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

J Proteome Res. 2009 Jan;8(1):374-9. doi: 10.1021/pr800635m.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Databases, Protein
  • HeLa Cells
  • Humans
  • Mass Spectrometry / methods
  • Molecular Sequence Data
  • Peptides / chemistry*
  • Protein Processing, Post-Translational
  • Proteins / analysis
  • Proteomics / methods
  • Reproducibility of Results
  • Software
  • Tandem Mass Spectrometry / methods*

Substances

  • Peptides
  • Proteins