Data requirements for protein identification using chemically-assisted fragmentation and tandem mass spectrometry

Eur. J. Mass Spectrom. 11, 161–167 (2005)
DOI: 10.1255/ejms.758

Data requirements for protein identification using chemically-assisted fragmentation and tandem mass spectrometry

Kenton D. Juhlin, Dionne D. Swift, Martin P. Lacey, Paul E. Correa and Thomas W. Keough
The Procter & Gamble Company, PO Box 538707, Cincinnati, OH 45253-8707, USA

ABSTRACT:

Many laboratories identify proteins by searching tandem mass spectrometry data against genomic or protein sequence databases. These database searches typically use the measured peptide masses or the derived peptide sequence and, in this paper, we focus on the latter. We study the minimum peptide sequence data requirements for definitive protein identification from protein sequence databases. Accurate mass measurements are not needed for definitive protein identification, even when a limited amount of sequence data is available for searching. This information has implications for the mass spectrometry performance (and cost), data base search strategies and proteomics research.

Keywords: peptide sequencing, protein identification, tandem mass spectrometry, chemically assisted fragmentation (CAF), database searching

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