subject:*PEFF progress and call next week and beyond
>
>     Hi everyone, we would like to set up some regular calls to carry
>     PEFF over the finish line. We had a good discussion at the PSI
>     meeting, so we just need to keep some momentum to get it finished.
>
>     I would like to set up a time next week to have conference call to
>     discuss some of the open issues. If you are interested in working
>     to help complete and resubmit PEFF, please complete the Doodle
>     poll below (even if you cannot attend at the suggested times next
>     week) and I will keep you in the loop for continuing development
>     on this. I have sent this to the list of coauthors on the
>     specification and other vocal participants at the workshop that I
>     recall. Anyone else is welcome to join the effort even if I forgot
>     to add you to the list above.
>
>     http://doodle.com/but4z7ihv75byyp7
>
>     Attached are the latest document and the notes I took during the
>     PSI workshop.
>
>     Please respond to the doodle poll and I will email some specific
>     agenda point in advance of the meeting.
>
>     We should probably paste some more information here:
>
>     http://www.psidev.info/peff
>
>     Please email me if you have specific agenda items or other
>     questions or comments.
>
>     thanks,
>
>     Eric
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

[Binz Pierre-A. <Pie...@ch...>]

Hi Juan,
Great to have Emanuele on board, welcome !
It would be nice to confirm that our latest proposal to separate simple variants (single amino acid replacement) from complex variants (everything else) is not blocking. I wouldn’t believe it is, but it is good to have an idea from the various users of UniProt, who are not only proteomics users (same can be true for neXtProt btw).

Cheers
Pierre-Alain

De : Juan Antonio Vizcaino [mailto:ju...@eb...]
Envoyé : jeudi 18 juin 2015 18:25
À : Eric Deutsch
Cc : Binz Pierre-Alain; jim...@th...; Patrick Pedrioli; en...@uw...; Robert Chalkley; xia...@va...; Lydie Lane; Matt Chambers; Harald Barsnes; David Creasy; Eugene Kapp; Ger...@gm...; Andy Jones; Yasset Perez-Riverol; Karl Clauser; Emanuele Alpi; Mass spectrometry standard development; psi...@li...
Objet : Re: PEFF call Thursday 8am Seattle, 4pm UK time

Hi all,

I am now including also Emanuele Alpi in the loop. He is representing the UniProt team in the EBI and will join the calls. They are very interested in supporting PEFF in the future, since there is increasing demand from UniProt users for them to provide a better support for variation information and they were already thinking about ways to do this.

He will also coordinate efforts with the UniProt development team here to produce additional example files (in addition to the human ones provided by neXtProt).

Cheers,

Juan



On 18 Jun 2015, at 15:29, Eric Deutsch <ede...@sy...<mailto:ede...@sy...>> wrote:

Hi everyone, I know we had planned to call again today to discuss PEFF, but I am behind on the preparations I wanted to get done before the call. And I didn’t send a reminder or anything. So let’s plan on meeting next Thursday at the regular time. In the next week I will send out the revised documents and repository where all the materials are, so that everyone has a chance to review the documents before the call.

Thanks,
Eric


From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Thursday, May 28, 2015 3:32 PM
To: Pierre-Alain Binz; jim...@th...<mailto:jim...@th...>; Patrick Pedrioli; en...@uw...<mailto:en...@uw...>; cha...@cg...<mailto:cha...@cg...>; xia...@va...<mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi...<mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb...<mailto:ju...@eb...>; Ger...@gm...<mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
Cc: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; Eric Deutsch
Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time

Hi everyone, here are my notes from the second PEFF call today. Please let me know if I captured anything incorrectly.

Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Harald, Karl, Juan Antonio, Simon, Julian, Gerhard,
Did I miss anyone?

Agenda:

- Review conclusions from last time
+ Explicitly do not support the (CTRL+A) multi-header delimiter
+ For variants, deprecate existing term and create two new terms, one for simple single amino acid substitutions, and another for more complex indels and extended replacements, etc.
+ nonsense mutation supported via * character
+ No regular expressions for the simple SAAV term, but do allow regexp for the more complex

- Discuss degree of PTM complexity to support
+ Proposed format for PTMs is (startPosition|endPosition|accession|name)
+ Two reasons for start and end: 1) there can be modifications that span multiple residues, 2) only one way to encode for all
+ Would we encode not just the position, but also the residue that can be modified?
+ PSI-MOD has implicit reference of which amino acid is being modified
+ tricky issue
+ Consensus: do not encode the amino acid being modified. Let it be implicit from the CV or inferred by the reading software
+ Describe explicitly how different start and stop positions would be used with examples in the spec doc

- Support for UniMod vs. PSI-MOD
+ Existing two terms ModRes and ModResPSI
+ ModResPSI requires PSI-MOD identifier
+ Proposal to just support UniMod instead
+ Karl suggests that we should have explicit names in addition to a modification so that it is human readable
+ Pierre-Alain says that the reason for the two terms is that some resources already use PSI-MOD and some use UniMod. Conversion between the two is difficult.
+ Do neXtProt/UniProt already support PSI-MOD and RESID? So conversion to UniMod might be difficult?
+ It is not possible to have a one-to-one mapping between PSI-MOD and UniMod. Many-to-may mapping is possible.
+ One problem with readability is that PSI-MOD names are very long
+ Is it true that in the UniMod.obo that all term names are unique? We hope so. Is required by OBO format?
+ Continue to use ModResPSI and use a four-part entry (startposition|endposition|accession|name)
+ Add ModResUnimod term and support that
+ But also keep the original ModRes. Discourage use of this except when UniMod and PSI-MOD not feasible
+ Suggest for a single PEFF file, only one of these terms should be used. Don’t mix terms.
+ Settle on (startPosition|endPosition|accession|name)
+ This allows for significant complexity, and we should explicitly allow readers to determine the level of complexity they will support

We ran out of time again here.

Major action items:
+ Capture all these sentiments in the spec doc as well as the example files and circulate in advance of the next telecall in 3 weeks time

- Review examples of PEFF
- Review PEFF-supporting software
- Central location for all supporting documentation
- Another call in 2-3 weeks to review progress on the action items?
+ Yes, same time in 3 weeks




From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Wednesday, May 27, 2015 4:15 PM
To: Pierre-Alain Binz; jim...@th...<mailto:jim...@th...>; Patrick Pedrioli; en...@uw...<mailto:en...@uw...>; cha...@cg...<mailto:cha...@cg...>; xia...@va...<mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi...<mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb...<mailto:ju...@eb...>; Ger...@gm...<mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
Cc: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; Eric Deutsch
Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time

Hi everyone, this is a reminder that we planned a call Thursday 8am Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can get through the rest of the agenda this time. I have another hard stop at 55 minutes past the hour, so we’ll try to finish efficiently.

Dial in numbers:
+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ Generic international: +44 2083222500 (UK number)
+ US: 877-420-0272

access code: 297427 #

Agenda:

- Review conclusions from last time
- Discuss degree of PTM complexity to support
- Support for UniMod vs. PSI-MOD
- Review examples of PEFF
- Review PEFF-supporting software
- Central location for all supporting documentation
- Listing of action items

Thanks,
Eric



From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Thursday, May 21, 2015 11:26 AM
To: Pierre-Alain Binz; jim...@th...<mailto:jim...@th...>; Patrick Pedrioli; en...@uw...<mailto:en...@uw...>; cha...@cg...<mailto:cha...@cg...>; xia...@va...<mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi...<mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb...<mailto:ju...@eb...>; Ger...@gm...<mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
Cc: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; Eric Deutsch
Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time

Hi everyone, here are my notes from the PEFF call today. Please let me know if I captured anything incorrectly.

Note that we agreed to continue to the second part of the posted agenda, which we did not finish today, next Thursday at the same timeslot.

Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben, Yasset, Karl, Juan Antonio
Did I miss anyone?

Agenda:

- Review what remains to be done
+ We need to finish spec doc, the extant single hand-crafted example (~dozen entries), and the OBO file
+ neXtProt has been generating PEFF files regularly (not quite compliant the spec as previously written, but are now actively fixing the neXtProt exporter so this discussion is timely)
+ Writer from Alain Gateau? This is the neXtProt exporter?
+ Reader from Harald
+ Settle the open issues below and then update all these elements
+ Full manuscript?
+ General tool to work with PEFF files? Add/subtract elements, adjust annotations? Would be great but not required.

