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MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications
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.
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Cited by
Comet: An open‐source MS / MS sequence database search tool
Eng, J. K., Jahan, T. A., & Hoopmann, M. R. (2013) · PROTEOMICS · doi:10.1002/pmic.201200439 · Cited by 1,474
Dieterich, D. C., Link, A. J., Graumann, J., Tirrell, D. A., & Schuman, E. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601637103 · Cited by 874
Self-citationPRIDE: The proteomics identifications database
Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., & Apweiler, R. (2005) · PROTEOMICS · doi:10.1002/pmic.200401303 · Cited by 594
Identification of long-lived proteins reveals exceptional stability of essential cellular structures
Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., & Hetzer, M. W. (2013) · Cell · doi:10.1016/j.cell.2013.07.037 · Cited by 572
Shoulders, M. D., Ryno, L. M., Genereux, J. C., Moresco, J. J., Tu, P. G., Wu, C., Yates, J. R., Su, A. I., Kelly, J. W., & Wiseman, R. L. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.03.024 · Cited by 554
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Metadata
- Authors
- McDonald, W. H., Tabb, D. L., Sadygov, R. G., MacCoss, M. J., Venable, J., Graumann, J., Johnson, J. R., Cociorva, D., & Yates, J. R.
- Venue
- Rapid Communications in Mass Spectrometry
- Publisher
- Wiley
- Published
- 2004-08-13
- Volume
- 18
- Issue
- 18
- Pages
- 2162-2168
- ISSN
- 0951-4198 (ISSN-L)
- 1097-0231
- OpenAlex
- W2132811240
- Cited by
- 345
- References
- 0
- FWCI
- 4.45
- Type
- journal article
- Language
- en
- Open access
- closed
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- McDonald, W. H., Tabb, D. L., Sadygov, R. G., MacCoss, M. J., Venable, J., Graumann, J., Johnson, J. R., Cociorva, D., & Yates, J. R. (2004). MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Communications in Mass Spectrometry. https://doi.org/10.1002/rcm.1603
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