psidev-qc-dev — PSI-QC working group mailinglist

Re: [Psidev-qc-dev] Upcoming teleconference Friday 16/06

[Tenzer, S. <te...@un...>]

Hi everybody,

unfortunately I will not be able to attend the TC, as I will be on holiday with my family. My apologies!

Best wishes,

Stefan




Am 13.06.2017 um 15:47 schrieb Wout Bittremieux <wou...@ua...<mailto:wou...@ua...>>:

Dear colleagues,

This is a reminder that our next teleconference is scheduled for Friday, June 16th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China).

You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

Provisional agenda items are:
- follow-up on the CV and MIAPE-QC work by Martin & Jinmeng (cfr. Martin's mail from last month and Jinmeng's update here<https://github.com/Jinmeng-QC/MIAPE-QC/blob/master/summary_update.md>)
- evaluate the CV in terms of OpenMS & iMonDB use cases and requirements
- report on new developments at ASMS
- any additional items that need to be discussed...

I hope to talk to all of you on Friday.

Best,
Wout
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[Psidev-qc-dev] Upcoming teleconference Friday 16/06

[Wout B. <wou...@ua...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for Friday, June 16th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China).

You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

Provisional agenda items are:
- follow-up on the CV and MIAPE-QC work by Martin & Jinmeng (cfr. Martin's mail from last month and Jinmeng's update here <https://github.com/Jinmeng-QC/MIAPE-QC/blob/master/summary_update.md>)
- evaluate the CV in terms of OpenMS & iMonDB use cases and requirements
- report on new developments at ASMS
- any additional items that need to be discussed...

I hope to talk to all of you on Friday.

Best,
Wout

[Psidev-qc-dev] MIAPE-QC update

[Jinmeng J. <jia...@16...>]

Dear colleagues,I have made several changes to the old version of MIAPE-QC document. Please find the new document here: https://github.com/Jinmeng-QC/MIAPE-QC/blob/master/MIAPE-QC.md. Meanwhile, you can find a summary containing statictics of current checklist, details about the changes, advices/questions/interests from community and other information about MIAPE-QC and qcCV through: https://github.com/Jinmeng-QC/MIAPE-QC/blob/master/summary_update.md.

According to dissusion at last week's teleconference, I will let Mathias upload these files to qcML-development repository. (many thanks, Mathias~) 




Best,
Jinmeng


--

Jinmeng, Jia
Ph.D. candidate,Tieliu Shi's Lab
Center for Bioinformatics and Computational Biology
Shanghai Key Laboratory of Regulatory Biology
Institute of Biomedical Sciences and School of Life Sciences
East China Normal University
Minhang Campus: 500 Dongchuan RD., Shanghai 200241

Re: [Psidev-qc-dev] Upcoming teleconference on Friday

[Bittremieux W. <wou...@ua...>]

Dear colleagues,

Please find the meeting notes of last week's teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20170519_telco.md

In particular some action points are listed at the bottom. These will be picked up during our next teleconference next month.

Best,
Wout

> On 16 May 2017, at 09:49, Bittremieux Wout <wou...@ua...> wrote:
> 
> Dear colleagues,
> 
> As agreed during the annual PSI meeting last month in Beijing we will keep in close contact with each other through monthly teleconferences. These teleconferences will take place each third Friday of the month at 9:00 GMT.
> 
> Our first teleconference is scheduled for next Friday, May 19th, at 9:00 GMT (11:00 Western Europe & South Africa, 17:00 China).
> 
> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
> 
> Provisional agenda items are:
> - follow-up on crafting an example qcML file incorporating the proposed changes
> - follow-up on converting the list of identified QC metrics to the CV
> - ASMS attendance and meet-up
> - any additional items that need to be discussed...
> 
> I hope to talk to all of you on Friday.
> 
> Best,
> Wout
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference on Friday

[Martin E. <mar...@ru...>]

Dear QC colleagues,

 

unexpectedly (and unfortunately) I cannot attend 

the Hangout.

 

Attached is a slightly updated obo file.

I will add the other metrics from our Excel, other NIST metrics and

metrics from MIAPE QC document. 

Together with Gerhard I will start to assemble a CV mapping 

file for the CV validator. Therefore we need the crafted qcML file (from
github).

 

>From current point of view I will not attend ASMS.

