[Psidev-pi-dev] Minutes phone call mzIdentML cross-linking April 28th

[Juan A. V. <ju...@eb...>]

Hi all,

Summary of the call yesterday. 

People attending:
I apologise because I am missing at least one person (I did not get who she was) -> Andy, Oliver and the rest of the Tuebingen people (Mathias, Timo, etc), Gerhard, Robert, Alexander, Lutz, Juan. 

-> After reviewing the specification document (Figure 3 there):

1)- At the moment, at the peptide level restrict the specification to "pairs". 
In the future, new CV params could be added to support the cases where a single linker connects multiple peptides in multiple positions. Loop links in the same peptide and more than two peptides linked by different linkers are supported right now.

2) Change in the CV the term “receiver” to the more correct (from a chemical point of view) “acceptor”.

3) The specification document needs to be updated with the latest version of the figures (including hyphenated cross-link terms and the correct accession numbers for the CV terms). Andy will do it.


After reviewing the list of cross-linkers (generated by Lutz, available at https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv <https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv>).

4) Some improvements need to be done: long name for some of the reagents needs to be agreed in some cases (for instance L-Photo-Leucine is not a systematic name), ideally publications or CAS numbers should be available as a more stable reference).
This discussion will continue off-line via e-mail between Lutz, Oliver and others.
At this point, we just need a identifier and a long name. Other details can be updated later. This would be version 1.0 of the CV. 

5) Keep the file it as a csv file at the moment.

Discussion about protein-protein interaction (PPI) evidences (Figure 4 in the specification document):

6) Not all the complexity related to PPI should be encoded in mzIdentML. The right balance needs to be kept. If more complexity is needed, links to external PSI MI and/or PSI XML files could be added. So, it should be enough adding which proteins are interacting plus some scores. 

7) There was one proposal made in the GitHub issues page (https://github.com/HUPO-PSI/mzIdentML/issues/2 <https://github.com/HUPO-PSI/mzIdentML/issues/2>). However, in order to capture more structural information (for instance the position of the interaction for each protein), this information needs to go at the Protein level (ProteinDetectionHypothesis), not at the ProteinGroup level. Andy has already posted in GitHub a possible solution.


TO DO next:

1) Lutz -> Update examples with real CV terms, and check that the validator works. Use temporary CV terms for the scores, that have not been added yet to the PSI MS CV (which also needs to be done).

2) Tuebingen -> Not far from having example files. Check with the validator. 


Next phone call next Wednesday May 4th at 4 pm UK time.


Best regards,

Juan