- Discuss (CTRL+A) header delimiter
+ Not new perhaps, this already exists in FASTA!
+ Or maybe not in the FASTA specification is there is one, but seen in the wild
+ Original NCBI nr already has these (CTRL+A)
+ This PEFF feature was mainly motivated by the fact that this feature is already existing out there in the field, by NCBI nr at least
+ For software implementations, there are several things that could happen when faced with this, which is not good.
+ Some on the call feel this is a problematic feature that should be avoided
+ General consensus is that this should be an explicitly disallowed feature. Keep it simple. Repeat the sequence.
+ Could add a header keyvalue that could point to other redundant entries?

- Discuss degree of sequence variant complexity to support
+ Explicit examples of usage should be written into the specification. This is not there yet.
+ Discussion at PSI workshop last month moved strongly toward excluding advanced variations completely
+ Karl proposed having two different tags, one for simple substitutions, and one for indels and other complex things
+ Gerben in favor of including indels in separate tags
+ Pierre-Alain okay to splitting into two tags as Karl suggested
+ Karl stands by his suggestion. And also suggests deprecating existing term to avoid confusion
+ Explicitly require that SAAV changes be in the simple SAAV term, and NOT in the more complex term
+ Xiaojing asks what about nonsense mutation?
+ In the simple SAAV, could allow a change to an asterisk: (223:*) General agreement on this.
+ (223|225|KPA) goes in the more complex term
+ There were rumblings that regular expressions should not be supported anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex. Eric is not sure if there was a consensus on this.

Ran out of time here. Skipped to last agenda item. Will continue here next week.

- Discuss degree of PTM complexity to support
- Support for UniMod vs. PSI-MOD
- Review examples of PEFF
- Review PEFF-supporting software
- Central location for all supporting documentation

- Time slot for future calls
+ Broad agreement that Thursday at this time is good. We will meet again at this time next week and continue with the agenda.







From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Wednesday, May 20, 2015 4:18 PM
To: Pierre-Alain Binz; jim...@th...<mailto:jim...@th...>; Patrick Pedrioli; en...@uw...<mailto:en...@uw...>; cha...@cg...<mailto:cha...@cg...>; xia...@va...<mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi...<mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb...<mailto:ju...@eb...>; Ger...@gm...<mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol
Cc: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; Eric Deutsch
Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time

Hi everyone, just a reminder about the PEFF call tomorrow, see below for details. Dial-in information:

Dial in numbers:
+ Germany: 08001012079
+ Switzerland: 0800000860
+ UK: 08081095644
+ Generic international: +44 2083222500 (UK number)
+ US: 877-420-0272

access code: 297427 #


From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Monday, May 18, 2015 2:36 PM
To: Pierre-Alain Binz; jim...@th...<mailto:jim...@th...>; Patrick Pedrioli; en...@uw...<mailto:en...@uw...>; cha...@cg...<mailto:cha...@cg...>; xia...@va...<mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi...<mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb...<mailto:ju...@eb...>; Ger...@gm...<mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol
Cc: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>; Eric Deutsch
Subject: PEFF call Thursday 8am Seattle, 4pm UK time

Hi everyone, it appears that we have near consensus for Thursday at the earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.

Agenda:
- Review what remains to be done
- Discuss (CTRL+A) header delimiter
- Discuss degree of sequence variant complexity to support
- Discuss degree of PTM complexity to support
- Support for UniMod vs. PSI-MOD
- Review examples of PEFF
- Review PEFF-supporting software
- Central location for all supporting documentation
- Time slot for future calls

We may not get through this all, but let’s tackle as much as we can and continue at the next call. I’m presenting at the top of the next hour, so I’d like to limit this call to 55 mins.

I will send out dial-in information and reminder as we get closer.

Thanks,
Eric


From: Eric Deutsch [mailto:ede...@sy...<mailto:ede...@sy...>]
Sent: Friday, May 15, 2015 10:05 AM
To: Pierre-Alain Binz; jim...@th...<mailto:jim...@th...>; Patrick Pedrioli; en...@uw...<mailto:en...@uw...>; cha...@cg...<mailto:cha...@cg...>; xia...@va...<mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi...<mailto:Har...@bi...>; David Creasy; Eugene Kapp; Eric Deutsch; ju...@eb...<mailto:ju...@eb...>; Ger...@gm...<mailto:Ger...@gm...>
Cc: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...>
Subject: PEFF progress and call next week and beyond

Hi everyone, we would like to set up some regular calls to carry PEFF over the finish line. We had a good discussion at the PSI meeting, so we just need to keep some momentum to get it finished.

I would like to set up a time next week to have conference call to discuss some of the open issues. If you are interested in working to help complete and resubmit PEFF, please complete the Doodle poll below (even if you cannot attend at the suggested times next week) and I will keep you in the loop for continuing development on this. I have sent this to the list of coauthors on the specification and other vocal participants at the workshop that I recall. Anyone else is welcome to join the effort even if I forgot to add you to the list above.

http://doodle.com/but4z7ihv75byyp7

Attached are the latest document and the notes I took during the PSI workshop.

Please respond to the doodle poll and I will email some specific agenda point in advance of the meeting.

We should probably paste some more information here:
http://www.psidev.info/peff

Please email me if you have specific agenda items or other questions or comments.

thanks,
Eric

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

[Juan A. V. <ju...@eb...>]

Hi all,

I am now including also Emanuele Alpi in the loop. He is representing the UniProt team in the EBI and will join the calls. They are very interested in supporting PEFF in the future, since there is increasing demand from UniProt users for them to provide a better support for variation information and they were already thinking about ways to do this. 

He will also coordinate efforts with the UniProt development team here to produce additional example files (in addition to the human ones provided by neXtProt).

