The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra*S
- Ignat V. Shilov‡,
- Sean L. Seymour‡§,
- Alpesh A. Patel,
- Alex Loboda,
- Wilfred H. Tang,
- Sean P. Keating¶,
- Christie L. Hunter,
- Lydia M. Nuwaysir and
- Daniel A. Schaeffer
- §To whom correspondence should be addressed: Applied Biosystems/MDS Sciex, 850 Lincoln Centre Dr., Foster City, CA 94404. Tel.: 510-708-9483; Fax: 650-638-6223; E-mail: seymousl{at}appliedbiosystems.com
Abstract
The Paragon™ Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2–5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.
Footnotes
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Published, MCP Papers in Press, May 27, 2007, DOI 10.1074/mcp.T600050-MCP200
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↵ 1 Seymour, S. L., Loboda, A., Tang, W. H., Nimkar, S., and Schaeffer, D. A. (2004) Poster presented at the 52nd ASMS Conference on Mass Spectrometry and Allied Topics, Nashville, TN (May 23–27, 2004).
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2 Seymour, S. L. (2005) PowerPoint presentation at the MCP Workshop: Criteria for Publication of Proteomic Data, Paris, France (May 12–13, 2005) (www.mcponline.org/misc/PariReport_PP.shtml).
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↵ 3 S. L. Seymour, A. Loboda, W. H. Tang, A. A. Patel, I. V. Shilov, and D. A. Schaeffer, manuscript in preparation.
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↵ 4 The abbreviations used are: STV, Sequence Temperature Value; ROC, receiver operating characteristic; ID, identification; SS, Search Space; CDS, Celera Discovery System.
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↵* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
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↵S The on-line version of this article (available at http://www.mcponline.org) contains supplemental material.
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↵‡ Both authors made equal contributions to this work.
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↵¶ Present address: Molecular Devices Corp., Union City, CA 94587.
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- Received September 12, 2006.
- Revision received May 26, 2007.
- © 2007 The American Society for Biochemistry and Molecular Biology
