A statistical model of proteolytic digestion

I. J. Wang; C. P. Diehl; F. J. Pineda

doi:10.1109/CSB.2003.1227390

A statistical model of proteolytic digestion

I. J. Wang, C. P. Diehl, F. J. Pineda

Bloomberg School of Public Health

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

3 Scopus citations

Abstract

We present a stochastic model of proteolytic digestion of a proteome, assuming the distribution of parent protein lengths in the proteome, the relative abundances of the 20 amino acids in the proteome, and the digestion "rules" of the enzyme used in the digestion. We derived a closed form expression for the fragment mass distribution for a large class of enzymes including the widely used trypsin. The expression uses the distribution of lengths in a mixture of proteins taken from a proteome, as well as the relative abundances of the 20 amino acids in the proteome. The agreement between theory and the in silica digest is excellent.

Original language	English (US)
Title of host publication	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	506-508
Number of pages	3
ISBN (Electronic)	0769520006, 9780769520001
DOIs	https://doi.org/10.1109/CSB.2003.1227390
State	Published - Jan 1 2003
Event	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States Duration: Aug 11 2003 → Aug 14 2003

Publication series

Name	Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

Other

Other	2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Country/Territory	United States
City	Stanford
Period	8/11/03 → 8/14/03

ASJC Scopus subject areas

Electrical and Electronic Engineering
Computer Science Applications

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10.1109/CSB.2003.1227390

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A statistical model of proteolytic digestion. / Wang, I. J.; Diehl, C. P.; Pineda, F. J.

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 506-508 1227390 (Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Wang, IJ, Diehl, CP & Pineda, FJ 2003, A statistical model of proteolytic digestion. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227390, Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003, Institute of Electrical and Electronics Engineers Inc., pp. 506-508, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 8/11/03. https://doi.org/10.1109/CSB.2003.1227390

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AB - We present a stochastic model of proteolytic digestion of a proteome, assuming the distribution of parent protein lengths in the proteome, the relative abundances of the 20 amino acids in the proteome, and the digestion "rules" of the enzyme used in the digestion. We derived a closed form expression for the fragment mass distribution for a large class of enzymes including the widely used trypsin. The expression uses the distribution of lengths in a mixture of proteins taken from a proteome, as well as the relative abundances of the 20 amino acids in the proteome. The agreement between theory and the in silica digest is excellent.

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BT - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003

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ER -

A statistical model of proteolytic digestion

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