Abstract

The two central problems in protein identification by searching a protein sequence collection with MS data are the optimal use of experimental information to allow for identification of low abundance proteins and the accurate assignment of the probability that a result is false. For comprehensive MS-based protein identification, it is necessary to choose an appropriate algorithm and optimal search conditions. We report a systematic study of the quality of PMF-based protein identifications under different sequence collection search conditions using the Probity algorithm, which assigns the statistical significance to each result. We employed 2244 PMFs from 2-DE-separated human blood plasma proteins, and performed identification under various search constraints: mass accuracy (0.01-0.3 Da), maximum number of missed cleavage sites (0-2), and size of the sequence collection searched (5.6 x 10(4)-1.8 x 10(5)). By counting the number of significant results (significance levels 0.05, 0.01, and 0.001) for each condition, we demonstrate the search condition impact on the successful outcome of proteome analysis experiments. A mass correction procedure utilizing mass deviations of albumin matching peptides was tested in an attempt to improve the statistical significance of identifications and iterative searching was employed for identification of multiple proteins from each PMF

Published in

Proteomics
2006, Volume: 6, number: 7, pages: 2079-2085
Publisher: WILEY-V C H VERLAG GMBH

SLU Authors

• Ossipova, Elena

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

• Eriksson, Jan

  • Department of Molecular Sciences, Swedish University of Agricultural Sciences
    

Publication identifier

DOI: https://doi.org/10.1002/pmic.200500484

Permanent link to this page (URI)

https://res.slu.se/id/publ/9579