Warning: The NCBI web site requires JavaScript to function. more...

My NCBI Sign In

J Proteome Res. 2008 Sep;7(9):3838-46. Epub 2008 Jul 17.

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.

Tabb DL, Ma ZQ, Martin DB, Ham AJ, Chambers MC.

Source

Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8575, USA. david.l.tabb@vanderbilt.edu

Abstract

In shotgun proteomics, tandem mass spectra of peptides are typically identified through database search algorithms such as Sequest. We have developed DirecTag, an open-source algorithm to infer partial sequence tags directly from observed fragment ions. This algorithm is unique in its implementation of three separate scoring systems to evaluate each tag on the basis of peak intensity, m/ z fidelity, and complementarity. In data sets from several types of mass spectrometers, DirecTag reproducibly exceeded the accuracy and speed of InsPecT and GutenTag, two previously published algorithms for this purpose. The source code and binaries for DirecTag are available from http://fenchurch.mc.vanderbilt.edu.

PMID:: 18630943; [PubMed - indexed for MEDLINE]
PMCID: PMC2810657

Free PMC Article

Images from this publication.See all images (7) Free text

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

MeSH Terms

Substances

Peptides

Grant Support

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Click here to read

Click here to read

Related citations

SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry. [J Proteome Res. 2011]
SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry.
Li W, Ji L, Goya J, Tan G, Wysocki VH. J Proteome Res. 2011 Apr 1; 10(4):1593-602. Epub 2011 Feb 23.
A ranking-based scoring function for peptide-spectrum matches. [J Proteome Res. 2009]
A ranking-based scoring function for peptide-spectrum matches.
Frank AM. J Proteome Res. 2009 May; 8(5):2241-52.
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. [J Proteome Res. 2007]
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.
Tabb DL, Fernando CG, Chambers MC. J Proteome Res. 2007 Feb; 6(2):654-61.
Review Overview of tandem mass spectrometry (MS/MS) database search algorithms. [Curr Protoc Protein Sci. 2007]
Review Overview of tandem mass spectrometry (MS/MS) database search algorithms.
Kapp E, Schütz F. Curr Protoc Protein Sci. 2007 Aug; Chapter 25:Unit25.2.
Review Protein identification by tandem mass spectrometry and sequence database searching. [Methods Mol Biol. 2007]
Review Protein identification by tandem mass spectrometry and sequence database searching.
Nesvizhskii AI. Methods Mol Biol. 2007; 367:87-119.

See reviews... See all...

Cited by 6 PubMed Central articles

ProbPS: a new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity. [BMC Bioinformatics. 2011]
ProbPS: a new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity.
Zhang S, Wang Y, Bu D, Zhang H, Sun S. BMC Bioinformatics. 2011 Aug 17; 12:346. Epub 2011 Aug 17.
Review A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. [J Proteomics. 2010]
Review A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.
Nesvizhskii AI. J Proteomics. 2010 Oct 10; 73(11):2092-123. Epub 2010 Sep 8.
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry. [BMC Bioinformatics. 2010]
A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.
Pan C, Park BH, McDonald WH, Carey PA, Banfield JF, VerBerkmoes NC, Hettich RL, Samatova NF. BMC Bioinformatics. 2010 Mar 5; 11:118. Epub 2010 Mar 5.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring.
J Proteome Res. 2008 Sep ;7(9):3838-46. Epub 2008 Jul 17 .

PubMed
Infant care patterns at epidemiologic study of cystic fibrosis sites that achiev...
Infant care patterns at epidemiologic study of cystic fibrosis sites that achieve superior childhood lung function.
Pediatrics. 2007 Mar ;119(3):e531-7.

PubMed
In vivo profile of the human leukocyte microRNA response to endotoxemia.
In vivo profile of the human leukocyte microRNA response to endotoxemia.
Biochem Biophys Res Commun. 2009 Mar 13 ;380(3):437-41. Epub 2009 Jan 29 .

PubMed
Mesenteric adenitis and portal vein thrombosis due to Fusobacterium nucleatum.
Mesenteric adenitis and portal vein thrombosis due to Fusobacterium nucleatum.
Eur J Gastroenterol Hepatol. 2004 Oct ;16(10):1063-6.

PubMed
Estimating the undetected burden of influenza hospitalizations in children.
Estimating the undetected burden of influenza hospitalizations in children.
Epidemiol Infect. 2007 Aug ;135(6):951-8. Epub 2006 Dec 7 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

You are here: NCBI > Literature > PubMed

Write to the Help Desk