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

TLDR

Proteomic laboratories increasingly confront data storage and processing bottlenecks as shotgun experiments generate tens of thousands of spectra daily, and storing each spectrum and its identification as separate files strains resources, especially when relational databases are impractical for many academic settings. The authors aim to introduce unified text file formats that consolidate spectral data (MS1 and MS2) and search results (SQT) into compact, easily parsed files. These formats are designed as simple, machine‑ and human‑readable text files that can be flexibly integrated with new algorithms and data‑mining strategies. The resulting formats are compact, readily parsed, and adaptable for future computational developments. © 2004 John Wiley & Sons, Ltd.

Abstract

Abstract 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. Copyright © 2004 John Wiley & Sons, Ltd.