Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting

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

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...
Cc: eug...@tu...; le...@im...; Andrea Sinz <and...@ph...>; Robert Chalkley <cha...@cg...>; eli...@ug...; ju...@ed...; 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

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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