QuaMeter: Multivendor performance metrics for LC-MS/MS proteomics instrumentation

Ze Qiang Ma; Kenneth O. Polzin; Surendra Dasari; Matthew C. Chambers; Birgit Schilling; Bradford W. Gibson; Bao Q. Tran; Lorenzo Vega-Montoto; Daniel C. Liebler; David L. Tabb

doi:10.1021/ac300629p

QuaMeter: Multivendor performance metrics for LC-MS/MS proteomics instrumentation

Ze Qiang Ma, Kenneth O. Polzin, Surendra Dasari, Matthew C. Chambers, Birgit Schilling, Bradford W. Gibson, Bao Q. Tran, Lorenzo Vega-Montoto, Daniel C. Liebler, David L. Tabb

Quantitative Health Sciences

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

43 Scopus citations

Abstract

LC-MS/MS-based proteomics studies rely on stable analytical system performance that can be evaluated by objective criteria. The National Institute of Standards and Technology (NIST) introduced the MSQC software to compute diverse metrics from experimental LC-MS/MS data, enabling quality analysis and quality control (QA/QC) of proteomics instrumentation. In practice, however, several attributes of the MSQC software prevent its use for routine instrument monitoring. Here, we present QuaMeter, an open-source tool that improves MSQC in several aspects. QuaMeter can directly read raw data from instruments manufactured by different vendors. The software can work with a wide variety of peptide identification software for improved reliability and flexibility. Finally, QC metrics implemented in QuaMeter are rigorously defined and tested. The source code and binary versions of QuaMeter are available under Apache 2.0 License at http://fenchurch.mc.vanderbilt.edu.

Original language	English (US)
Pages (from-to)	5845-5850
Number of pages	6
Journal	Analytical Chemistry
Volume	84
Issue number	14
DOIs	https://doi.org/10.1021/ac300629p
State	Published - Jul 17 2012

ASJC Scopus subject areas

Analytical Chemistry

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10.1021/ac300629p

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title = "QuaMeter: Multivendor performance metrics for LC-MS/MS proteomics instrumentation",

abstract = "LC-MS/MS-based proteomics studies rely on stable analytical system performance that can be evaluated by objective criteria. The National Institute of Standards and Technology (NIST) introduced the MSQC software to compute diverse metrics from experimental LC-MS/MS data, enabling quality analysis and quality control (QA/QC) of proteomics instrumentation. In practice, however, several attributes of the MSQC software prevent its use for routine instrument monitoring. Here, we present QuaMeter, an open-source tool that improves MSQC in several aspects. QuaMeter can directly read raw data from instruments manufactured by different vendors. The software can work with a wide variety of peptide identification software for improved reliability and flexibility. Finally, QC metrics implemented in QuaMeter are rigorously defined and tested. The source code and binary versions of QuaMeter are available under Apache 2.0 License at http://fenchurch.mc.vanderbilt.edu.",

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AU - Ma, Ze Qiang

AU - Polzin, Kenneth O.

AU - Dasari, Surendra

AU - Chambers, Matthew C.

AU - Schilling, Birgit

AU - Gibson, Bradford W.

AU - Tran, Bao Q.

AU - Vega-Montoto, Lorenzo

AU - Liebler, Daniel C.

AU - Tabb, David L.

PY - 2012/7/17

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AB - LC-MS/MS-based proteomics studies rely on stable analytical system performance that can be evaluated by objective criteria. The National Institute of Standards and Technology (NIST) introduced the MSQC software to compute diverse metrics from experimental LC-MS/MS data, enabling quality analysis and quality control (QA/QC) of proteomics instrumentation. In practice, however, several attributes of the MSQC software prevent its use for routine instrument monitoring. Here, we present QuaMeter, an open-source tool that improves MSQC in several aspects. QuaMeter can directly read raw data from instruments manufactured by different vendors. The software can work with a wide variety of peptide identification software for improved reliability and flexibility. Finally, QC metrics implemented in QuaMeter are rigorously defined and tested. The source code and binary versions of QuaMeter are available under Apache 2.0 License at http://fenchurch.mc.vanderbilt.edu.

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QuaMeter: Multivendor performance metrics for LC-MS/MS proteomics instrumentation

Abstract

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