 

  Best regards

     Martin

 

 

Von: Bittremieux Wout [mailto:wou...@ua...] 
Gesendet: Dienstag, 16. Mai 2017 09:49
An: psi...@li...
Betreff: [Psidev-qc-dev] Upcoming teleconference on Friday

 

Dear colleagues,

 

As agreed during the annual PSI meeting last month in Beijing we will keep
in close contact with each other through monthly teleconferences. These
teleconferences will take place each third Friday of the month at 9:00 GMT.

 

Our first teleconference is scheduled for next Friday, May 19th, at 9:00 GMT
(11:00 Western Europe & South Africa, 17:00 China).

 

You can connect to our teleconference on Google Hangouts through the
following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

 

Provisional agenda items are:

- follow-up on crafting an example qcML file incorporating the proposed
changes

- follow-up on converting the list of identified QC metrics to the CV

- ASMS attendance and meet-up

- any additional items that need to be discussed...

 

I hope to talk to all of you on Friday.

 

Best,

Wout

[Psidev-qc-dev] REMINDER: HUPO PSI recommendation document (file format proBAM), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

this is a reminder, that the 60-days public comments 

and external review phase ends in two weeks on 31st May!

 

See below for details of your contribution.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Donnerstag, 30. März 2017 09:50
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format proBAM), 60-days
public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

A recommendation document specifying the proBAM file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBAM-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 31st May 2017).

 

The format represents output from proteogenomic studies,

mapping the MS-based proteomics PSM information to 

the genome. Background: The proBAM format builds upon the structure of the

original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)

by extending it with other mandatory fields to accommodate unique features

on MS-based proteomics peptide-spectrum matches (PSMs) information.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBAM-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

[Psidev-qc-dev] Upcoming teleconference on Friday

[Bittremieux W. <wou...@ua...>]

Dear colleagues,

As agreed during the annual PSI meeting last month in Beijing we will keep in close contact with each other through monthly teleconferences. These teleconferences will take place each third Friday of the month at 9:00 GMT.

Our first teleconference is scheduled for next Friday, May 19th, at 9:00 GMT (11:00 Western Europe & South Africa, 17:00 China).

You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

Provisional agenda items are:
- follow-up on crafting an example qcML file incorporating the proposed changes
- follow-up on converting the list of identified QC metrics to the CV
- ASMS attendance and meet-up
- any additional items that need to be discussed...

I hope to talk to all of you on Friday.

Best,
Wout

[Psidev-qc-dev] HUPO-PSI Beijing meeting notes

[Bittremieux W. <wou...@ua...>]

Dear colleagues,

First of all I want to thank everyone that attended last week's HUPO-PSI meeting in Beijing for their efforts. We succeeded in getting some good work done in our QC working group!

You can find the meeting notes on our official GitHub repository here<https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20170424_Beijing.md>.

I especially want to highlight that we have decided to schedule monthly teleconferences to further coordinate the work on the qcML format. These teleconferences will take place on the third Friday of the month at 9:00 GMT. We tried to strike a balance to accommodate our international collaborators. The first teleconference will take place on Friday May 19, and I hope to talk to many of you on that occasion. An explicit announcement of this teleconference with practical details will follow soon.

I tried to record the names of all the people that attended our sessions (see the meeting notes), but I think I might have missed a few and I likely made a few mistakes as well. If you see that someone is missing or that I misspelled a name, please let me know. Your engagement is instrumental to the success of the working group, so it is important to stay in touch.

Let's keep the momentum going!

Thank you,
Wout

Re: [Psidev-qc-dev] PSI annual meeting agenda

[David T. <dt...@su...>]

Hi, Mathias.

I agree entirely that doing a CV / qcML markup session as early as
possible is entirely necessary.

If you are willing to take a lead on shaping the agenda, that will
certainly be helpful to me.  I am besieged with local tasks in the
run-up to this meeting, so I won't be able to spend as much time on it
as I should.

Thanks,
Dave

On 4/12/2017 1:12 PM, Mathias Walzer wrote:
> Dear all,
>
> The PSI annual meeting agenda for 'our' track looks like this right now:
>
> Track 4 - Quality Control
>
> Tue - morning:
> qcML / minimal requirements
> Minimal reporting requirements
>
> Tue - afternoon:
> Software support
> Implementation in repositories
>
> Wed - morning:
> Break-outs based on interests
> Break-outs based on interests
> Summary, wrap-up
>
> I would, however, very much like to discuss how we are going to integrate our collection of metrics into the cv (or do the CV from scratch), the cv into the schema and the minimum requirements in all of this *before* we go on about software and repository integration.
> Depending on how detailed the cv terms are going to be in 'final' will influence how lax we can be on the schema side.
> Because, and I will stress this ever so often, one goal should be machine readability *without* ethereal knowledge of how some certain bit of data is meant. In the end, we want to support the widespread adoption of (comparable?) quality metrics for which it might be detrimental if reported metrics are ambiguous/unintelligible without the context of the particular software.
>
> TL;DR: I suggest to have a CV definitions session on Tuesday afternoon and move the other points thereafter.
>
> Please respond soon, deadline for agenda fix and print is soon (this week!), otherwise, I will go ahead with the changes.
>
> best,
>    mths
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev


