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

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I certainly believe that we agreed for simplicity that all SIILists should have "MS:1002439:final PSM list UNDER DISCUSSION" or the “intermediate PSM list” term, even those most files are not using combined search engine approaches. I think this was agreed in case other cases arise where intermediate results for some other pre-processing are kept in the file.

I don’t know how to interpret the error message, possibly a bug?

From: Lutz Fischer [mailto:lfi...@st...]
Sent: 12 February 2015 18:55
To: psi...@li...; Jones, Andy
Cc: mayerg97
Subject: Re: [Psidev-pi-dev] Minutes call today (February 6th)

Hi all,

sorry missed last weeks meeting. I had an tooth-op and somehow for the rest of the day I was not really very usable - meaning I plainly forgot about it.

I have a question about "MS:1002439:final PSM list UNDER DISCUSSION".

With the 1.4.8 version of the validator I got an error message, that I have to put this in at least one list. So I added the code to do so. Only now I get a complain with version 1.4.10:
Message 1:
    Rule ID: SpectrumIdentificationList_rule
    Level: INFO
    Context(/cvParam/@accession ) in 2 locations
    --> Not all of the 1 values SpectrumIdentificationList's CV terms ['MS:1002439'] found using the Xpath '/cvParam/@accession' matched any of the 1 CvTerm(s):
  - Any children term of MS:1001184 (search statistics). The term can be repeated. The matching value has to be the identifier of the term, not its name.

So I wonder what is the current state of that? Should I put the term in - even so I have only one list or leave it out?

Lutz

On 05/02/15 19:29, Juan Antonio Vizcaino wrote:
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

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