Cheers,

Juan



> On 18 Jun 2015, at 15:29, Eric Deutsch <ede...@sy...> wrote:
> 
> Hi everyone, I know we had planned to call again today to discuss PEFF, but I am behind on the preparations I wanted to get done before the call. And I didn’t send a reminder or anything. So let’s plan on meeting next Thursday at the regular time. In the next week I will send out the revised documents and repository where all the materials are, so that everyone has a chance to review the documents before the call.
>  
> Thanks,
> Eric
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Thursday, May 28, 2015 3:32 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, here are my notes from the second PEFF call today. Please let me know if I captured anything incorrectly.
>  
> Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Harald, Karl, Juan Antonio, Simon, Julian, Gerhard, 
> Did I miss anyone?
>  
> Agenda:
>  
> - Review conclusions from last time
> + Explicitly do not support the (CTRL+A) multi-header delimiter
> + For variants, deprecate existing term and create two new terms, one for simple single amino acid substitutions, and another for more complex indels and extended replacements, etc.
> + nonsense mutation supported via * character
> + No regular expressions for the simple SAAV term, but do allow regexp for the more complex
>  
> - Discuss degree of PTM complexity to support
> + Proposed format for PTMs is (startPosition|endPosition|accession|name)
> + Two reasons for start and end: 1) there can be modifications that span multiple residues, 2) only one way to encode for all
> + Would we encode not just the position, but also the residue that can be modified?
> + PSI-MOD has implicit reference of which amino acid is being modified
> + tricky issue
> + Consensus: do not encode the amino acid being modified. Let it be implicit from the CV or inferred by the reading software
> + Describe explicitly how different start and stop positions would be used with examples in the spec doc
>  
> - Support for UniMod vs. PSI-MOD
> + Existing two terms ModRes and ModResPSI
> + ModResPSI requires PSI-MOD identifier
> + Proposal to just support UniMod instead 
> + Karl suggests that we should have explicit names in addition to a modification so that it is human readable
> + Pierre-Alain says that the reason for the two terms is that some resources already use PSI-MOD and some use UniMod. Conversion between the two is difficult.
> + Do neXtProt/UniProt already support PSI-MOD and RESID? So conversion to UniMod might be difficult?
> + It is not possible to have a one-to-one mapping between PSI-MOD and UniMod. Many-to-may mapping is possible.
> + One problem with readability is that PSI-MOD names are very long
> + Is it true that in the UniMod.obo that all term names are unique? We hope so. Is required by OBO format?
> + Continue to use ModResPSI and use a four-part entry (startposition|endposition|accession|name)
> + Add ModResUnimod term and support that
> + But also keep the original ModRes. Discourage use of this except when UniMod and PSI-MOD not feasible
> + Suggest for a single PEFF file, only one of these terms should be used. Don’t mix terms.
> + Settle on (startPosition|endPosition|accession|name)
> + This allows for significant complexity, and we should explicitly allow readers to determine the level of complexity they will support
>  
> We ran out of time again here.
>  
> Major action items:
> + Capture all these sentiments in the spec doc as well as the example files and circulate in advance of the next telecall in 3 weeks time
>  
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
> - Another call in 2-3 weeks to review progress on the action items?
> + Yes, same time in 3 weeks
>  
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Wednesday, May 27, 2015 4:15 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, this is a reminder that we planned a call Thursday 8am Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can get through the rest of the agenda this time. I have another hard stop at 55 minutes past the hour, so we’ll try to finish efficiently.
>  
> Dial in numbers:
> + Germany: 08001012079
> + Switzerland: 0800000860
> + UK: 08081095644
> + Generic international: +44 2083222500 (UK number)
> + US: 877-420-0272
>  
> access code: 297427 #
>  
> Agenda:
>  
> - Review conclusions from last time
> - Discuss degree of PTM complexity to support
> - Support for UniMod vs. PSI-MOD
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
> - Listing of action items
>  
> Thanks,
> Eric
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Thursday, May 21, 2015 11:26 AM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, here are my notes from the PEFF call today. Please let me know if I captured anything incorrectly.
>  
> Note that we agreed to continue to the second part of the posted agenda, which we did not finish today, next Thursday at the same timeslot.
>  
> Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben, Yasset, Karl, Juan Antonio
> Did I miss anyone?
>  
> Agenda:
>  
> - Review what remains to be done
> + We need to finish spec doc, the extant single hand-crafted example (~dozen entries), and the OBO file
> + neXtProt has been generating PEFF files regularly (not quite compliant the spec as previously written, but are now actively fixing the neXtProt exporter so this discussion is timely)
> + Writer from Alain Gateau? This is the neXtProt exporter?
> + Reader from Harald
> + Settle the open issues below and then update all these elements
> + Full manuscript?
> + General tool to work with PEFF files? Add/subtract elements, adjust annotations? Would be great but not required.
>  
> - Discuss (CTRL+A) header delimiter
> + Not new perhaps, this already exists in FASTA!
> + Or maybe not in the FASTA specification is there is one, but seen in the wild
> + Original NCBI nr already has these (CTRL+A)
> + This PEFF feature was mainly motivated by the fact that this feature is already existing out there in the field, by NCBI nr at least
> + For software implementations, there are several things that could happen when faced with this, which is not good.
> + Some on the call feel this is a problematic feature that should be avoided
> + General consensus is that this should be an explicitly disallowed feature. Keep it simple. Repeat the sequence.
> + Could add a header keyvalue that could point to other redundant entries?
>  
> - Discuss degree of sequence variant complexity to support
> + Explicit examples of usage should be written into the specification. This is not there yet.
> + Discussion at PSI workshop last month moved strongly toward excluding advanced variations completely
> + Karl proposed having two different tags, one for simple substitutions, and one for indels and other complex things
> + Gerben in favor of including indels in separate tags
> + Pierre-Alain okay to splitting into two tags as Karl suggested
> + Karl stands by his suggestion. And also suggests deprecating existing term to avoid confusion
> + Explicitly require that SAAV changes be in the simple SAAV term, and NOT in the more complex term
> + Xiaojing asks what about nonsense mutation?
> + In the simple SAAV, could allow a change to an asterisk: (223:*) General agreement on this.
> + (223|225|KPA) goes in the more complex term
> + There were rumblings that regular expressions should not be supported anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex. Eric is not sure if there was a consensus on this.
>  
> Ran out of time here. Skipped to last agenda item. Will continue here next week.
>  
> - Discuss degree of PTM complexity to support
> - Support for UniMod vs. PSI-MOD
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
>  
> - Time slot for future calls
> + Broad agreement that Thursday at this time is good. We will meet again at this time next week and continue with the agenda.
>  
>  
>  
>  
>  
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Wednesday, May 20, 2015 4:18 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: RE: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, just a reminder about the PEFF call tomorrow, see below for details. Dial-in information:
>  
> Dial in numbers:
> + Germany: 08001012079
> + Switzerland: 0800000860
> + UK: 08081095644
> + Generic international: +44 2083222500 (UK number)
> + US: 877-420-0272
>  
> access code: 297427 #
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Monday, May 18, 2015 2:36 PM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>; Jones, Andy; Yasset Perez-Riverol
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>; Eric Deutsch
> Subject: PEFF call Thursday 8am Seattle, 4pm UK time
>  
> Hi everyone, it appears that we have near consensus for Thursday at the earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.
>  
> Agenda:
> - Review what remains to be done
> - Discuss (CTRL+A) header delimiter
> - Discuss degree of sequence variant complexity to support
> - Discuss degree of PTM complexity to support
> - Support for UniMod vs. PSI-MOD
> - Review examples of PEFF
> - Review PEFF-supporting software
> - Central location for all supporting documentation
> - Time slot for future calls
>  
> We may not get through this all, but let’s tackle as much as we can and continue at the next call. I’m presenting at the top of the next hour, so I’d like to limit this call to 55 mins.
>  
> I will send out dial-in information and reminder as we get closer.
>  
> Thanks,
> Eric
>  
>  
> From: Eric Deutsch [mailto:ede...@sy... <mailto:ede...@sy...>] 
> Sent: Friday, May 15, 2015 10:05 AM
> To: Pierre-Alain Binz; jim...@th... <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... <mailto:en...@uw...>; cha...@cg... <mailto:cha...@cg...>; xia...@va... <mailto:xia...@va...>; Lydie Lane; Matt Chambers; Har...@bi... <mailto:Har...@bi...>; David Creasy; Eugene Kapp; Eric Deutsch; ju...@eb... <mailto:ju...@eb...>; Ger...@gm... <mailto:Ger...@gm...>
> Cc: Mass spectrometry standard development; psi...@li... <mailto:psi...@li...>
> Subject: PEFF progress and call next week and beyond
>  
> Hi everyone, we would like to set up some regular calls to carry PEFF over the finish line. We had a good discussion at the PSI meeting, so we just need to keep some momentum to get it finished.
>  
> I would like to set up a time next week to have conference call to discuss some of the open issues. If you are interested in working to help complete and resubmit PEFF, please complete the Doodle poll below (even if you cannot attend at the suggested times next week) and I will keep you in the loop for continuing development on this. I have sent this to the list of coauthors on the specification and other vocal participants at the workshop that I recall. Anyone else is welcome to join the effort even if I forgot to add you to the list above.
>  
> http://doodle.com/but4z7ihv75byyp7 <http://doodle.com/but4z7ihv75byyp7>
>  
> Attached are the latest document and the notes I took during the PSI workshop.
>  
> Please respond to the doodle poll and I will email some specific agenda point in advance of the meeting.
>  
> We should probably paste some more information here:
> http://www.psidev.info/peff <http://www.psidev.info/peff>
>  
> Please email me if you have specific agenda items or other questions or comments.
>  
> thanks,
> Eric

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, I know we had planned to call again today to discuss PEFF, but
I am behind on the preparations I wanted to get done before the call. And I
didn’t send a reminder or anything. So let’s plan on meeting next Thursday
at the regular time. In the next week I will send out the revised documents
and repository where all the materials are, so that everyone has a chance
to review the documents before the call.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, May 28, 2015 3:32 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol; Karl Clauser
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, here are my notes from the second PEFF call today. Please let
me know if I captured anything incorrectly.



Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Harald, Karl, Juan
Antonio, Simon, Julian, Gerhard,

Did I miss anyone?



Agenda:



- Review conclusions from last time

+ Explicitly do not support the (CTRL+A) multi-header delimiter

+ For variants, deprecate existing term and create two new terms, one for
simple single amino acid substitutions, and another for more complex indels
and extended replacements, etc.

+ nonsense mutation supported via * character

+ No regular expressions for the simple SAAV term, but do allow regexp for
the more complex



- Discuss degree of PTM complexity to support

+ Proposed format for PTMs is (startPosition|endPosition|accession|name)

+ Two reasons for start and end: 1) there can be modifications that span
multiple residues, 2) only one way to encode for all

+ Would we encode not just the position, but also the residue that can be
modified?

