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Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS

Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS
Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS
A database of 5448 peptide tandem mass spectra acquired in a quadrupole time-of-flight mass spectrometer was generated for peptides derived from proteins digested with trypsin. Peptides were identified from their mass spectra by the Mascot algorithm. Statistical models were then used to investigate factors influencing the abundance of ions formed. Separate models were formulated for b and y ions as it was thought that different factors may influence the formation of each type of ion. Several factors were found to have a highly significant influence on the abundance of ions formed. These include the actual mass of the ion formed after fragmentation as well as the location of the cleavage. The composition of the fragmenting peptide was also found to be important, and amino acids either side of the fragmentation site influenced the abundance of ions produced. To increase understanding of fragmentation mechanisms, the effect of several physicochemical properties of these residues was also investigated in a separate model. In conclusion, the models formulated for b and y ions provide useful characterization of the abundance of ions formed, and this information could be used to develop improved algorithms for peptide identification.
algorithms, amino acids, chemistry, data Interpretation statistical databases, protein ions models, statistical, peptides, probability tandem mass spectrometry, trypsin
0003-2700
5601-5607
Barton, Sheila J.
4f674382-ca0b-44ad-9670-e71a0b134ef0
Richardson, Sylvia
7cf66912-960b-4b71-a55a-e38c9f20ccfa
Perkins, David N.
d3302880-a7c5-4188-a4f3-48e73fdb7d23
Bellahn, Inga
8a275b7e-c27f-4e78-82d6-2710da9e1ed4
Bryant, Trevor N.
142eb783-abb6-4fa6-b3d9-46a24308cda1
Whittaker, John C.
39199258-46b8-420d-8a4d-9092c12d971a
Barton, Sheila J.
4f674382-ca0b-44ad-9670-e71a0b134ef0
Richardson, Sylvia
7cf66912-960b-4b71-a55a-e38c9f20ccfa
Perkins, David N.
d3302880-a7c5-4188-a4f3-48e73fdb7d23
Bellahn, Inga
8a275b7e-c27f-4e78-82d6-2710da9e1ed4
Bryant, Trevor N.
142eb783-abb6-4fa6-b3d9-46a24308cda1
Whittaker, John C.
39199258-46b8-420d-8a4d-9092c12d971a

Barton, Sheila J., Richardson, Sylvia, Perkins, David N., Bellahn, Inga, Bryant, Trevor N. and Whittaker, John C. (2007) Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS. Analytical Chemistry, 79 (15), 5601-5607. (doi:10.1021/ac0700272).

Record type: Article

Abstract

A database of 5448 peptide tandem mass spectra acquired in a quadrupole time-of-flight mass spectrometer was generated for peptides derived from proteins digested with trypsin. Peptides were identified from their mass spectra by the Mascot algorithm. Statistical models were then used to investigate factors influencing the abundance of ions formed. Separate models were formulated for b and y ions as it was thought that different factors may influence the formation of each type of ion. Several factors were found to have a highly significant influence on the abundance of ions formed. These include the actual mass of the ion formed after fragmentation as well as the location of the cleavage. The composition of the fragmenting peptide was also found to be important, and amino acids either side of the fragmentation site influenced the abundance of ions produced. To increase understanding of fragmentation mechanisms, the effect of several physicochemical properties of these residues was also investigated in a separate model. In conclusion, the models formulated for b and y ions provide useful characterization of the abundance of ions formed, and this information could be used to develop improved algorithms for peptide identification.

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More information

Published date: 1 August 2007
Keywords: algorithms, amino acids, chemistry, data Interpretation statistical databases, protein ions models, statistical, peptides, probability tandem mass spectrometry, trypsin

Identifiers

Local EPrints ID: 66423
URI: https://eprints.soton.ac.uk/id/eprint/66423
ISSN: 0003-2700
PURE UUID: dd9267fe-5b84-438c-98df-9cc3a1d7ee77
ORCID for Sheila J. Barton: ORCID iD orcid.org/0000-0003-4963-4242

Catalogue record

Date deposited: 12 Jun 2009
Last modified: 20 Jul 2019 01:05

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