[Psidev-pi-dev] Minutes call today (February 6th)

[Juan A. V. <jav...@gm...>]

Hi all,

Please, let me know if I missed anything.

Present: Andy, Gerhard, Julian, Eric, Harald, Juan Antonio


The whole conference was devoted to checking some of the example files of mzIdentML 1.2 (which can be donwloaded from the SVN under examples 1.2):

1- Multi-search example (generated by Liverpool):

<additionalsearchparams> needs to contain an extra CVparam to indicate that the file contains results coming from different search engines in different PSM lists

The final PSM list CV could be put at the beginning, to facilitate the work of some readers. However, this would imply a schema change, so keep it in mind in the long list of possible improvements.

 <cvParam cvRef="PSI-MS" accession="MS:1002439" name="final PSM list UNDER DISCUSSION"></cvParam>

TO DO: Julian to generate a new example file containing intermediate PSM lists.
Andy -> Update spec documentation (section 5.3.1 for listing all the search engines in the AnalysisProtocol)


2- Example containing peptide scores (generated by Liverpool):

<AdditionalSearchParams>
      <cvParam cvRef="PSI-MS" accession="MS:1001211" name="parent mass type mono"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1001256" name="fragment mass type mono"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002490" name="peptide-level scoring"></cvParam>
      <cvParam cvRef="PSI-MS" accession="MS:1002496" name="group PSMs by sequence"></cvParam>
    </AdditionalSearchParams>

Does the validator do anything with this information? It seems to be the case but it needs to be checked.


TO DO:
The validator needs to be corrected since it gives an error related to “de novo”.
Andy to post in the list his detailed solution to the current validation errors related to the peptide scores.


3- PeptideShaker example: it contains results from several search engines, peptide scores and mod localization scores in the same file.

- The validator needs to work out which CVterm to look for the regex (mod positition and related scores).

- Parent terms needs to be added in the CV for those that are peptide level and mod localization scores at the same time.

- Solution found to report peptide objects containing the final location of the mod, without taking into account the ones from the individual PSMs.

TO DO: Andy and Harald to try validator with the current examples to test it properly.
<additionalsearchparams> needs to contain an extra CVparam to indicate that the file contains results coming from different search engines in different PSM lists


4- Cross-linking related example.

Cross-linking example. Work ongoing by Lutz.

TO DO: Andy to get x-linkers added to the PSI-MS list. 



Next call next Thursday at the same time.

Cheers,

Juan Antonio