Using Excel or TSV files to create spectra libraries

Using Excel or TSV files to create spectra libraries anna kwasnik  2019-03-06

Dear Skyline Team, can anyone advice if it would be possible to use the Excel or TSV saved spectra to create spectra libraries in format for example BLIB or SPLC (SLC) in Skyline? Any advice will be greatly appreciated.

Brendan MacLean responded:  2019-03-06

The tabular format we support for custom spectral library building is called SSL. It is described here: input and output file formats

It seems to be getting a lot of use recently. So it should work for you, but let us know if you run into any issues.

anna kwasnik responded:  2019-03-06

Many thanks for prompt reply Brendan, its greatly appreciated. I think I wasn't specific enough with my question. I am designing an experiment and for few peptides I don't have spectra libraries. The spectra for individual peptides can be found on PeptideAtlas (for example linked in here[145]SEYTYGASYR&assumed_charge=2&chimera_level=&sample_id=6081spectrum_name=TCGA_D8-A13Y_A8-A076_AO-A126_117C_W_BI_20130617_H-PM_f16.09267.09267.2).
This spectra can be downloaded in two formats TSV or Excel and I am wondering if it is possible to convert them to the format of spectra libraries for example BLIB or SPLC (SLC) using Skyline?

Brendan MacLean responded:  2019-03-06

Hi Anna,
We don't yet have anything that supports either of these formats. The best I can offer you is to figure out what spectral library on PeptideAtlas contains this peptide spectrum match.

Download that entire library and use it as described in the Targeted Method Editing tutorial:

We will continue to consider our integration with external sources of spectrum information. Thanks for clarifying your request.