+ PSI-MOD has implicit reference of which amino acid is being modified

+ tricky issue

+ Consensus: do not encode the amino acid being modified. Let it be
implicit from the CV or inferred by the reading software

+ Describe explicitly how different start and stop positions would be used
with examples in the spec doc



- Support for UniMod vs. PSI-MOD

+ Existing two terms ModRes and ModResPSI

+ ModResPSI requires PSI-MOD identifier

+ Proposal to just support UniMod instead

+ Karl suggests that we should have explicit names in addition to a
modification so that it is human readable

+ Pierre-Alain says that the reason for the two terms is that some
resources already use PSI-MOD and some use UniMod. Conversion between the
two is difficult.

+ Do neXtProt/UniProt already support PSI-MOD and RESID? So conversion to
UniMod might be difficult?

+ It is not possible to have a one-to-one mapping between PSI-MOD and
UniMod. Many-to-may mapping is possible.

+ One problem with readability is that PSI-MOD names are very long

+ Is it true that in the UniMod.obo that all term names are unique? We hope
so. Is required by OBO format?

+ Continue to use ModResPSI and use a four-part entry
(startposition|endposition|accession|name)

+ Add ModResUnimod term and support that

+ But also keep the original ModRes. Discourage use of this except when
UniMod and PSI-MOD not feasible

+ Suggest for a single PEFF file, only one of these terms should be used.
Don’t mix terms.

+ Settle on (startPosition|endPosition|accession|name)

+ This allows for significant complexity, and we should explicitly allow
readers to determine the level of complexity they will support



We ran out of time again here.



Major action items:

+ Capture all these sentiments in the spec doc as well as the example files
and circulate in advance of the next telecall in 3 weeks time



- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Another call in 2-3 weeks to review progress on the action items?

+ Yes, same time in 3 weeks









*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, May 27, 2015 4:15 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol; Karl Clauser
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, this is a reminder that we planned a call Thursday 8am
Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can get
through the rest of the agenda this time. I have another hard stop at 55
minutes past the hour, so we’ll try to finish efficiently.



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*



Agenda:



- Review conclusions from last time

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Listing of action items



Thanks,

Eric







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, May 21, 2015 11:26 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol; Karl Clauser
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, here are my notes from the PEFF call today. Please let me know
if I captured anything incorrectly.



Note that we agreed to continue to the second part of the posted agenda,
which we did not finish today, next Thursday at the same timeslot.



Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben,
Yasset, Karl, Juan Antonio

Did I miss anyone?



Agenda:



- Review what remains to be done

+ We need to finish spec doc, the extant single hand-crafted example
(~dozen entries), and the OBO file

+ neXtProt has been generating PEFF files regularly (not quite compliant
the spec as previously written, but are now actively fixing the neXtProt
exporter so this discussion is timely)

+ Writer from Alain Gateau? This is the neXtProt exporter?

+ Reader from Harald

+ Settle the open issues below and then update all these elements

+ Full manuscript?

+ General tool to work with PEFF files? Add/subtract elements, adjust
annotations? Would be great but not required.



- Discuss (CTRL+A) header delimiter

+ Not new perhaps, this already exists in FASTA!

+ Or maybe not in the FASTA specification is there is one, but seen in the
wild

+ Original NCBI nr already has these (CTRL+A)

+ This PEFF feature was mainly motivated by the fact that this feature is
already existing out there in the field, by NCBI nr at least

+ For software implementations, there are several things that could happen
when faced with this, which is not good.

+ Some on the call feel this is a problematic feature that should be avoided

+ General consensus is that this should be an explicitly disallowed
feature. Keep it simple. Repeat the sequence.

+ Could add a header keyvalue that could point to other redundant entries?



- Discuss degree of sequence variant complexity to support

+ Explicit examples of usage should be written into the specification. This
is not there yet.

+ Discussion at PSI workshop last month moved strongly toward excluding
advanced variations completely

+ Karl proposed having two different tags, one for simple substitutions,
and one for indels and other complex things

+ Gerben in favor of including indels in separate tags

+ Pierre-Alain okay to splitting into two tags as Karl suggested

+ Karl stands by his suggestion. And also suggests deprecating existing
term to avoid confusion

+ Explicitly require that SAAV changes be in the simple SAAV term, and NOT
in the more complex term

+ Xiaojing asks what about nonsense mutation?

+ In the simple SAAV, could allow a change to an asterisk: (223:*) General
agreement on this.

+ (223|225|KPA) goes in the more complex term

+ There were rumblings that regular expressions should not be supported
anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex.
Eric is not sure if there was a consensus on this.



Ran out of time here. Skipped to last agenda item. Will continue here next
week.



- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation



- Time slot for future calls

+ Broad agreement that Thursday at this time is good. We will meet again at
this time next week and continue with the agenda.















*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, May 20, 2015 4:18 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, just a reminder about the PEFF call tomorrow, see below for
details. Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 18, 2015 2:36 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, it appears that we have near consensus for Thursday at the
earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.



Agenda:

- Review what remains to be done

- Discuss (CTRL+A) header delimiter

- Discuss degree of sequence variant complexity to support

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Time slot for future calls



We may not get through this all, but let’s tackle as much as we can and
continue at the next call. I’m presenting at the top of the next hour, so
I’d like to limit this call to 55 mins.



I will send out dial-in information and reminder as we get closer.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
psi...@li...
*Subject:* PEFF progress and call next week and beyond



Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, here are my notes from the second PEFF call today. Please let
me know if I captured anything incorrectly.



Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Harald, Karl, Juan
Antonio, Simon, Julian, Gerhard,

Did I miss anyone?



Agenda:



- Review conclusions from last time

+ Explicitly do not support the (CTRL+A) multi-header delimiter

+ For variants, deprecate existing term and create two new terms, one for
simple single amino acid substitutions, and another for more complex indels
and extended replacements, etc.

+ nonsense mutation supported via * character

+ No regular expressions for the simple SAAV term, but do allow regexp for
the more complex



- Discuss degree of PTM complexity to support

+ Proposed format for PTMs is (startPosition|endPosition|accession|name)

+ Two reasons for start and end: 1) there can be modifications that span
multiple residues, 2) only one way to encode for all

+ Would we encode not just the position, but also the residue that can be
modified?

+ PSI-MOD has implicit reference of which amino acid is being modified

+ tricky issue

+ Consensus: do not encode the amino acid being modified. Let it be
implicit from the CV or inferred by the reading software

+ Describe explicitly how different start and stop positions would be used
with examples in the spec doc



- Support for UniMod vs. PSI-MOD

+ Existing two terms ModRes and ModResPSI

+ ModResPSI requires PSI-MOD identifier

+ Proposal to just support UniMod instead

+ Karl suggests that we should have explicit names in addition to a
modification so that it is human readable

+ Pierre-Alain says that the reason for the two terms is that some
resources already use PSI-MOD and some use UniMod. Conversion between the
two is difficult.

+ Do neXtProt/UniProt already support PSI-MOD and RESID? So conversion to
UniMod might be difficult?

+ It is not possible to have a one-to-one mapping between PSI-MOD and
UniMod. Many-to-may mapping is possible.

+ One problem with readability is that PSI-MOD names are very long

+ Is it true that in the UniMod.obo that all term names are unique? We hope
so. Is required by OBO format?

+ Continue to use ModResPSI and use a four-part entry
(startposition|endposition|accession|name)

+ Add ModResUnimod term and support that

+ But also keep the original ModRes. Discourage use of this except when
UniMod and PSI-MOD not feasible

+ Suggest for a single PEFF file, only one of these terms should be used.
Don’t mix terms.

+ Settle on (startPosition|endPosition|accession|name)

+ This allows for significant complexity, and we should explicitly allow
readers to determine the level of complexity they will support



We ran out of time again here.



Major action items:

+ Capture all these sentiments in the spec doc as well as the example files
and circulate in advance of the next telecall in 3 weeks time



- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Another call in 2-3 weeks to review progress on the action items?

+ Yes, same time in 3 weeks









*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, May 27, 2015 4:15 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol; Karl Clauser
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, this is a reminder that we planned a call Thursday 8am
Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can get
through the rest of the agenda this time. I have another hard stop at 55
minutes past the hour, so we’ll try to finish efficiently.



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*



Agenda:



- Review conclusions from last time

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Listing of action items



Thanks,

Eric







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, May 21, 2015 11:26 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol; Karl Clauser
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, here are my notes from the PEFF call today. Please let me know
if I captured anything incorrectly.



Note that we agreed to continue to the second part of the posted agenda,
which we did not finish today, next Thursday at the same timeslot.



Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben,
Yasset, Karl, Juan Antonio

Did I miss anyone?