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[Psidev-qc-dev] PSI annual meeting agenda

[Mathias W. <wa...@in...>]

Dear all, 

The PSI annual meeting agenda for 'our' track looks like this right now:
	
Track 4 - Quality Control

Tue - morning:
qcML / minimal requirements
Minimal reporting requirements

Tue - afternoon:
Software support
Implementation in repositories

Wed - morning:
Break-outs based on interests
Break-outs based on interests
Summary, wrap-up

I would, however, very much like to discuss how we are going to integrate our collection of metrics into the cv (or do the CV from scratch), the cv into the schema and the minimum requirements in all of this *before* we go on about software and repository integration.
Depending on how detailed the cv terms are going to be in 'final' will influence how lax we can be on the schema side.
Because, and I will stress this ever so often, one goal should be machine readability *without* ethereal knowledge of how some certain bit of data is meant. In the end, we want to support the widespread adoption of (comparable?) quality metrics for which it might be detrimental if reported metrics are ambiguous/unintelligible without the context of the particular software. 

TL;DR: I suggest to have a CV definitions session on Tuesday afternoon and move the other points thereafter.

Please respond soon, deadline for agenda fix and print is soon (this week!), otherwise, I will go ahead with the changes. 
	
best, 
  mths

[Psidev-qc-dev] HUPO PSI recommendation document (file format proBAM), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

http://www.psidev.info for an overview of activities).

 

A recommendation document specifying the proBAM file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBAM-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 31st May 2017).

 

The format represents output from proteogenomic studies,

mapping the MS-based proteomics PSM information to 

the genome. Background: The proBAM format builds upon the structure of the

original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)

by extending it with other mandatory fields to accommodate unique features

on MS-based proteomics peptide-spectrum matches (PSMs) information.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBAM-in-docproc) 

or send them directly to martin.eisenacher: at : rub.de for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

[Psidev-qc-dev] namespace in mzIdentML

[Witold E W. <wew...@gm...>]

Sorry if this is not the appropriate list but did not find any list
dedicated for users here: http://www.psidev.info/mailing-lists

I just have a brief question. I am trying to write the following
xpath/xquery statement

db:open("extracted","20160312_15_B1_myrimatch_2_2_140.mzid")/*:MzIdentML/*:SequenceCollection/*:Peptide

and would like to be more specific about the namespace than to use the *.

However, namespaces  are not mentioned even once in the
http://www.psidev.info/sites/default/files/mzIdentML1.1.0.pdf

Thanks

[Psidev-qc-dev] REVISED VERSION R1: PSI recommendation document (file format proBed), 14-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

I received a revised version (R1) of the proBed format specification:

http://www.psidev.info/proBed-in-docproc

A “responses to reviewers” document is also included.

 

It would be great to receive your comments within two 

weeks (13th March 2017).

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

 

 

Von: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Donnerstag, 20. Oktober 2016 11:11
An: psi...@li...;
psi...@li...; psi...@li...;
ps...@eb...; psi...@eb...
Betreff: [Psidev-qc-dev] PSI recommendation document (file format proBed),
60-days public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying the proBed file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBed-in-docproc

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 

now goes through 60-days public comments and external 

review phase (end: 19th December 2016).

 

"The format represents systematically the output of proteogenomics

analyses, by mapping peptide identification data retrieved from 

mass spectrometry (MS)-based experiments to the genome."

(see also Cover Letter attached to the submission page)

 

The format is based on the BED format (Browser Extensive Data,

 <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>
https://genome.ucsc.edu/FAQ/FAQformat.html#format1),

developed by the UCSC (University of California, Santa Cruz) team.

 

The public comment period enables the wider community to provide 

feedback on a proposed standard before it is formally accepted, and 

thus is an important step in the standardisation process.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

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

 



 

Re: [Psidev-qc-dev] Join

[walzer <wa...@in...>]

As you successfully posted the request to the mailinglist - I'd declare 
success!

Welcome back!

