From: Jones, A. <And...@li...> - 2016-04-21 09:04:06
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More answers in-line: From: Lutz Fischer [mailto:lfi...@st...] Sent: 20 April 2016 16:13 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: short examples for different cross-linker peptide combinations Hi I attached some example representations of different cross-linked peptide configuration - as image and xml examples. One thing that I realised we probably need to change the description and the possibly validator a bit. If we want to have anything else then "two peptides, one cross-linker" then the current wording in the draft is not really working (the blue box under 5.3.5) - it enforces two peptides and two spectrumidentificationitems. I think the only rule I would see is that for each donor-modification has to be at least one zero-mass receptor modification. Okay – if the validator is enforcing only case 1, then this is not correct. Have you tried some of the other examples – do they fail validation? I certainly intended that cases 1-4 would be completely standardly supported. I can see that case 5 is potentially representable but would break the one donor – one receiver rule (per pair of Modification elements), which works for cases 1-4. Is such an example realistic at the present time? I don’t fully understand what you are showing in Case 6, and quite possibly this would break some other part of mzIdentML. Again, is this a realistic case we need to support now? Best wishes Andy A loop link has only one peptide - other structures would need more peptide. But otherwise I think we can represent basically anything I could think of right now. I have 5 examples. 1) standard cross-link - two peptides, one cross-linker 2) loop link - one peptide, one cross-linker then the more fancy examples start 3) two peptides two cross-linker 4) three peptides two cross-linker 5) a very fancy pentameric cross-linker - its just an example to show we can represent other things then dimeric cross-linker 6) 4 chains with 16 disulfid bounds - I thing three years ago at the PSI-meeting somebody had the question whether antibodies would be representable - so we can say yes Some examples are a bit far fetched - but I think it is worthwhile having these as a reference. At some point people will look for other things then "2 peptides, one cross-linker". E.g. try to record an anti-body. Any comments/corrections are welcome. 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 |