Research Article

Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides

  1. Swaminathan Jagannath1,†,
  2. Varatharajan Sabareesh2,*

Article first published online: 20 AUG 2007

DOI: 10.1002/rcm.3179

Issue

Rapid Communications in Mass Spectrometry

Rapid Communications in Mass Spectrometry

Volume 21, Issue 18, pages 3033–3038, 30 September 2007

Additional Information

How to Cite

Jagannath, S. and Sabareesh, V. (2007), Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides. Rapid Communications in Mass Spectrometry, 21: 3033–3038. doi: 10.1002/rcm.3179

Author Information

  1. 1

    Department of Biotechnology, Vellore Institute of Technology, Vellore 632 014, India

  2. 2

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India

  1. †

    Department of Biotechnology, Indian Institute of Technology, Chennai 600 036, India.

*Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Publication History

  1. Issue published online: 20 AUG 2007
  2. Article first published online: 20 AUG 2007
  3. Manuscript Accepted: 10 JUL 2007
  4. Manuscript Revised: 6 JUL 2007
  5. Manuscript Received: 21 MAR 2007

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Abstract

The software Peptide Fragment Ion Analyser (PFIA) aids in the analysis and interpretation of tandem mass spectrometric data of peptides. The software package has been designed to facilitate the analysis of product ions derived from acyclic and cyclic peptide natural products that possess unusual amino acid residues and are heavily post-translationally modified. The software consists of two programmes: (a) PFIA-I lists the amino acid compositions and their corresponding product ion types for ‘a queried m/z value’ (z = +1) and (b) PFIA-II displays fragmentation pattern diagram(s) and lists all sequence-specific product ion types for the protonated adduct of ‘a queried sequence’. The unique feature of PFIA-II is its ability to handle cyclic peptides. The two programmes used in combination can prove helpful for deriving peak assignments in the de novo sequencing of novel peptides. Copyright © 2007 John Wiley & Sons, Ltd.

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