On 22.02.2017 14:48, Julian Uszkoreit wrote:
> Hi,
>
> Please add me to the PSI-QC mailing list.
>
> Cheers,
> Julian
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] Join

[Julian U. <jul...@ru...>]

Hi,

Please add me to the PSI-QC mailing list.

Cheers,
Julian

Re: [Psidev-qc-dev] quality metrics

[walzer <wa...@in...>]

Dear all,

as interest in a telco is not putting doodle or me in a difficult spot 
to pick a date, maybe a little digest of the newest metrics we could 
discuss, will kindle some more interest 
(http://doodle.com/poll/bv36kwe3hfmgwm8v).

CPTAC labeling QC
We haven't touched upon QC for labeling techniques, and the CPTAC study 
considerations seem like a good start (thanks to Karl Clauser). 
Summarised, these would cover ideally the completeness of labellings 
(counting the number of labeled vs. unlabeled termini) Also, considering 
the S/N of not only all spectra (as we would now with MS2-2) but also of 
only those with reporter ions seems to be a good idea. MassUP - QC 
MassUp covers base with a number of metrics that also we use (e.g. the 
name of the sample, number of spectra, min. Mass, max. Mass, avg. 
Masses, ...) but also ask for a classas label of the sample - as already 
mentioned this is highly interesting to bring the experimental design 
into the loop to do proper QC for a set of several measurements.They 
also define POPXX as a the number of peaks with Percentage of Presence- 
so I am not that familiar with MALDI, but it seems to be a a good idea 
in general to also look at the replication success on a spectrum and 
peaks level! though I am not sure which kind of peaks they are 
considering in this MALID setting with MassUp analysis. msPurity Lawson 
et al. published an interesting metric to assist with spectral library 
search result assessments in metabolomics. The metric assesses the 
purity of the precursor producing a tandem spectrum. Having more than 
just the targeted ion species in your selection for fragmentation messes 
with the lookup of your spectrum in a library with (assumedly) pure 
spectra. But I think this is also useful in other context, at least I 
come across some mixed spectra sometimes, especially when sample 
abundance or ionisation yield is low and the fill times go up to the 
max. set. They calculate this metric as a ratio of precursor intensity 
and sum. intensity of the respective isolation window. As I read it, it 
is assumed that the highest peak in the isolation window is the targeted 
precursor peak, and it's intensity for the MS2 is interpolated from the 
intensity in the neighboring MS1. I think it would also be good to have 
a classification of analysis metrics and acquisition metrics. I think it 
came up in Ghent, but our metrics list was not long enough to make such 
separations. This goes in the same direction as what Robert was saying 
in his mail, that there might be as well a lot of good/reliable results 
in bad runs. After all, often times analysis algorithms are robust 
enough to navigate around bits of bad data. The ID(free) classification 
goes in that direction, but I think analysis metrics would comprise more.

best,

   Mathias

On 07.02.2017 21:05, Mathias Walzer wrote:
> Dear all,
>
> let's discuss new QC metrics and definition refinement of old ones here. We might start here:
>
> There are some interesting new developments:
> There is the Mass-Up framework ( http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0752-4 ) for Maldi TOF QC, see Davids post on Quality control in Mass-Up
>
> And also new developments from the metabolomics side with msPurity (http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358)
>
> For labelled experiments, Spectrum Mill is using quality control metrics proven on CPTAC breast cancer proteome dataset (http://www.nature.com/nature/journal/v534/n7605/abs/nature18003.html , see Karl Clausers Re: [Psidev-qc-dev] HUPO PSI Quality Control Working Group post with the SpectrumMill documentation attached)
>
> Or, which would be much to my delight, revise the collection of more general LC-MS/MS metrics already in use in qcML (https://github.com/mwalzer/qcML-development/blob/feature/QC-CV-Metric_overview/cv/qc-metric-collection.md).
>
> So to the matter, how do you think do any metrics from the above fit in our CV definition schema? Would some need generalisation for the sake of minimising redundancy/overlap, or on the other side are some not specific enough?
> Do you have a great metric that is missing in our discussions?
>
> best,
>    Mathias
>
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Re: [Psidev-qc-dev] qcML format evolution

[walzer <wa...@in...>]

Dear all,


you may have seen the activity on github regarding the metrics 
definitions as implemented in one way or the other by previous software 
and the mailing list thread about new metrics.


My suggestion would be, that we have our first telco next week or the 
following to discuss the metrics and their representation.

What about the following dates?

