IngentaConnect Mass Spectrometry Data Analysis in the Proteomics Era

Authors: Forner, Francesca¹; Foster, Leonard J.¹; Toppo, Stefano¹

Source: Current Bioinformatics, Volume 2, Number 1, January 2007 , pp. 63-93(31)

Publisher: Bentham Science Publishers

Abstract:

With the advent of whole genome sequencing, large-scale proteomics has rapidly come to dominate the postgenomic age. As such, tandem mass spectrometry has emerged as the most promising and powerful technique in this area but analysis of raw spectra remains one of the principle bottlenecks to making effective use of the technology. Analytical approaches for identifying proteins from MS/MS data fall into two categories: comparing measured fragment spectra to theoretical spectra from sequence databases and de novo peptide sequencing. Available methods still have weaknesses, highlighting the need for new powerful algorithms that are able to exploit the enormous volume of data generated by proteomic experiments. Recent efforts have also been directed towards the identification of post-translational modifications, biomarker discovery and quantitative proteomics. Overall, the intended goal of this review is to give as thorough as possible an overview of state-of-the-art approaches and tools developed to analyze tandem mass spectra in different fields and discuss future directions aimed at overcoming the limits of present methods.

Keywords: Mass spectrometry; proteomics; database searching algorithms; spectra analysis; de novo sequencing; quantitative proteomics

Document Type: Research article

DOI: 10.2174/157489307779314285

Affiliations: 1: Department of Biological Chemistry, University of Padova, V.le G. Colombo 3, I-35121 Padova, Italy.

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