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Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting
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From: Jones, A. <And...@li...> - 2016-05-18 14:57:50
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Hi all, Apologies I may be a few minutes late, please start without me – taking a look through the issues etc. Best wishes Andy From: Jones, Andy Sent: 17 May 2016 09:31 To: 'psi...@li...' <psi...@li...> Cc: 'eug...@tu...' <eug...@tu...>; 'le...@im...' <le...@im...>; 'Andrea Sinz' <and...@ph...>; 'Robert Chalkley' <cha...@cg...>; 'eli...@ug...' <eli...@ug...>; 'ju...@ed...' <ju...@ed...>; 'sul...@ug...' <sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Hi all, Just confirming we will have the call tomorrow at 4pm UK, 5pm EU, 8am California to discuss progress on cross-linking in mzid 1.2. Agenda: - Update on CV (Lutz – can you join the call, and/or send an update in advance - Update on example files (Lutz/Eugen) and tests against the validator. Please raise an issue if have any problems with the validator - Work through issues on list: https://github.com/HUPO-PSI/mzIdentML/issues I feel we are almost complete on all other mzid 1.2 issues, and cross-linking is the one outstanding features. As such, I would appreciate a push from everyone at this point to get this done, so we can submit the specifications to the document process. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 11 May 2016 16:56 To: 'psi...@li...' <psi...@li...<mailto:psi...@li...>> Cc: 'eug...@tu...' <eug...@tu...<mailto:eug...@tu...>>; 'le...@im...' <le...@im...<mailto:le...@im...>>; 'Andrea Sinz' <and...@ph...<mailto:and...@ph...>>; 'Robert Chalkley' <cha...@cg...<mailto:cha...@cg...>>; 'eli...@ug...' <eli...@ug...<mailto:eli...@ug...>>; 'ju...@ed...' <ju...@ed...<mailto:ju...@ed...>>; 'sul...@ug...' <sul...@ug...<mailto:sul...@ug...>> Subject: RE: Cross-linking discussions at PSI meeting Hi all (crosslinking people specifically), We would like to schedule the next crosslinking-mzid call for Wed 18th at 4pm (UK); 5pm EU – please can you let me know if this suits. Best wishes Andy From: Jones, Andy Sent: 04 May 2016 17:06 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Hi all, Brief summary from the call: 1. Agreed that expMassToCharge, calcMassToCharge and chargeState should be identical for alpha and beta PSMs, reflecting the overall values for the cross-linked molecules; a. Also agreed that for consensus spectrum approach, there should be one SpectrumIdentificationItem per peptide chain identified, we acknowledge potential for some loss of information, but probably impossible to second guess everything that people want to encode 2. General agreement over my proposal for interaction scores as per issue pdf 3. Agreed for Lutz to make a provisional release of a very simple CV e.g. XLMOD.1.0.1.csv; and have a second working copy where ideas can be developed; Detail can be added over time, as people need specific terms 4. Proteogenomics – Agreed to move chromosome name and strand to DBSequence (protein-level), also move Genome reference version to DBSequence; Remove “peptide start position on chromosome” as redundant info, this is not needed for the encoding 5. Decide to leave the issue open for now for people to vote on, not enough people on the call to take a decision Proposed date for next call, same time slot next Wed 11th May – please let me know if you can make it. Plan to discuss mzid items, not including cross-linking next week. Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 04 May 2016 14:27 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, The main items to work through today are as follows: 1. The XL encoding with consensus spectra, and more generally what values should go in expMassToCharge, calcMassToCharge and chargeState: https://github.com/HUPO-PSI/mzIdentML/issues/19, as we identified a flaw in the proposed specs a. For background see Section 5.2.8 of the spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx 2. How to encode protein-level interaction evidence: https://github.com/HUPO-PSI/mzIdentML/issues/24 3. Any issues around CV of reagents: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv. Looks like it hasn’t been updated since last week – Lutz, any developments here? Time permitting, I would like sign off one or two non-XL issues: 4. Proteogenomics: https://github.com/HUPO-PSI/mzIdentML/issues/4; Specifically encoding of genome reference version; and whether to keep CV term for “peptide start on chromosome” since info is redundant 5. Multiple search engine encoding: https://github.com/HUPO-PSI/mzIdentML/issues/5 Speak in 1.5 hours, Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 03 May 2016 14:58 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, As a reminder, we will have our next mzid 1.2 call tomorrow at 4pm UK time/5pm EU/8am California for those of you who can join: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160504T16&p1=301&ah=1 The dial in details are as usual (below) – Juan, is there someone at the EBI who can start the call for us? Agenda: 1. XL encoding and CV issues (before the call I will update issues and documentation in GitHub) 2. Work through other mzid 1.2 issues (time permitting): https://github.com/HUPO-PSI/mzIdentML/issues 3. Any other business Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 28 April 2016 15:37 To: 'Jones, Andy' <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Summary of items we will discuss on the call (30 mins time): 1. Overview of encoding as written in spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx (section 5.2.8 and Figure 3 and Figure 4) a. Note Figure 4 is subject to change following our discussions 2. Work through issues flagged here, particularly those mentioned by Lutz: https://github.com/HUPO-PSI/mzIdentML/issues/2; a. For this we will also need to look at the proposed XL CV: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv 3. Action points towards getting the XL part of mzid 1.2 complete Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 27 April 2016 10:22 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1 The main topic for discussion will be encoding cross-linking in mzIdentML 1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here: https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open issues around cross-linking by tomorrow. The current version of the specifications are here (rather long I’m afraid) along with a powerpoint explaining the encodings for new features: https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2 If Lutz is able to create a CV file for reagents before the call, we will also post that online for discussions. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 19 April 2016 15:56 To: tobias <to...@eb...<mailto:to...@eb...>> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; sul...@ug...<mailto:sul...@ug...>; ju...@ed...<mailto:ju...@ed...>; eli...@ug...<mailto:eli...@ug...>; Lutz Fischer <lfi...@st...<mailto:lfi...@st...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Juan Antonio Vizcaino <ju...@eb...<mailto:ju...@eb...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; psi...@li...<mailto:psi...@li...> Subject: Cross-linking discussions at PSI meeting Hi all, This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list. The major outcomes from today are as follows: 1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info. 2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format) 3. Some additions to mzid 1.2 to cover: - cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism) - Adding protein-level interaction evidence - Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity 4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2 5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship 6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper. I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look. ACTION items: - We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec - Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub) - Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered - Andy to continue cleaning and updating specification document I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it. best wishes Andy |