Tue. 21.02. - 14.00 CEST

Tue. 21.02. - 18.00 CEST (hangouts only)

Wed 22.02. - 14.00 CEST
Wed 22.02. - 18.00 CEST (hangouts only)

Mon. 27.02. - 14.00 CEST

Mon 27.02. - 18.00 CEST (hangouts only)

Tue 28.02. - 14.00 CEST


I would suggest also to have the discussion via hangouts, alternatively 
via EBI teleconference system (however there, someone has to be 
physically at EBI, which excludes the evening dates).

If you want to participate, please take the doodle 
(http://doodle.com/poll/bv36kwe3hfmgwm8v) so we can find a date that 
fits most. If you cannot make any of the dates, please let me know.

best,
   Mathias

On 07.02.2017 19:24, Mathias Walzer wrote:
> Hi all,
>
> as the last two post were closely related to new metrics, I'll create 
> a new thread for metrics ([Psidev-qc-dev] metrics) and forward 
> (repost) the respective posts.
>
> Now, as no feedback whatsoever about the changes (after last spring 
> meeting, that is > 0.7) reached me, I will go ahead and make this a 
> pre-release on which we can base our next step on - metrics 
> development and refinement. But keep in mind that it is pretty hard to 
> define a community standard format without feedback.
>
> I'd like to take this opportunity to paraphrase my latter question
> > And shall we have a regular telco/hangouts/... (bi- or tri-weekly)?
>
> We should have a regular teleconference. We can use google hangouts 
> or, after consulting with Juanan, the EBI 0800 telco system for that. 
> I will circulate date suggestions soon.
>
> I added a visual review to github a while back for folks to make it 
> easier to express their ideas/opinions on the _next iteration_ of 
> schema evolution. 
> (https://github.com/HUPO-PSI/qcML-development/tree/master/schema/v0_0_9)
>
>
>
> best,
>
>   Mathias
>

[Psidev-qc-dev] quality metrics

[Mathias W. <wa...@in...>]

Dear all, 

let's discuss new QC metrics and definition refinement of old ones here. We might start here:

There are some interesting new developments: 
There is the Mass-Up framework ( http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0752-4 ) for Maldi TOF QC, see Davids post on Quality control in Mass-Up 

And also new developments from the metabolomics side with msPurity (http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358) 

For labelled experiments, Spectrum Mill is using quality control metrics proven on CPTAC breast cancer proteome dataset (http://www.nature.com/nature/journal/v534/n7605/abs/nature18003.html , see Karl Clausers Re: [Psidev-qc-dev] HUPO PSI Quality Control Working Group post with the SpectrumMill documentation attached)

Or, which would be much to my delight, revise the collection of more general LC-MS/MS metrics already in use in qcML (https://github.com/mwalzer/qcML-development/blob/feature/QC-CV-Metric_overview/cv/qc-metric-collection.md).

So to the matter, how do you think do any metrics from the above fit in our CV definition schema? Would some need generalisation for the sake of minimising redundancy/overlap, or on the other side are some not specific enough?
Do you have a great metric that is missing in our discussions?

best,
  Mathias

[Psidev-qc-dev] Goals/Milestones

[Mathias W. <wa...@in...>]

Dear all, 


to keep track of our efforts, this new thread might help us. 
I'll start by summarising and comment on our milestones from the WG charter so far. 


1. The first goal to submit a perspective manuscript is done, the review is already back in. Reacting might or might not demand some work on the next milestones in advance. For more, see the conversation on the manuscript. Next would be the preparation for qcML submission into the PSI process. 
2-5. We already did some re-evaluation of the current version of qcML while and after Ghent. Major point is, that due to the close intertwining of how metrics are represented and how they are defined, we are likely best off using an iterative looping approach of tackling this milestone and the next. Which is, to re-evaluate our QC controlled vocabulary with the metrics definitions and consolidate with other existing definitions. After this, we would have to see for software implementations. It would be of course nice to have this already available to support the iterations of previous two steps and in response to the reviewer comments. This is a moving target and tedious for developers to keep up, but I made some efforts as I saw some of the reviewer comments coming. Basically the first iteration of goals 2,3,4,5. To have a consolidated list of older metrics, our efforts from Ghent, the NIST metrics in a cv update AND to have them calculated and processed by OpenMS with some tangible output. Therefore, see github (https://github.com/mwalzer/qcML-development/blob/feature/QC-CV-Metric_overview/cv/README.md, https://github.com/mwalzer/qcML-development/blob/feature/QC-CV-Metric_overview/cv/qc-metric-collection.md). 
6. Our final goal will be to chaperone qcML through the PSI standardisation process after we deem the metrics definition, the CV, and the format sufficiently aligned and implemented. 


