MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications.

By W. McDonald, David L. Tabb, Rovshan G. Sadygov, Michael J. MacCoss, John D. Venable, Johannes Graumann, Jeffrey R. Johnson, Daniel Cociorva, John R. Yates III. Rapid Communications in Mass Spectrometry, 2004

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Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0 (2016, methodology): “Converting the RAW files to two separate files in the MS1 and MS2 formats [19], respectively, was done with ProteoWizard [20] with vendor peak picking for the MS2 spectra and all other options left at their default values.”
Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline (2012, methodology): “Bioinformatic Database Searches for LTQ FT-ICR— MS1 and MS2 files were derived from the raw files using Make MS2 (28) and then searched using an in-house pipeline with the Sequest algorithm (version 2.7).”
Comet: An open‐source MS/MS sequence database search tool (2013, methodology): “We have collaborated with Proteome Software to ensure that its SQT output can be imported into Scaffold [21].”