Journal
JOURNAL OF PROTEOME RESEARCH
Volume 7, Issue 8, Pages 3382-3395Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr800140v
Keywords
proteomics; LC-MS/MS; sequence similarity searches; background spectra filtering; de novo sequencing; MS BLAST
Categories
Funding
- NIGMS NIH HHS [R01 GM070986, R01 GM070986-04, 1 R01 GM 070986-01A1] Funding Source: Medline
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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.
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