Need to improve the validation information in the reports.

[jflucier]

Hello,

I was wandering what are the criterias for the call made for the validation column in the PSM report file. What is considered for this?

My guess is search engine algorithm evalue associated to match, are there any other criterias. I have look in documents on https://compomics.com/bioinformatics-for-proteomics/ but cannot seem to find this information. In exported documentation of ReportCli, its only written:

Validation Indicates the validation level of the retained PSM.

thank you in advance for your help.

JF

[mvaudel]

Hi JF,

Sorry the details are mainly displayed in the GUI, I see that I need to improve the exports for command line users. Will put this on our list for the coming releases :)

The validation levels are as follows:

• Non Validated for PSMs that do not pass the validation threshold (1% FDR by default)
• Doubtful for PSMs that pass the validation threshold but not the quality filters (Filters can be edited, defaults for a doubtful hit are: (1) precursor mass deviation with a probability under 0.01% to be within the distribution of deviations or (2) <30% of the sequence covered by fragment ions)
• Confident for PSMs that pass the validation threshold and the quality filters.

[jflucier]

My opinion: an easy way to add this info would be to include it on the documentation export of the ReportCli.

tks for your response Marc, very appreciated.