Agenda:



- Review what remains to be done

+ We need to finish spec doc, the extant single hand-crafted example
(~dozen entries), and the OBO file

+ neXtProt has been generating PEFF files regularly (not quite compliant
the spec as previously written, but are now actively fixing the neXtProt
exporter so this discussion is timely)

+ Writer from Alain Gateau? This is the neXtProt exporter?

+ Reader from Harald

+ Settle the open issues below and then update all these elements

+ Full manuscript?

+ General tool to work with PEFF files? Add/subtract elements, adjust
annotations? Would be great but not required.



- Discuss (CTRL+A) header delimiter

+ Not new perhaps, this already exists in FASTA!

+ Or maybe not in the FASTA specification is there is one, but seen in the
wild

+ Original NCBI nr already has these (CTRL+A)

+ This PEFF feature was mainly motivated by the fact that this feature is
already existing out there in the field, by NCBI nr at least

+ For software implementations, there are several things that could happen
when faced with this, which is not good.

+ Some on the call feel this is a problematic feature that should be avoided

+ General consensus is that this should be an explicitly disallowed
feature. Keep it simple. Repeat the sequence.

+ Could add a header keyvalue that could point to other redundant entries?



- Discuss degree of sequence variant complexity to support

+ Explicit examples of usage should be written into the specification. This
is not there yet.

+ Discussion at PSI workshop last month moved strongly toward excluding
advanced variations completely

+ Karl proposed having two different tags, one for simple substitutions,
and one for indels and other complex things

+ Gerben in favor of including indels in separate tags

+ Pierre-Alain okay to splitting into two tags as Karl suggested

+ Karl stands by his suggestion. And also suggests deprecating existing
term to avoid confusion

+ Explicitly require that SAAV changes be in the simple SAAV term, and NOT
in the more complex term

+ Xiaojing asks what about nonsense mutation?

+ In the simple SAAV, could allow a change to an asterisk: (223:*) General
agreement on this.

+ (223|225|KPA) goes in the more complex term

+ There were rumblings that regular expressions should not be supported
anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex.
Eric is not sure if there was a consensus on this.



Ran out of time here. Skipped to last agenda item. Will continue here next
week.



- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation



- Time slot for future calls

+ Broad agreement that Thursday at this time is good. We will meet again at
this time next week and continue with the agenda.















*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, May 20, 2015 4:18 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, just a reminder about the PEFF call tomorrow, see below for
details. Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 18, 2015 2:36 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, it appears that we have near consensus for Thursday at the
earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.



Agenda:

- Review what remains to be done

- Discuss (CTRL+A) header delimiter

- Discuss degree of sequence variant complexity to support

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Time slot for future calls



We may not get through this all, but let’s tackle as much as we can and
continue at the next call. I’m presenting at the top of the next hour, so
I’d like to limit this call to 55 mins.



I will send out dial-in information and reminder as we get closer.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
psi...@li...
*Subject:* PEFF progress and call next week and beyond



Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

[Psidev-ms-dev] New version 3.76.0 of psi-ms.obo

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

Dear proteomics community,

attached you find the new version 3.76.0 of the psi-ms.obo file.


Changed CV terms in version 3.76.0 of psi-ms.obo:
=================================================
************ Added is_a: MS:1002484 ! peptide-level statistical threshold
************ Updated definition
[Term]
id: MS:1001868
name: distinct peptide-level q-value
def: "Estimation of the q-value for distinct peptides once redundant 
identifications of the same peptide have been removed (id est multiple 
PSMs, possibly with different mass modifications, mapping to the same 
sequence have been collapsed to one entry)." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ Obsoleted the following term because of id clash with 
MS:1002289 (ProteinProphet)
[Term]
id: MS:1002289
name: ASAPRatio
def: "OBSOLETE A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on 2-channel isotope-labelled data such 
as ICAT, SILAC, etc." [PSI:PI]
comment: This term was made obsolete because of id clash with the term 
MS:1002289 (ProteinProphet) - use term MS:1002574 (ASAPRatio) instead.
is_a: MS:1002286 ! Trans-Proteomic Pipeline software
is_obsolete: true


New CV terms in version 3.76.0 of psi-ms.obo:
=============================================
************ Term with new id for ASAPRatio
[Term]
id: MS:1002574
name: ASAPRatio
def: "A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on 2-channel isotope-labelled data such 
as ICAT, SILAC, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

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] PEFF call Thursday 8am Seattle, 4pm UK time

[Lydie L. <lyd...@is...>]

Hi everyone,

I have to catch a train at 5:40 tonight. I will try to arrive in advance 
at the train station and join the call from there from 5:00 to 5.30.

I got some precisions from my team regarding neXtProt's Peff generator:

- the source code is publicly available but conceived to communicate 
with neXtProt (uses neXtProt's new  API)
- as is, it is not applicable on UniProt entries. Adaptation to UniProt 
content would require rewriting the DAO classes (links between database 
and services).

If you need to generate Peff from (non human) Swiss-Prot entries, I'd 
suggest you to contact the Swiss-Prot development team.

