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          Institute: MPI für molekulare Zellbiologie und Genetik     Collection: Publikationen MPI-CBG 2008     Display Documents

ID: 414358.0, MPI für molekulare Zellbiologie und Genetik / Publikationen MPI-CBG 2008
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification
Authors:Junqueira, Magno; Spirin, Victor; Balbuena, Tiago Santana; Waridel, Patrice; Surendranath, Vineeth; Kryukov, Grigoriy; Adzhubei, Ivan; Thomas, Henrik; Sunyaev, Shamil; Shevchenko, Andrej
Date of Publication (YYYY-MM-DD):2008
Title of Journal:Journal of Proteome Research
Issue / Number:8
Start Page:3382
End Page:3395
Copyright:not available
Audience:Experts Only
Intended Educational Use:No
Abstract / Description:Only a small fraction of spectra acquired in LC-MS/MS runs matches peptides from target proteins upon database searches. The remaining, operationally termed background, spectra originate from a variety of poorly controlled sources and affect the throughput and confidence of database searches. Here, we report an algorithm and its software implementation that rapidly removes background spectra, regardless of their precise origin. The method estimates the dissimilarity distance between screened MS/MS spectra and unannotated spectra from a partially redundant background library compiled from several control and blank runs. Filtering MS/MS queries enhanced the protein identification capacity when searches lacked spectrum to sequence matching specificity. In sequence-similarity searches it reduced by, on average, 30-fold the number of orphan hits, which were not explicitly related to background protein contaminants and required manual validation. Removing high quality background MS/MS spectra, while preserving in the data set the genuine spectra from target proteins, decreased the false positive rate of stringent database searches and improved the identification of low-abundance proteins.
External Publication Status:published
Document Type:Article
Communicated by:n.n.
Affiliations:MPI f�r molekulare Zellbiologie und Genetik
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