DTASelect and contrast: Tools for assembling and comparing protein identifications from shotgun proteomics

被引：1141

作者：

Tabb, DL ^{[1
]}

McDonald, WH

Yates, JR

机构：

[1] Univ Washington, Dept Mol Biotechnol, Seattle, WA 98195 USA

[2] Scripps Res Inst, Dept Cell Biol SR11, La Jolla, CA 92037 USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2002年 / 1卷 / 01期

关键词：

proteomics; protein identification; SEQUEST; data analysis; software; differential analysis; subtractive analysis; MudPIT; assembly;

D O I：

10.1021/pr015504q

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST algorithm. Inferring a mixture's source proteins requires that the identified peptides be reassociated. This process becomes more challenging as the number of peptides increases. DTASelect, a new software package, assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed and precision of proteomic data analysis.

引用

页码：21 / 26

页数：6

共 17 条

[1] AN APPROACH TO CORRELATE TANDEM MASS-SPECTRAL DATA OF PEPTIDES WITH AMINO-ACID-SEQUENCES IN A PROTEIN DATABASE [J].

ENG, JK ;

MCCORMACK, AL ;

YATES, JR .

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1994, 5 (11) :976-989

[2] Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography microspray and nanospray mass spectrometry [J].

Gatlin, CL ;

Kleemann, GR ;

Hays, LG ;

Link, AJ ;

Yates, JR .

ANALYTICAL BIOCHEMISTRY, 1998, 263 (01) :93-101

[3] Coronin promotes the rapid assembly and cross-linking of actin filaments and may link the actin and microtubule cytoskeletons in yeast [J].

Goode, BL ;

Wong, JJ ;

Butty, AC ;

Peter, M ;

McCormack, AL ;

Yates, JR ;

Drubin, DG ;

Barnes, G .

JOURNAL OF CELL BIOLOGY, 1999, 144 (01) :83-98

[4] Quantitative analysis of complex protein mixtures using isotope-coded affinity tags [J].

Gygi, SP ;

Rist, B ;

Gerber, SA ;

Turecek, F ;

Gelb, MH ;

Aebersold, R .

NATURE BIOTECHNOLOGY, 1999, 17 (10) :994-999

[5] IDENTIFYING PROTEINS FROM 2-DIMENSIONAL GELS BY MOLECULAR MASS SEARCHING OF PEPTIDE-FRAGMENTS IN PROTEIN-SEQUENCE DATABASES [J].

HENZEL, WJ ;

BILLECI, TM ;

STULTS, JT ;

WONG, SC ;

GRIMLEY, C ;

WATANABE, C .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993, 90 (11) :5011-5015

[6] PROTEIN SEQUENCING BY TANDEM MASS-SPECTROMETRY [J].

HUNT, DF ;

YATES, JR ;

SHABANOWITZ, J ;

WINSTON, S ;

HAUER, CR .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1986, 83 (17) :6233-6237

[7] Direct analysis of protein complexes using mass spectrometry [J].

Link, AJ ;

Eng, J ;

Schieltz, DM ;

Carmack, E ;

Mize, GJ ;

Morris, DR ;

Garvik, BM ;

Yates, JR .

NATURE BIOTECHNOLOGY, 1999, 17 (07) :676-682

[8] A strategy for the identification of proteins localized to subcellular spaces: Application to E-coli periplasmic proteins [J].

Link, AJ ;

Carmack, E ;

Yates, JR .

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 1997, 160 (1-3) :303-316

[9] Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level [J].

McCormack, AL ;

Schieltz, DM ;

Goode, B ;

Yang, S ;

Barnes, G ;

Drubin, D ;

Yates, JR .

ANALYTICAL CHEMISTRY, 1997, 69 (04) :767-776

[10] Mgm101p is a novel component of the mitochondrial nucleoid that binds DNA and is required for the repair of oxidatively damaged mitochondrial DNA [J].

Meeusen, S ;

Tieu, QT ;

Wong, E ;

Weiss, E ;

Schieltz, D ;

Yates, JR ;

Nunnari, J .

JOURNAL OF CELL BIOLOGY, 1999, 145 (02) :291-304

← 1 2 →