Best,

Lydie


On 28.05.2015 01:15, Eric Deutsch wrote:
>
> Hi everyone, this is a reminder that we planned a call Thursday 8am 
> Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can 
> get through the rest of the agenda this time. I have another hard stop 
> at 55 minutes past the hour, so we’ll try to finish efficiently.
>
> Dial in numbers:
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + Generic international: +44 2083222500 (UK number)
>
> + US: 877-420-0272
>
> *access code: 297427 #*
>
> Agenda:
>
> - Review conclusions from last time
>
> - Discuss degree of PTM complexity to support
>
> - Support for UniMod vs. PSI-MOD
>
> - Review examples of PEFF
>
> - Review PEFF-supporting software
>
> - Central location for all supporting documentation
>
> - Listing of action items
>
> Thanks,
>
> Eric
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Thursday, May 21, 2015 11:26 AM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; 
> Ger...@gm... <mailto:Ger...@gm...>; 
> Jones, Andy; Yasset Perez-Riverol; Karl Clauser
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>; Eric Deutsch
> *Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
> Hi everyone, here are my notes from the PEFF call today. Please let me 
> know if I captured anything incorrectly.
>
> Note that we agreed to continue to the second part of the posted 
> agenda, which we did not finish today, next Thursday at the same timeslot.
>
> Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, 
> Gerben, Yasset, Karl, Juan Antonio
>
> Did I miss anyone?
>
> Agenda:
>
> - Review what remains to be done
>
> + We need to finish spec doc, the extant single hand-crafted example 
> (~dozen entries), and the OBO file
>
> + neXtProt has been generating PEFF files regularly (not quite 
> compliant the spec as previously written, but are now actively fixing 
> the neXtProt exporter so this discussion is timely)
>
> + Writer from Alain Gateau? This is the neXtProt exporter?
>
> + Reader from Harald
>
> + Settle the open issues below and then update all these elements
>
> + Full manuscript?
>
> + General tool to work with PEFF files? Add/subtract elements, adjust 
> annotations? Would be great but not required.
>
> - Discuss (CTRL+A) header delimiter
>
> + Not new perhaps, this already exists in FASTA!
>
> + Or maybe not in the FASTA specification is there is one, but seen in 
> the wild
>
> + Original NCBI nr already has these (CTRL+A)
>
> + This PEFF feature was mainly motivated by the fact that this feature 
> is already existing out there in the field, by NCBI nr at least
>
> + For software implementations, there are several things that could 
> happen when faced with this, which is not good.
>
> + Some on the call feel this is a problematic feature that should be 
> avoided
>
> + General consensus is that this should be an explicitly disallowed 
> feature. Keep it simple. Repeat the sequence.
>
> + Could add a header keyvalue that could point to other redundant entries?
>
> - Discuss degree of sequence variant complexity to support
>
> + Explicit examples of usage should be written into the specification. 
> This is not there yet.
>
> + Discussion at PSI workshop last month moved strongly toward 
> excluding advanced variations completely
>
> + Karl proposed having two different tags, one for simple 
> substitutions, and one for indels and other complex things
>
> + Gerben in favor of including indels in separate tags
>
> + Pierre-Alain okay to splitting into two tags as Karl suggested
>
> + Karl stands by his suggestion. And also suggests deprecating 
> existing term to avoid confusion
>
> + Explicitly require that SAAV changes be in the simple SAAV term, and 
> NOT in the more complex term
>
> + Xiaojing asks what about nonsense mutation?
>
> + In the simple SAAV, could allow a change to an asterisk: (223:*) 
> General agreement on this.
>
> + (223|225|KPA) goes in the more complex term
>
> + There were rumblings that regular expressions should not be 
> supported anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) 
> in complex. Eric is not sure if there was a consensus on this.
>
> Ran out of time here. Skipped to last agenda item. Will continue here 
> next week.
>
> - Discuss degree of PTM complexity to support
>
> - Support for UniMod vs. PSI-MOD
>
> - Review examples of PEFF
>
> - Review PEFF-supporting software
>
> - Central location for all supporting documentation
>
> - Time slot for future calls
>
> + Broad agreement that Thursday at this time is good. We will meet 
> again at this time next week and continue with the agenda.
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Wednesday, May 20, 2015 4:18 PM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; 
> Ger...@gm... <mailto:Ger...@gm...>; 
> Jones, Andy; Yasset Perez-Riverol
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>; Eric Deutsch
> *Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
> Hi everyone, just a reminder about the PEFF call tomorrow, see below 
> for details. Dial-in information:
>
> Dial in numbers:
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + Generic international: +44 2083222500 (UK number)
>
> + US: 877-420-0272
>
> *access code: 297427 #*
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Monday, May 18, 2015 2:36 PM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; 
> Ger...@gm... <mailto:Ger...@gm...>; 
> Jones, Andy; Yasset Perez-Riverol
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>; Eric Deutsch
> *Subject:* PEFF call Thursday 8am Seattle, 4pm UK time
>
> Hi everyone, it appears that we have near consensus for Thursday at 
> the earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.
>
> Agenda:
>
> - Review what remains to be done
>
> - Discuss (CTRL+A) header delimiter
>
> - Discuss degree of sequence variant complexity to support
>
> - Discuss degree of PTM complexity to support
>
> - Support for UniMod vs. PSI-MOD
>
> - Review examples of PEFF
>
> - Review PEFF-supporting software
>
> - Central location for all supporting documentation
>
> - Time slot for future calls
>
> We may not get through this all, but let’s tackle as much as we can 
> and continue at the next call. I’m presenting at the top of the next 
> hour, so I’d like to limit this call to 55 mins.
>
> I will send out dial-in information and reminder as we get closer.
>
> Thanks,
>
> Eric
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Friday, May 15, 2015 10:05 AM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; Eric Deutsch; ju...@eb... 
> <mailto:ju...@eb...>; Ger...@gm... 
> <mailto:Ger...@gm...>
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>
> *Subject:* PEFF progress and call next week and beyond
>
> Hi everyone, we would like to set up some regular calls to carry PEFF 
> over the finish line. We had a good discussion at the PSI meeting, so 
> we just need to keep some momentum to get it finished.
>
> I would like to set up a time next week to have conference call to 
> discuss some of the open issues. If you are interested in working to 
> help complete and resubmit PEFF, please complete the Doodle poll below 
> (even if you cannot attend at the suggested times next week) and I 
> will keep you in the loop for continuing development on this. I have 
> sent this to the list of coauthors on the specification and other 
> vocal participants at the workshop that I recall. Anyone else is 
> welcome to join the effort even if I forgot to add you to the list above.
>
> http://doodle.com/but4z7ihv75byyp7
>
> Attached are the latest document and the notes I took during the PSI 
> workshop.
>
> Please respond to the doodle poll and I will email some specific 
> agenda point in advance of the meeting.
>
> We should probably paste some more information here:
>
> http://www.psidev.info/peff
>
> Please email me if you have specific agenda items or other questions 
> or comments.
>
> thanks,
>
> Eric
>


-- 
Lydie Lane, Ph. D
CALIPHO group co-director
SIB-Swiss Institute of Bioinformatics
Department of Human Protein Sciences, University of Geneva
CMU, Michel-Servet 1,
1211 Geneva 4,
Switzerland
+ 41 (0) 22 379 58 41

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, this is a reminder that we planned a call Thursday 8am
Seattle, 4pm UK time to continue our discussion on PEFF. I hope we can get
through the rest of the agenda this time. I have another hard stop at 55
minutes past the hour, so we’ll try to finish efficiently.



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*



Agenda:



- Review conclusions from last time

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Listing of action items



Thanks,

Eric







*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Thursday, May 21, 2015 11:26 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol; Karl Clauser
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, here are my notes from the PEFF call today. Please let me know
if I captured anything incorrectly.



Note that we agreed to continue to the second part of the posted agenda,
which we did not finish today, next Thursday at the same timeslot.



Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben,
Yasset, Karl, Juan Antonio

Did I miss anyone?



Agenda:



- Review what remains to be done

+ We need to finish spec doc, the extant single hand-crafted example
(~dozen entries), and the OBO file

+ neXtProt has been generating PEFF files regularly (not quite compliant
the spec as previously written, but are now actively fixing the neXtProt
exporter so this discussion is timely)

+ Writer from Alain Gateau? This is the neXtProt exporter?

+ Reader from Harald

+ Settle the open issues below and then update all these elements

+ Full manuscript?

+ General tool to work with PEFF files? Add/subtract elements, adjust
annotations? Would be great but not required.



- Discuss (CTRL+A) header delimiter

+ Not new perhaps, this already exists in FASTA!

+ Or maybe not in the FASTA specification is there is one, but seen in the
wild

+ Original NCBI nr already has these (CTRL+A)

+ This PEFF feature was mainly motivated by the fact that this feature is
already existing out there in the field, by NCBI nr at least

+ For software implementations, there are several things that could happen
when faced with this, which is not good.

+ Some on the call feel this is a problematic feature that should be avoided

+ General consensus is that this should be an explicitly disallowed
feature. Keep it simple. Repeat the sequence.

+ Could add a header keyvalue that could point to other redundant entries?



- Discuss degree of sequence variant complexity to support

+ Explicit examples of usage should be written into the specification. This
is not there yet.

+ Discussion at PSI workshop last month moved strongly toward excluding
advanced variations completely

+ Karl proposed having two different tags, one for simple substitutions,
and one for indels and other complex things

+ Gerben in favor of including indels in separate tags

+ Pierre-Alain okay to splitting into two tags as Karl suggested

+ Karl stands by his suggestion. And also suggests deprecating existing
term to avoid confusion

+ Explicitly require that SAAV changes be in the simple SAAV term, and NOT
in the more complex term

+ Xiaojing asks what about nonsense mutation?

+ In the simple SAAV, could allow a change to an asterisk: (223:*) General
agreement on this.

+ (223|225|KPA) goes in the more complex term

+ There were rumblings that regular expressions should not be supported
anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex.
Eric is not sure if there was a consensus on this.



Ran out of time here. Skipped to last agenda item. Will continue here next
week.



- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation



- Time slot for future calls

+ Broad agreement that Thursday at this time is good. We will meet again at
this time next week and continue with the agenda.















*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, May 20, 2015 4:18 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, just a reminder about the PEFF call tomorrow, see below for
details. Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 18, 2015 2:36 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, it appears that we have near consensus for Thursday at the
earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.



Agenda:

- Review what remains to be done

- Discuss (CTRL+A) header delimiter

- Discuss degree of sequence variant complexity to support

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Time slot for future calls



We may not get through this all, but let’s tackle as much as we can and
continue at the next call. I’m presenting at the top of the next hour, so
I’d like to limit this call to 55 mins.



I will send out dial-in information and reminder as we get closer.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
psi...@li...
*Subject:* PEFF progress and call next week and beyond



Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

[Psidev-ms-dev] pepXML Perl parser

[Felipe da V. L. <fe...@le...>]

Dear All,

I just released a Perl implementation of a pepXML parser using modern Perl
programming. The parser also provides top level methods to access the data.

https://metacpan.org/pod/release/LEPREVOST/PepXML-Parser-0.02/README.pod

https://github.com/Leprevost/PepXML-Parser

Please fell free to contact me if there is any questions.

best regards

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

[David C. <dc...@ma...>]

Hi Everyone,

Sorry I couldn't make the call, and good work for moving this forward. 
Yes, protein databases from NCBI have multiple title lines for identical 
sequences. Concerning the idea of just repeating the sequences, some 
numbers from the current complete nr file to be aware of:

File size              : 40,231,392,221
Number of sequences    :     66,926,000
Number of title lines  :    170,713,645
Average sequence length: 360 residues

So, duplicating the sequences would change the file size by roughly
   (170,713,645 - 66,926,000) * 360 =  37,363,552,200
So, nearly doubling the size of the 38Gb file. Obviously this will 
almost certainly make search engines, blast etc. slower and may have an 
adverse effect on the stats for some tools.

