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LCMS-Spectator is a Windows program for visualizing LC-MS/MS spectra and identified peptides from MSGF+ or identified proteoforms from MSPathFinder.

MS Data can be loaded from Thermo raw files (*.raw) or MzML files. The software displays MS and MS/MS spectra as well as precursor and product ion chromatograms as resizable, floatable tabbed-documents.

Identification and target files can also be loaded to show the spectral and chromatographic evidence. The tool currently supports MS-GF+ and MSPathFinder results (.mzid MzIdentML files), plus also the tab-delimited _IcTda.tsv file created by MSPathFinder.

Loading MS-GF+ results

To visualize peptides identified by MS-GF+, select "Open Id File" on the main screen. Next, select the .mzid file from MS-GF+ (also supports .mzid.gz files). Then select the Thermo .raw file or the .mzML file. LCMS-Spectator will then create a .PBF file, which is an indexed form of the instrument file (.raw or .mzML). This indexing can take several minutes for large files.

Alternatively, use "Open Data Set" on the main screen. On the next window select:

• The instrument data file (.raw or .mzML)
• The MS-GF+ results file (.mzid or .mzid.gz)
• Optional: The FASTA file (protein sequences)

Leave the "Parameter File" and "Feature File" textboxes empty

Loading MSPathFinder results

To visualize proteoforms identified by MSPathFinder, use "Open Data Set" on the main screen. On the next window select:

• The MSPathFinder parameter file (.param)
• The instrument data file (.raw or .mzML)
• The feature file created by ProMex (.ms1ft)
• The MSPathFinder results file (.mzid, .mzid.gz, or tab-delimited _IcTda.tsv)
• The FASTA file (protein sequences)

LCMS-Spectator will then create a .PBF file, which is an indexed form of the instrument file (.raw or .mzML). This indexing can take several minutes for large files.

Note: ProMex is used in conjunction with MSPathFinder. ProMex characterizes the "features" in the mass spectral data, finding data points that appear to come from the same proteoform as they co-elute (isotopic clusters that have a different charge state, but similar elution profiles). MSPathFinder's input is the features file created by ProMex.

Additional Buttons

The "Open Feature File" button can be used to load a .ms1ft file from ProMex and instrument data (.raw or .mzML) but no identifications.

The "Open from DMS" button only works on PNNL's internal network.

Screenshots

Screenshots of LCMS-Spectator with descriptions