But least not to forget after the PSI process to extend our collection of metrics and support for new techniques. This is, of course, a very tempting task to skip ahead to, but let's not forget to cover our bases with the milestones before. 


best, 
Mathias

Re: [Psidev-qc-dev] qcML format evolution

[Mathias W. <wa...@in...>]

Hi all, 

as the last two post were closely related to new metrics, I'll create a new thread for metrics ([Psidev-qc-dev] metrics) and forward (repost) the respective posts. 

Now, as no feedback whatsoever about the changes (after last spring meeting, that is > 0.7) reached me, I will go ahead and make this a pre-release on which we can base our next step on - metrics development and refinement. But keep in mind that it is pretty hard to define a community standard format without feedback. 

I'd like to take this opportunity to paraphrase my latter question 
> And shall we have a regular telco/hangouts/... (bi- or tri-weekly)? 
We should have a regular teleconference. We can use google hangouts or, after consulting with Juanan , the EBI 0800 telco system for that. I will circulate date suggestions soon. 
I added a visual review to github a while back for folks to make it easier to express their ideas/opinions on the _next iteration_ of schema evolution. (https://github.com/HUPO-PSI/qcML-development/tree/master/schema/v0_0_9) 





best, 
Mathias 

Re: [Psidev-qc-dev] Quality control in Mass-Up (and other topics)

[Mathias W. <wa...@in...>]

Hi all, 
great news! 
But communications seem a little convoluted to me. Mostly all in one - schema, agenda, and review. I will try to entangle the different topics as much as possible to maintain clear threads. Or was I maybe missed out on some conversations? 


So I will answer in the respective threads, or open new ones. For reference: 

[Psidev-qc-dev] qcML format evolution, [Psidev-qc-dev] HUPO-PSI QC WG manuscript, *new* [Psidev-qc-dev] Goals/milestones, and *new*[PSIdev-qc-dev] metrics. 
If no one minds, I will more or less frequently keep an eye on the thread moderation. 

best, 
Mathias 

Re: [Psidev-qc-dev] Quality control in Mass-Up (and other topics)

[Tabb, D. P. <dt...@su...>]

Hi, all.

A couple of weeks ago, I gave a talk at Semmering, Austria, on some ideas for quality control making its presence felt more broadly, supporting experiments beyond the usual run of LC-MS/MS shotgun workflows (attached).  I am pleased to report that one of the attendees of the meeting had already made substantial in-roads to putting MALDI-TOF profiling on firmer footing in QC.  Hugo Lopez Fernandez published his Mass-Up framework (http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0752-4) with a module intended explicitly for QC in the MALDI.  It can recognize when a particular profile matches relatively few m/z values for the other replicates for a sample or when a sample has low overlap with other samples.  We probably want to cite this in Wout's manuscript (now due on Valentine's Day) as an example of a framework that we hope will communicate with qcML, once it is standardized.

Wout, congratulations on passing your defense!

Mathias Walzer, how do matters sit with qcML updates?  What steps stand between now and document submission?  We have a HUPO-PSI meeting at Beijing in less than three months!

Thanks,
Dave

-----Original Message-----
From: Hugo López Fernández [mailto:hlf...@uv...] 
Sent: Friday, 20 January 2017 13:32
To: Tabb, David, Prof <dt...@su...>
Subject: Quality control in Mass-Up (and other topics)

Hello David,

I am Hugo, we met last week in Semmering. I hope this email finds you well and that you had a good trip to back home.

As we talked in the EuBIC, I am writing you to let you know more about the quality control analysis that we have included in Mass-Up (http://sing-group.org/mass-up/). This quality control is intended to work with peak lists. We would like to incorporate quality control for raw data, specially to detect batch effects as I also commented you.

Basically, the quality control (which is explained with most details in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at two
levels: at the replicates leve and at the samples level, which includes additional information from the intra-sample m/z matching process and consensus spectrum creation (this is because our collaborators usually want to reduce replicates spectra to a unique sample "consensus" 
spectrum). You can find attached the quality control image included in the paper.

At the replicates level, the user can check basic information about each individual spectrum (i.e. peak count, m/z range, intensity ranges, etc.) and compare all spectra in the dataset. At the samples level, the user can check the performance of the intra-sample peak matching process, by comparing the percentages of presence (POP) counts (i.e.: the counts of peaks that are present in, for example, 60%, 80% or 100% of replicates) and the POPs of each sample.