Hope this helps somewhat...

David


On 21/05/2015 19:26, Eric Deutsch wrote:
>
> Hi everyone, here are my notes from the PEFF call today. Please let me 
> know if I captured anything incorrectly.
>
> Note that we agreed to continue to the second part of the posted 
> agenda, which we did not finish today, next Thursday at the same timeslot.
>
> Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, 
> Gerben, Yasset, Karl, Juan Antonio
>
> Did I miss anyone?
>
> Agenda:
>
> - Review what remains to be done
>
> + We need to finish spec doc, the extant single hand-crafted example 
> (~dozen entries), and the OBO file
>
> + neXtProt has been generating PEFF files regularly (not quite 
> compliant the spec as previously written, but are now actively fixing 
> the neXtProt exporter so this discussion is timely)
>
> + Writer from Alain Gateau? This is the neXtProt exporter?
>
> + Reader from Harald
>
> + Settle the open issues below and then update all these elements
>
> + Full manuscript?
>
> + General tool to work with PEFF files? Add/subtract elements, adjust 
> annotations? Would be great but not required.
>
> - Discuss (CTRL+A) header delimiter
>
> + Not new perhaps, this already exists in FASTA!
>
> + Or maybe not in the FASTA specification is there is one, but seen in 
> the wild
>
> + Original NCBI nr already has these (CTRL+A)
>
> + This PEFF feature was mainly motivated by the fact that this feature 
> is already existing out there in the field, by NCBI nr at least
>
> + For software implementations, there are several things that could 
> happen when faced with this, which is not good.
>
> + Some on the call feel this is a problematic feature that should be 
> avoided
>
> + General consensus is that this should be an explicitly disallowed 
> feature. Keep it simple. Repeat the sequence.
>
> + Could add a header keyvalue that could point to other redundant entries?
>
> - Discuss degree of sequence variant complexity to support
>
> + Explicit examples of usage should be written into the specification. 
> This is not there yet.
>
> + Discussion at PSI workshop last month moved strongly toward 
> excluding advanced variations completely
>
> + Karl proposed having two different tags, one for simple 
> substitutions, and one for indels and other complex things
>
> + Gerben in favor of including indels in separate tags
>
> + Pierre-Alain okay to splitting into two tags as Karl suggested
>
> + Karl stands by his suggestion. And also suggests deprecating 
> existing term to avoid confusion
>
> + Explicitly require that SAAV changes be in the simple SAAV term, and 
> NOT in the more complex term
>
> + Xiaojing asks what about nonsense mutation?
>
> + In the simple SAAV, could allow a change to an asterisk: (223:*) 
> General agreement on this.
>
> + (223|225|KPA) goes in the more complex term
>
> + There were rumblings that regular expressions should not be 
> supported anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) 
> in complex. Eric is not sure if there was a consensus on this.
>
> Ran out of time here. Skipped to last agenda item. Will continue here 
> next week.
>
> - Discuss degree of PTM complexity to support
>
> - Support for UniMod vs. PSI-MOD
>
> - Review examples of PEFF
>
> - Review PEFF-supporting software
>
> - Central location for all supporting documentation
>
> - Time slot for future calls
>
> + Broad agreement that Thursday at this time is good. We will meet 
> again at this time next week and continue with the agenda.
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Wednesday, May 20, 2015 4:18 PM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; 
> Ger...@gm... <mailto:Ger...@gm...>; 
> Jones, Andy; Yasset Perez-Riverol
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>; Eric Deutsch
> *Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time
>
> Hi everyone, just a reminder about the PEFF call tomorrow, see below 
> for details. Dial-in information:
>
> Dial in numbers:
>
> + Germany: 08001012079
>
> + Switzerland: 0800000860
>
> + UK: 08081095644
>
> + Generic international: +44 2083222500 (UK number)
>
> + US: 877-420-0272
>
> *access code: 297427 #*
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Monday, May 18, 2015 2:36 PM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; ju...@eb... <mailto:ju...@eb...>; 
> Ger...@gm... <mailto:Ger...@gm...>; 
> Jones, Andy; Yasset Perez-Riverol
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>; Eric Deutsch
> *Subject:* PEFF call Thursday 8am Seattle, 4pm UK time
>
> Hi everyone, it appears that we have near consensus for Thursday at 
> the earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.
>
> Agenda:
>
> - Review what remains to be done
>
> - Discuss (CTRL+A) header delimiter
>
> - Discuss degree of sequence variant complexity to support
>
> - Discuss degree of PTM complexity to support
>
> - Support for UniMod vs. PSI-MOD
>
> - Review examples of PEFF
>
> - Review PEFF-supporting software
>
> - Central location for all supporting documentation
>
> - Time slot for future calls
>
> We may not get through this all, but let’s tackle as much as we can 
> and continue at the next call. I’m presenting at the top of the next 
> hour, so I’d like to limit this call to 55 mins.
>
> I will send out dial-in information and reminder as we get closer.
>
> Thanks,
>
> Eric
>
> *From:*Eric Deutsch [mailto:ede...@sy... 
> <mailto:ede...@sy...>]
> *Sent:* Friday, May 15, 2015 10:05 AM
> *To:* Pierre-Alain Binz; jim...@th... 
> <mailto:jim...@th...>; Patrick Pedrioli; en...@uw... 
> <mailto:en...@uw...>; cha...@cg... 
> <mailto:cha...@cg...>; xia...@va... 
> <mailto:xia...@va...>; Lydie Lane; Matt Chambers; 
> Har...@bi... <mailto:Har...@bi...>; 
> David Creasy; Eugene Kapp; Eric Deutsch; ju...@eb... 
> <mailto:ju...@eb...>; Ger...@gm... 
> <mailto:Ger...@gm...>
> *Cc:* Mass spectrometry standard development; 
> psi...@li... 
> <mailto:psi...@li...>
> *Subject:* PEFF progress and call next week and beyond
>
> Hi everyone, we would like to set up some regular calls to carry PEFF 
> over the finish line. We had a good discussion at the PSI meeting, so 
> we just need to keep some momentum to get it finished.
>
> I would like to set up a time next week to have conference call to 
> discuss some of the open issues. If you are interested in working to 
> help complete and resubmit PEFF, please complete the Doodle poll below 
> (even if you cannot attend at the suggested times next week) and I 
> will keep you in the loop for continuing development on this. I have 
> sent this to the list of coauthors on the specification and other 
> vocal participants at the workshop that I recall. Anyone else is 
> welcome to join the effort even if I forgot to add you to the list above.
>
> http://doodle.com/but4z7ihv75byyp7
>
> Attached are the latest document and the notes I took during the PSI 
> workshop.
>
> Please respond to the doodle poll and I will email some specific 
> agenda point in advance of the meeting.
>
> We should probably paste some more information here:
>
> http://www.psidev.info/peff
>
> Please email me if you have specific agenda items or other questions 
> or comments.
>
> thanks,
>
> Eric
>

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, here are my notes from the PEFF call today. Please let me know
if I captured anything incorrectly.



Note that we agreed to continue to the second part of the posted agenda,
which we did not finish today, next Thursday at the same timeslot.



Present: Eric, Pierre-Alain, Jim, Robert, Xiaojing, Lydie, Harald, Gerben,
Yasset, Karl, Juan Antonio

Did I miss anyone?



Agenda:



- Review what remains to be done

+ We need to finish spec doc, the extant single hand-crafted example
(~dozen entries), and the OBO file

+ neXtProt has been generating PEFF files regularly (not quite compliant
the spec as previously written, but are now actively fixing the neXtProt
exporter so this discussion is timely)

+ Writer from Alain Gateau? This is the neXtProt exporter?

+ Reader from Harald

+ Settle the open issues below and then update all these elements

+ Full manuscript?

+ General tool to work with PEFF files? Add/subtract elements, adjust
annotations? Would be great but not required.



- Discuss (CTRL+A) header delimiter

+ Not new perhaps, this already exists in FASTA!

+ Or maybe not in the FASTA specification is there is one, but seen in the
wild

+ Original NCBI nr already has these (CTRL+A)

+ This PEFF feature was mainly motivated by the fact that this feature is
already existing out there in the field, by NCBI nr at least

+ For software implementations, there are several things that could happen
when faced with this, which is not good.

+ Some on the call feel this is a problematic feature that should be avoided

+ General consensus is that this should be an explicitly disallowed
feature. Keep it simple. Repeat the sequence.

