PEPTIDE FRAGMENT ION ANALYSER

A simple and versatile tool for the interpretation of tandem mass spectral data of peptides and de novo sequencing

Interpretation of tandem mass spectra for de novo sequencing of peptides has led to the development of a plethora of softwares, tools and various algorithms over the past few decades. Peptide Fragment Ion Analyser (PFIA) is an attempt to simplify the problem at the grass root levels.

This software is made up of two parts :

(1) Peptide Fragment Ion Analyser - I (PFIA-I) evaluates the amino acid compositions for the queried m/z value (for z = +1). The list includes the various fragment ions [a, b, c, x, y, z ] and sum of various amino acid residues combinations, which matches the queried value. N-terminus, C-terminus, cysteine, sulphation and phosphorylation modifications have been included and one or many of these modifications can be used upon the users’ discretion. A choice of monoisotopic or average mass of amino acids is also provided. The search can be narrowed to display either by fragment ion types or by amino acids. Narrowing the search by amino acids, displays only those results containing that particular amino acid queried. A number of unusual amino acids such as hydroxyproline, alpha-aminoisobutyric acid, etc. are also considered. A special option is provided, wherein the user defined amino acid residue mass can be entered, which would also be included in the search results. The mass range that can be queried without any modifications is m/z 30 - 1101 (z = +1) with an accuracy upto 5 places of decimal. The programme evaluates amino acid compositions only up to 4 amino acid residues.

(2) Peptide Fragment Ion Analyser - II (PFIA-II) displays the theoretical fragmentation pattern diagram and/or lists out the fragment ions for the queried sequence. This helps in confirming the proposed sequences from the tandem mass spectral data of the peptide. Both linear and cyclic peptides are considered. N-terminus, C-terminus, various cysteine modifications, sulphation / phosphorylation of Ser / Thr / Tyr have been included; and one or many of these modifications can be used upon the users’ discretion. A number of unusual amino acids such as hydroxyproline, alpha-aminoisobutyric acid, etc. are also considered. A special option is provided, wherein the user defined amino acid residue mass can be entered, which would also be incorporated in the query and the subsequent results. All ion types including immonium ions and sidechain fragment ions of Leu / Ile (d, v, w type ions), can be displayed. A maximum peptide length of up to 25 amino acid residues can be entered.

The residue mass of the usual and unusual amino acids considered along with their nomenclature has been included in the Help section. This section also contains information about, how to use the programmes, the nomenclature used for representing the fragment ions and features about the fragmentation pattern diagram.

Note: In this programme, the m/z values of c- and z- type ions are calculated, based on those chemical structures that can be anticipated from collision induced dissociation (CID) or collisionally activated dissociation (CAD). The chemical structures of all the product ion types, (including that of c- and z-) arising from the cleavage of peptides' backbone due to CID (or CAD) are given in 'Help' section

A software, PFIA, compatible to both Windows and Linux platform combining the features of both PFIA - I and II is also available for download. The back-end programming is done by using ActiveState ActivePerl 5.8. A Java interface for the web based interface and Tk-perl module for graphical user interface has been used. Validation of the programmes has been done with the data obtained from Mass spectrometry facility and Proteomics facility at Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Programmed by : Jagannath. S, Department of Biotechnology, Vellore Institute of Technology, Vellore, India

Research Supervisor : Prof P. Balaram, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India

Research and Consultancy : V.Sabareesh, Molecular Biophysiscs Unit, Indian Institute of Science, Bangalore, India

Acknowledgements : Prof N.Srinivasan, [Molecular Biophysics Unit, Indian Institute of Science]; Abhishek Tiwari, [Vellore Institute of Technology, Vellore, India]; O. Krishna Dev [Molecular Biophysics Unit, Indian Institute of Science]

Links : Peptide Fragment Ion Analyser - I    Peptide Fragment Ion Analyser - II  Snapshots for Software   Help    PFIA software (for download)

Please contact us for suggestions and queries : Jagannath.S , V.Sabareesh

PFIA has been cited in : Rapid Commun. Mass Spectrom. (2008) Vol 22, 1889-1898.

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Page created in Oct. 2006. Last modified in July 2007.