Computational proteomics analysis system (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

Adam Rauch; Matthew Bellew; Jimmy Eng; Matthew Fitzgibbon; Ted Holzman; Peter Hussey; Mark Igra; Brendan Maclean; Chen Wei Lin; Andrea Detter; Ruihua Fang; Vitor Faca; Phil Gafken; Heidi Zhang; Jeffrey Whitaker; David States; Sam Hanash; Amanda Paulovich; Martin W. McIntosh

doi:10.1021/pr0503533

Computational proteomics analysis system (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

Adam Rauch, Matthew Bellew, Jimmy Eng, Matthew Fitzgibbon, Ted Holzman, Peter Hussey, Mark Igra, Brendan Maclean, Chen Wei Lin, Andrea Detter, Ruihua Fang, Vitor Faca, Phil Gafken, Heidi Zhang, Jeffrey Whitaker, David States, Sam Hanash, Amanda Paulovich, Martin W. McIntosh

Research output: Contribution to journal › Article › peer-review

175 Scopus citations

Abstract

The open-source Computational Proteomics Analysis System (CPAS) contains an entire data analysis and management pipeline for Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) proteomics, including experiment annotation, protein database searching and sequence management, and mining LC-MS/MS peptide and protein identifications. CPAS architecture and features, such as a general experiment annotation component, installation software, and data security management, make it useful for collaborative projects across geographical locations and for proteomics laboratories without substantial computational support.

Original language	English (US)
Pages (from-to)	112-121
Number of pages	10
Journal	Journal of Proteome Research
Volume	5
Issue number	1
DOIs	https://doi.org/10.1021/pr0503533
State	Published - Jan 2006
Externally published	Yes

Keywords

Adenocarcinoma
FuGE
Proteomics
X! Tandem
mzXML
pepXML

ASJC Scopus subject areas

Biochemistry
General Chemistry

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10.1021/pr0503533

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Rauch, A., Bellew, M., Eng, J., Fitzgibbon, M., Holzman, T., Hussey, P., Igra, M., Maclean, B., Lin, C. W., Detter, A., Fang, R., Faca, V., Gafken, P., Zhang, H., Whitaker, J., States, D., Hanash, S., Paulovich, A., & McIntosh, M. W. (2006). Computational proteomics analysis system (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. Journal of Proteome Research, 5(1), 112-121. https://doi.org/10.1021/pr0503533

Rauch, A, Bellew, M, Eng, J, Fitzgibbon, M, Holzman, T, Hussey, P, Igra, M, Maclean, B, Lin, CW, Detter, A, Fang, R, Faca, V, Gafken, P, Zhang, H, Whitaker, J, States, D, Hanash, S, Paulovich, A & McIntosh, MW 2006, 'Computational proteomics analysis system (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments', Journal of Proteome Research, vol. 5, no. 1, pp. 112-121. https://doi.org/10.1021/pr0503533

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abstract = "The open-source Computational Proteomics Analysis System (CPAS) contains an entire data analysis and management pipeline for Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) proteomics, including experiment annotation, protein database searching and sequence management, and mining LC-MS/MS peptide and protein identifications. CPAS architecture and features, such as a general experiment annotation component, installation software, and data security management, make it useful for collaborative projects across geographical locations and for proteomics laboratories without substantial computational support.",

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AU - Holzman, Ted

AU - Hussey, Peter

AU - Igra, Mark

AU - Maclean, Brendan

AU - Lin, Chen Wei

AU - Detter, Andrea

AU - Fang, Ruihua

AU - Faca, Vitor

AU - Gafken, Phil

AU - Zhang, Heidi

AU - Whitaker, Jeffrey

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AU - McIntosh, Martin W.

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Computational proteomics analysis system (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

Abstract

Keywords

ASJC Scopus subject areas

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