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

Michael T. Boyne, Benjamin A. Garcia, Mingxi Li, Leonid Zamdborg, Craig D. Wenger, Shannee Babai, Neil L. Kelleher

Research output: Contribution to journalArticlepeer-review

55 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)374-379
Number of pages6
JournalJournal of Proteome Research
Volume8
Issue number1
DOIs
StatePublished - Jan 2009

Keywords

  • High resolution
  • Human nuclei
  • Mass accuracy
  • Mass spectrometry
  • Post-translational modifications
  • Proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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