In spite of being a very simple quality control it allowed us to detect some problems with datasets and we encourage our collaborators to have a quick look at this quality control metrics before any other analysis. 
Unfortunately they usually don't but we must encourage good practices, which is the reason why I am developing this other software (http://www.sing-group.org/s2p/), also presented in other poster at the EuBIC. Basically it is a software to manage, process and integrate different data sources (Mascot identifications, MALDI plates, 2D-gel spots). It probably will not revolutionize bioinformatics but it is allowing the research group to process data efficiently and in a reproducible way, a totally different scenario than wen I came here six months ago.

As I mentioned previously we also would like to include quality control metrics for MALDI-TOF raw data, with special focus in batch effect detection (which seems to a common problem here). Regarding batch effect, I would like to apply this statistic
(http://dx.doi.org/10.1093/bioinformatics/btt480) based on guided principal component analysis to detect batch effects in MALDI-TOF data (some people applied it to LC-MS metabolomic data [http://dx.doi.org/10.1016/j.talanta.2014.07.031]). I would like to develop this work this year if I get public MALDI-TOF datasets where batch effect presence has been publicly reported (I found a few reported but I could not get the data to analyze it yet).

I will be happy to answer any question you may have or to receive any feedback from you. Looking forward to see you again, in other conference or wherever.

Best regards,

     Hugo.

--
----------------------------------------------------------------
Hugo López-Fernández, PhD
Email:hlf...@uv...
----------------------------------------------------------------
ESEI: Escuela Superior de Ingeniería Informática "Politécnico" Building, Room 306 "As Lagoas" Campus
32004 - Ourense - Spain
Web:http://www.sing-group.org/~hlfernandez/
----------------------------------------------------------------

Re: [Psidev-qc-dev] HUPO PSI Quality Control Working Group

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

Hi Dave,

 

Attached is the section of the Spectrum Mill v6.0 Manual that describes the
various Quality Metrics that I calculate, and the output table of the SM
quality metrics module for the CPTAC breast cancer proteome dataset from the
Mertins et all 2016 Nature paper. The table is included in the supplementary
materials that can be downloaded from the CPTAC DCC:

https://cptac-data-portal.georgetown.edu/cptac/s/S029 

select
Supplementary_Data_Proteome_Peptide_Spectrum_Match_results_SpectrumMill

 

Some metrics described in the manual, particularly the spectrum
identifiability metrics, are more recently developed and not included in the
example.

 

For iTRAQ and TMT labeling I believe the most important practical metrics
are for the completeness of labeling. N-termini are typically not completely
labeled. TMT labeling tends to be more complete than iTRAQ labeling, in our
hands. That is why we routinely search TMT and iTRAQ data allowing for the
peptide N-termini to be either labeled or unlabeled. When doing our label
check experiments we run more comprehensive searches which allow for Lysines
also to be either labeled or unlabeled.

 

One new metric that we are beginning to track and use as a filter for
inclusion in protein level quant calculations (but not yet described in the
manual or present in the example) is the median signal/noise of the reporter
ions MS/MS spectrum. I now extract that s/n value for each peak via the
Thermo MSFileReader API:

       FRAW::IXRawfile2Ptr pRawfile2 =  m_pRawfile;

       nRet = pRawfile2->GetLabelData(pvarLabels, pvarFlags, &nScanNumber);

I believe a similar metric was included in the most recent release of
Proteome Discoverer.

 

I hope this helps. Let me know if you have questions.

 

--Karl

 

From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Sent: Wednesday, November 30, 2016 7:39 AM
To: cl...@br...
Cc: psi...@li...
Subject: HUPO PSI Quality Control Working Group

 

Hi, Karl.

 

I am part of a working group at HUPO-PSI that seeks to further the use of
quality control pipelines in conjunction with proteomics and metabolomics
experiments.  We are pretty familiar with tool sets for dealing with general
identification data, but we would like to give some concrete examples of
experiments that are less well-covered by quality control tools.  iTRAQ and
TMT came to mind, and I recalled some conversations we had back in the CPTAC
Data Analysis teleconferences that touched on this subject.

 

Have you gone ahead to create tools for producing quality control metrics in
iTRAQ or TMT experiments?  For example, one might ask what fraction of MS/MS
scans include reporter ions from all four channels (if one uses the 4-way
reagent, of course).  I believe you were on your way to computing such
metrics.

