Making a Spectral Library from an .ssl file

Making a Spectral Library from an .ssl file david lewis2  2023-08-22 09:27

Hello Skyline Team,

I am looking to put together a spectral library using an .ssl file, and I was wondering if it is possible to create a spectral library using this file with MS2 scans that did not match from a database search? For example, instead of including the peptide sequence, when creating the spectral library, we can use different names, like this:

file scan charge sequence
demo.ms2 8 3 PrecursorID1
demo.ms2 1806 2 LAESITIEQGK
demo.ms2 2572 2 PrecursorID2
demo.ms2 3088 2 TTAGAVEATSEITEGK
demo.ms2 3266 2 DC[+57.0]EEVGADSNEGGEEEGEEC[+57.0]
demo.ms2 20919 3 VHINIVVIGHVDSGK
../elsewhere/spec.mzXML 00497 2 LKEPAQNTADNAK
../elsewhere/spec.mzXML 00680 2 ALEGPGPGEDAAHSENNPPR
../elsewhere/spec.mzXML 00965 2 FFSHEAEQK
../elsewhere/spec.mzXML 01114 2 C[+57.0]GPSQPL

In addition, can we only add the retention time column for this file and not add the score columns?

Thank you.


Brian Pratt responded:  2023-08-22 09:42

Not at the moment - I think we'd blow up on a sequence description that isn't a sequence - but I can see how this could work by allowing a combination of column headers for peptide and small molecules. "PrecursorID1" would appear in Skyline as a molecule defined only by its mass, and Skyline would have to operate in "Mixed" UI mode. The mass would be derived from the declared precursor m/z in the referenced MS2 scan.

If you'll put together a set of files, including a proposed SSL file and matching mass spec data, we could have a look at this.

david lewis2 responded:  2023-09-07 08:31

I have attached the MGF file that we get from PEAKS. The proposed SSL file is essentially the same format I sent earlier:

file scan charge sequence
demo.ms2 8 3 PrecursorID1
demo.ms2 1806 2 PrecursorID2
demo.ms2 2572 2 PrecursorID3
demo.ms2 3088 2 PrecursorID4
demo.ms2 3266 2 PrecursorID5
demo.ms2 9734 3 PrecursorID6
demo.ms2 20919 3 PrecursorID7
../elsewhere/spec.mzXML 00497 2 PrecursorID8
../elsewhere/spec.mzXML 00680 2 PrecursorID9
../elsewhere/spec.mzXML 00965 2 PrecursorID10
../elsewhere/spec.mzXML 01114 2 PrecursorID11

Please let me know if you need anything else.

Brian Pratt responded:  2023-09-08 13:23

I'll be able to help you better if you'll put together an actual small .ssl file that nominally agrees with the other provided files.