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

W. Hayes McDonald, David L. Tabb, Rovshan G. Sadygov, Michael J. MacCoss, John Venable, Johannes Graumann, Jeff R. Johnson, Daniel Cociorva, John R. Yates

Research output: Contribution to journalArticlepeer-review

299 Scopus citations


As the speed with which proteomic labs generate data increases along with the scale of projects they are undertaking, the resulting data storage and data processing problems will continue to challenge computational resources. This is especially true for shotgun proteomic techniques that can generate tens of thousands of spectra per instrument each day. One design factor leading to many of these problems is caused by storing spectra and the database identifications for a given spectrum as individual files. While these problems can be addressed by storing all of the spectra and search results in large relational databases, the infrastructure to implement such a strategy can be beyond the means of academic labs. We report here a series of unified text file formats for storing spectral data (MS1 and MS2) and search results (SQT) that are compact, easily parsed by both machine and humans, and yet flexible enough to be coupled with new algorithms and data-mining strategies.

Original languageEnglish (US)
Pages (from-to)2162-2168
Number of pages7
JournalRapid Communications in Mass Spectrometry
Issue number18
StatePublished - 2004
Externally publishedYes

ASJC Scopus subject areas

  • Analytical Chemistry
  • Spectroscopy
  • Organic Chemistry

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