Shotgun Protein Sequencing by Tandem Mass Spectra Assembly

peer-reviewed · Analytical Chemistry · 2004

peer-reviewed · Analytical Chemistry · 2004. Nuno Bandeira et al. The analysis of mass spectrometry data is still largely based on identification of single MS/MS spectra and…
Date 2004-12-01
Type peer-reviewed
Venue Analytical Chemistry
Publisher American Chemical Society (ACS)
Contribution algorithm
DOI 10.1021/ac0489162
Citations (OpenAlex) 52
Venue 2-year citedness 7.10

Abstract

The analysis of mass spectrometry data is still largely based on identification of single MS/MS spectra and does not attempt to make use of the extra information available in multiple MS/MS spectra from partially or completely overlapping peptides. Analysis of MS/MS spectra from multiple overlapping peptides opens up the possibility of assembling MS/MS spectra into entire proteins, similarly to the assembly of overlapping DNA reads into entire genomes. In this paper, we present for the first time a way to detect, score, and interpret overlaps between uninterpreted MS/MS spectra in an attempt to sequence entire proteins rather than individual peptides. We show that this approach not only extends the length of reconstructed amino acid sequences but also dramatically improves the quality of de novo peptide sequencing, even for low mass accuracy MS/MS data.

Authors

  1. Nuno Bandeira · University of California San Diego, University of California System
  2. Haixu Tang · Indiana University, Indiana University Bloomington, University of California San Diego
  3. Vineet Bafna · University of California San Diego
  4. Pavel A. Pevzner · Max Planck Institute of Molecular Cell Biology and Genetics, Saint Petersburg Academic University, St Petersburg University, St. Petersburg State University, University of California San Diego, University of Southern California

Methods and tools

  • Shotgun Protein Sequencing: Assembles overlapping MS/MS spectra of related peptides into contigs before any sequence is called, so a protein is sequenced from the assembly rather than from individual spectra. Tolerates mixtures and unanticipated modifications.

Cites (5)

Cited by (27)

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