+ Could add a header keyvalue that could point to other redundant entries?



- Discuss degree of sequence variant complexity to support

+ Explicit examples of usage should be written into the specification. This
is not there yet.

+ Discussion at PSI workshop last month moved strongly toward excluding
advanced variations completely

+ Karl proposed having two different tags, one for simple substitutions,
and one for indels and other complex things

+ Gerben in favor of including indels in separate tags

+ Pierre-Alain okay to splitting into two tags as Karl suggested

+ Karl stands by his suggestion. And also suggests deprecating existing
term to avoid confusion

+ Explicitly require that SAAV changes be in the simple SAAV term, and NOT
in the more complex term

+ Xiaojing asks what about nonsense mutation?

+ In the simple SAAV, could allow a change to an asterisk: (223:*) General
agreement on this.

+ (223|225|KPA) goes in the more complex term

+ There were rumblings that regular expressions should not be supported
anywhere? i.e. no (223|[KR]) for simple, no (223|225|[KR]PA) in complex.
Eric is not sure if there was a consensus on this.



Ran out of time here. Skipped to last agenda item. Will continue here next
week.



- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation



- Time slot for future calls

+ Broad agreement that Thursday at this time is good. We will meet again at
this time next week and continue with the agenda.















*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Wednesday, May 20, 2015 4:18 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* RE: PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, just a reminder about the PEFF call tomorrow, see below for
details. Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 18, 2015 2:36 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, it appears that we have near consensus for Thursday at the
earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.



Agenda:

- Review what remains to be done

- Discuss (CTRL+A) header delimiter

- Discuss degree of sequence variant complexity to support

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Time slot for future calls



We may not get through this all, but let’s tackle as much as we can and
continue at the next call. I’m presenting at the top of the next hour, so
I’d like to limit this call to 55 mins.



I will send out dial-in information and reminder as we get closer.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
psi...@li...
*Subject:* PEFF progress and call next week and beyond



Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

Re: [Psidev-ms-dev] PEFF call Thursday 8am Seattle, 4pm UK time

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

Hi everyone, just a reminder about the PEFF call tomorrow, see below for
details. Dial-in information:



Dial in numbers:

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ Generic international: +44 2083222500 (UK number)

+ US: 877-420-0272



*access code: 297427 #*





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Monday, May 18, 2015 2:36 PM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; ju...@eb...; Ger...@gm...; Jones, Andy; Yasset
Perez-Riverol
*Cc:* Mass spectrometry standard development;
psi...@li...; Eric Deutsch
*Subject:* PEFF call Thursday 8am Seattle, 4pm UK time



Hi everyone, it appears that we have near consensus for Thursday at the
earlier timeslot 8am PDT, 4pm UK time, so let’s plan on that.



Agenda:

- Review what remains to be done

- Discuss (CTRL+A) header delimiter

- Discuss degree of sequence variant complexity to support

- Discuss degree of PTM complexity to support

- Support for UniMod vs. PSI-MOD

- Review examples of PEFF

- Review PEFF-supporting software

- Central location for all supporting documentation

- Time slot for future calls



We may not get through this all, but let’s tackle as much as we can and
continue at the next call. I’m presenting at the top of the next hour, so
I’d like to limit this call to 55 mins.



I will send out dial-in information and reminder as we get closer.



Thanks,

Eric





*From:* Eric Deutsch [mailto:ede...@sy...]
*Sent:* Friday, May 15, 2015 10:05 AM
*To:* Pierre-Alain Binz; jim...@th...; Patrick Pedrioli;
en...@uw...; cha...@cg...; xia...@va...; Lydie
Lane; Matt Chambers; Har...@bi...; David Creasy; Eugene
Kapp; Eric Deutsch; ju...@eb...; Ger...@gm...
*Cc:* Mass spectrometry standard development;
psi...@li...
*Subject:* PEFF progress and call next week and beyond



Hi everyone, we would like to set up some regular calls to carry PEFF over
the finish line. We had a good discussion at the PSI meeting, so we just
need to keep some momentum to get it finished.



I would like to set up a time next week to have conference call to discuss
some of the open issues. If you are interested in working to help complete
and resubmit PEFF, please complete the Doodle poll below (even if you
cannot attend at the suggested times next week) and I will keep you in the
loop for continuing development on this. I have sent this to the list of
coauthors on the specification and other vocal participants at the workshop
that I recall. Anyone else is welcome to join the effort even if I forgot
to add you to the list above.



http://doodle.com/but4z7ihv75byyp7



Attached are the latest document and the notes I took during the PSI
workshop.



Please respond to the doodle poll and I will email some specific agenda
point in advance of the meeting.



We should probably paste some more information here:

http://www.psidev.info/peff



Please email me if you have specific agenda items or other questions or
comments.



thanks,

Eric

Re: [Psidev-ms-dev] Release candidate 3.76.0_rc1 of psi-ms.obo

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

HI Gerhard, thank you for fixing this!

Maybe the definition could be made more explicit that by distinct peptide we
mean aggregated over different mass modifications as well (if true?)

def: "Estimation of the q-value for distinct peptides once redundant
identifications of the same peptide have been removed (i. e., multiple PSMs,
possibly with different mass modifications, mapping to the same sequence
have been collapsed to one entry)." [PSI:PI]

thanks,
Eric


-----Original Message-----
From: mayerg97 [mailto:ger...@ru...]
Sent: Tuesday, May 19, 2015 2:49 AM
To: psi...@li...;
psi...@li...; psi...@li...
Subject: [Psidev-ms-dev] Release candidate 3.76.0_rc1 of psi-ms.obo

Dear proteomics community,

attached you find the release candidate 3.76.0_rc1 of the psi-ms.obo file.


Changed CV terms in version 3.76.0_rc1 of psi-ms.obo:
=====================================================
************ Added is_a: MS:1002484 ! peptide-level statistical threshold
[Term]
id: MS:1001868
name: distinct peptide-level q-value
def: "Estimation of the q-value 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]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ Obsoleted the following term because of id clash with
MS:1002289 (ProteinProphet)
[Term]
id: MS:1002289
name: ASAPRatio
def: "OBSOLETE A program in the TPP that calculates PSM, peptide, and
protein-level abundances based on 2-channel isotope-labelled data such
as ICAT, SILAC, etc." [PSI:PI]
comment: This term was made obsolete because of id clash with the term
MS:1002289 (ProteinProphet) - use term MS:1002574 (ASAPRatio) instead.
is_a: MS:1002286 ! Trans-Proteomic Pipeline software
is_obsolete: true



New CV terms in version 3.76.0_rc1 of psi-ms.obo:
=================================================
************ Term with new id for ASAPRatio
[Term]
id: MS:1002574
name: ASAPRatio
def: "A program in the TPP that calculates PSM, peptide, and
protein-level abundances based on 2-channel isotope-labelled data such
as ICAT, SILAC, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

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 3.76.0_rc1 of psi-ms.obo

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

Dear proteomics community,

attached you find the release candidate 3.76.0_rc1 of the psi-ms.obo file.


Changed CV terms in version 3.76.0_rc1 of psi-ms.obo:
=====================================================
************ Added is_a: MS:1002484 ! peptide-level statistical threshold
[Term]
id: MS:1001868
name: distinct peptide-level q-value
def: "Estimation of the q-value 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]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002484 ! peptide-level statistical threshold
relationship: has_units UO:0000166 ! parts per notation unit
relationship: has_units UO:0000187 ! percent
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

************ Obsoleted the following term because of id clash with 
MS:1002289 (ProteinProphet)
[Term]
id: MS:1002289
name: ASAPRatio
def: "OBSOLETE A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on 2-channel isotope-labelled data such 
as ICAT, SILAC, etc." [PSI:PI]
comment: This term was made obsolete because of id clash with the term 
MS:1002289 (ProteinProphet) - use term MS:1002574 (ASAPRatio) instead.
is_a: MS:1002286 ! Trans-Proteomic Pipeline software
is_obsolete: true



New CV terms in version 3.76.0_rc1 of psi-ms.obo:
=================================================
************ Term with new id for ASAPRatio
[Term]
id: MS:1002574
name: ASAPRatio
def: "A program in the TPP that calculates PSM, peptide, and 
protein-level abundances based on 2-channel isotope-labelled data such 
as ICAT, SILAC, etc." [PSI:PI]
is_a: MS:1002286 ! Trans-Proteomic Pipeline software

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