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Seek help building spectra library xfbubu  2019-02-21 14:56
 
Dear Skyline Team,

Greetings!

I was trying to build a library from ip2 search result (mzldent file), but run into "ERROR: .mzid file contains an unsupported score type". I have set the score cut-off to 0 but still could not solve this problem. I am wondering if you could help me with this? I have also attached the file used.

Thank you and I am looking forward to your reply!

Sincerely,
Xiaorui
 
 
Matt Chambers responded:  2019-02-22 14:24
Hi Xiaorui,

Thanks for the report. This will be a fixed in an upcoming patch.

Note that this file will be read as "PeptideShaker" input even though it hasn't been run through PeptideShaker. It looks like IP2 just added "PeptideShaker PSM confidence"=100 to every PSM to make it importable into BiblioSpec. So the assumption is that whatever created this file already did considerable confidence filtering and you're ok with all PSMs being imported.
 
xfbubu responded:  2019-03-05 01:01
Hi Matt,

Thank you very much for your fast response and I really appreciate it!

The ip2 search results were filtered with DTAselect, so I guess it makes sense that they set the PeptideShaker PSM confidence = 100... Thank you for looking into the file, and I will import all PSMs...

We have been using an in house script to convert the search results into ssl files and it seems work so far... we are currently using the Prolucid Xcorr Score (not probability type) to remove redundancy in the spectra library if a peptide was found in multiple searches... I am wondering if the upcoming patch will include some features that we could use to remove the redundancy as "PeptideShaker PSM confidence" are all set to be 100...?

Thank you and looking forward to your reply!

Sincerely,
Xiaorui