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

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

Hi Lutz,

I presume these messages are in response to things in the minutes? Elien did a fantastic job taking minutes for us (many thanks again for this!), but they were circulated before I had a chance to make some edits and clarifications.

Your comments are generally sensible, so for now, I wouldn’t take that version of the minutes to be a final record of discussions. I will write up all the final outcomes in the spec doc.

Hopefully later today.

Could everyone interested reply with regards to having a call next Thursday (28th April) at 4pm UK time, 5pm Europe, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160428T1500. If not, please let me know other slots you’re available, or I can setup a doodle poll if needed. Particularly it would be useful if Robert, Lutz and Alexander can join at the same time.

Best wishes
Andy

From: Lutz Fischer [mailto:lfi...@st...]
Sent: 20 April 2016 16:14
To: Elien Vandermarliere <Eli...@UG...>; Jones, Andy <jo...@li...>; tobias <to...@eb...>
Cc: eug...@tu...; le...@im...; Sule Yilmaz <Sul...@UG...>; Robert Chalkley <cha...@cg...>; Juan Antonio Vizcaino <ju...@eb...>; Yasset Perez-Riverol <yp...@eb...>; psi...@li...; Juri Rappsilber <jur...@ed...>
Subject: Re: Cross-linking discussions at PSI meeting

Hi

I have some quest to the summary document:
Homodimers:
    what do these have to do with loop links?
    Why no modification on one peptide - it should still have the zero mass receiver modification. Not every homodimer links exactly the same residue in both peptides...

Seems like residue pair information and protein pair information are to be stored.
- Is this optional?
- how are these to be stored?

Cross-links with DNA or RNA:
- stored as modification sounds rather insuficient to me. It works if you only look at short DNA or RNA stretches and you don't care about the identification and localisation of the DNS/RNA.
- what speaks against storing the DNA/RNA sequence as separate entity?
- the only thing I can see is the name of the xml-entities (e.g. peptide/peptideevidence).
- can we live with storing general sequence information in these?

Cross-linker into Unimod:
- we would need to store the different reaction specificities. That would possibly require a change to the unimod stores modifications
-Just looked at the unimod website maybe it can be handled with new classifications for specificity::
 - site1, site2, site3, ....
 - (will unimod support my pentameric example? - different mail)
 - is there a distinction between natural and induced cross-links (e.g. disulfide vs BS3)

Sorry for not being there and now possibly asking obvious/discarded questions...

Lutz


On 20/04/16 08:09, Elien Vandermarliere wrote:
Dear all

In attachment is the summary of the session on crosslinking.

Elien

Elien Vandermarliere, Dr
VIB Medical Biotechnology Center, Ugent
UGent faculteit Geneeskunde en Gezondheidswetenschappen
Albert Baertsoenkaai 3
B-9000 Gent
BELGIUM

Tel. +32 9 264 9359
Fax +32 9 264 9490
www.ugent.be<http://www.ugent.be>
www.vib.be<http://www.vib.be>

From: Jones, Andy [mailto:And...@li...]
Sent: dinsdag 19 april 2016 16:56
To: tobias
Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Sule Yilmaz; ju...@ed...<mailto:ju...@ed...>; Elien Vandermarliere; Lutz Fischer; Robert Chalkley; Juan Antonio Vizcaino; Yasset Perez-Riverol; 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






--

Lutz Fischer

lfi...@st...<mailto:lfi...@st...>

+44 131 6517057