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Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval.

ABSTRACT: A platform was developed to analyze MS/MS spectra from large peptides with low part-per-million mass accuracy, including a commercial-grade software suite. Termed Middle Down Proteomics, this platform identified 7454 peptides from 2-20 kDa (1472 unique) from 555 proteins after 23 LC-MS/MS injections of Lys-C digests of HeLa-S3 nuclear proteins. Along with greatly increased confidence for both peptide identification (expectation values from 10(-89) to 10(-4)) and characterization (up to 18% of peptides were modified in some LC-MS/MS runs), fragmentation data with <2 ppm accuracy enabled error tolerant and routine multiplexed database searching-all clearly demonstrated in this study.

SUBMITTER: Boyne MT

PROVIDER: S-EPMC2753674 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature

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Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval.

Boyne Michael T MT Garcia Benjamin A BA Li Mingxi M Zamdborg Leonid L Wenger Craig D CD Babai Shannee S Kelleher Neil L NL

Journal of proteome research 20090101 1

A platform was developed to analyze MS/MS spectra from large peptides with low part-per-million mass accuracy, including a commercial-grade software suite. Termed Middle Down Proteomics, this platform identified 7454 peptides from 2-20 kDa (1472 unique) from 555 proteins after 23 LC-MS/MS injections of Lys-C digests of HeLa-S3 nuclear proteins. Along with greatly increased confidence for both peptide identification (expectation values from 10(-89) to 10(-4)) and characterization (up to 18% of pe ...[more]

PMID: 19053528

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