 

I hope to include some concrete examples of how quality control becomes more
concrete in specialized areas of proteomics and metabolomics as part of a
manuscript we are fielding to Analytical Chemistry that introduces our
working group and its goals to a broader audience.

 

Thanks!

Dave

Re: [Psidev-qc-dev] HUPO-PSI Quality Control Working Group

[Robert C. <cha...@cg...>]

Hi David,

The publication guidelines are for making authors supply minimal 
information to allow assessment of the reliability of results. There is 
not necessarily a direct relationship between the quality of the data 
and quality of results: e.g. someone could have terrible chromatography 
and dirty samples, but still reliably identify all of the binding 
partners in an IP experiment.  Hence, for many studies the qcML file 
will not inform about the reliability of the results.  Where it does 
come into play is in comparative and quantitative studies; especially 
label-free studies, where chromatography and reproducible instrument 
performance are prerequisites.  I could see it as being required in SRM 
or other DIA studies, and could be added to our clinical guidelines.
What is not clear to me is whether this is something that the authors 
need to produce, or whether the repositories (PRIDE; MassIVE; PASSEL) 
should automatically create them.  There is also the ‘lowest common 
denominator’ problem of only being able to ask for it can be produced 
from all instrument files.  Is this derived from mzML files?
MCP has an Associate Editors meeting at the end of January.  I could 
potentially bring this up as a topic of discussion during the day if the 
paper is published by then, or if you send me it in whatever state it is 
in at the beginning of the New Year.

Robert


On 11/30/2016 4:19 AM, Tabb, David, Prof <dt...@su...> wrote:
>
> Hi, Sue and Robert.
>
> I am writing in connection with my work in the HUPO-PSI Quality 
> Control Working Group.  We were founded in April as a way to 
> facilitate the use of quality control workflows with proteomics and 
> metabolomics data sets.  Several groups have now produced tools to 
> generate proteomics quality metrics from raw data or raw data plus 
> identifications.  Our working group hopes to put forward standard ways 
> to communicate these metrics (particularly a file in an updated “qcML” 
> format), making it possible to make downstream decision-support tools 
> that are able to work with a variety of front-end metric generators.
>
> We believe one of the important ways we can leverage these metrics is 
> by ensuring that data sets that reach publication have some basic 
> quality information accompanying them (for some tools, this would mean 
> spending just a few minutes of CPU time to generate the qcML 
> document).  The qcML document could, for example, inform potential 
> users of the numbers of MS/MS scans acquired, the proportion of 
> precursors that were +2, or the distribution of TIC throughout the MS 
> scans.
>
> We submitted a manuscript to /Analytical Chemistry/ that introduced 
> the goals of the working group to solicit input from the broader 
> community.  A reviewer has suggested that we need to show greater 
> clarity on how we will interact with journals to nudge publication 
> guidelines to recommend the inclusion of qcML once the format is 
> finalized and the tools to produce them are easily acquired.  The two 
> of you came to my mind as great resources on how this evolution could 
> take place.
>
> Do you have some insights on how receptive ACS and ASBMB journals 
> would be to including this recommendation for proteomics and 
> metabolomics manuscripts?
>
> Thank you,
>
> Dave
>

-- 
Robert Chalkley PhD
Adjunct Professor
Genentech Hall, N474A
Tel: 415 476 5189
Fax: 415 502 1655

Mass Spectrometry Facility
University of California San Francisco
600 16th Street,
Genentech Hall, suite N472A
San Francisco, CA 94143-2240

[Psidev-qc-dev] HUPO PSI Quality Control Working Group

[Tabb, D. P. <dt...@su...>]

Hi, Karl.

I am part of a working group at HUPO-PSI that seeks to further the use of quality control pipelines in conjunction with proteomics and metabolomics experiments.  We are pretty familiar with tool sets for dealing with general identification data, but we would like to give some concrete examples of experiments that are less well-covered by quality control tools.  iTRAQ and TMT came to mind, and I recalled some conversations we had back in the CPTAC Data Analysis teleconferences that touched on this subject.

Have you gone ahead to create tools for producing quality control metrics in iTRAQ or TMT experiments?  For example, one might ask what fraction of MS/MS scans include reporter ions from all four channels (if one uses the 4-way reagent, of course).  I believe you were on your way to computing such metrics.

I hope to include some concrete examples of how quality control becomes more concrete in specialized areas of proteomics and metabolomics as part of a manuscript we are fielding to Analytical Chemistry that introduces our working group and its goals to a broader audience.

Thanks!
Dave