De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data

peer-reviewed · Methods in Molecular Biology · 2016

peer-reviewed · Methods in Molecular Biology · 2016. Mohammad Tawhidul Islam et al. High resolution mass spectrometry has revolutionized proteomics over the past decade, resulting in tremendous…
Date 2016-12-15
Type peer-reviewed
Venue Methods in Molecular Biology
Publisher Springer New York
Contribution review
DOI 10.1007/978-1-4939-6740-7_10
Citations (OpenAlex) 11
Venue 2-year citedness 1.14

Abstract

High resolution mass spectrometry has revolutionized proteomics over the past decade, resulting in tremendous amounts of data in the form of mass spectra, being generated in a relatively short span of time. The mining of this spectral data for analysis and interpretation though has lagged behind such that potentially valuable data is being overlooked because it does not fit into the mold of traditional database searching methodologies. Although the analysis of spectra by de novo sequences removes such biases and has been available for a long period of time, its uptake has been slow or almost nonexistent within the scientific community. In this chapter, we propose a methodology to integrate de novo peptide sequencing using three commonly available software solutions in tandem, complemented by homology searching, and manual validation of spectra. This simplified method would allow greater use of de novo sequencing approaches and potentially greatly increase proteome coverage leading to the unearthing of valuable insights into protein biology, especially of organisms whose genomes have been recently sequenced or are poorly annotated.

Authors

  1. Mohammad Tawhidul Islam · Macquarie University
  2. Abidali Mohamedali · Macquarie University
  3. Criselda Santan Fernandes · Macquarie University
  4. Mark S. Baker · Macquarie University
  5. Shoba Ranganathan · Macquarie University

Methods and tools

  • De novo deep mining protocol: Methods in Molecular Biology protocol for mining high-resolution MS data by de novo peptide sequencing rather than database search.

Cites (10)

Seen in the charts

Back to the full map

Back to top