Rapid Validation of Protein Identifications with the Borderline Statistical Confidence via De Novo Sequencing and MS BLAST Searches

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• 作者：Natalie Wielsch ; Henrik Thomas ; Vineeth Surendranath ; Patrice Waridel ; Ari Frank ; Pavel Pevzner ; Andrej Shevchenko
• 刊名：Journal of Proteome Research
• 出版年：2006
• 出版时间：September 2006
• 年：2006
• 卷：5
• 期：9
• 页码：2448 - 2456
• 全文大小：279K
• 年卷期：v.5,no.9(September 2006)
• ISSN：1535-3907

文摘

Protein identifications with the borderline statistical confidence are typically produced by matching afew marginal quality MS/MS spectra to database peptide sequences and represent a significantbottleneck in the reliable and reproducible characterization of proteomes. Here, we present a methodfor rapid validation of borderline hits that circumvents the need in, often biased, manual inspection ofraw MS/MS spectra. The approach takes advantage of the independent interpretation of correspondingMS/MS spectra by PepNovo de novo sequencing software followed by mass spectrometry-driven BLAST(MS BLAST) sequence-similarity database searches that utilize all partially inaccurate, degenerate andredundant candidate peptide sequences. In a case study involving the identification of more than 180Caenorhabditis elegans proteins by nanoLC -MS/MS analysis on a linear ion trap LTQ massspectrometer, the approach enabled rapid assignment (confirmation or rejection) of more than 70% ofMascot hits of borderline statistical confidence.