A Software Toolkit and Interface for Performing Stable Isotope Labeling and Top3 Quantification Using Progenesis LC-MS

被引：41

作者：

Qi, Da ^{[1
]}

Brownridge, Philip ^{[1
]}

Xia, Dong ^{[1
,2
]}

Mackay, Katherine ^{[1
]}

Gonzalez-Galarza, Faviel F. ^{[1
]}

Kenyani, Jenna ^{[2
]}

Harman, Victoria ^{[1
]}

Beynon, Robert J. ^{[1
]}

Jones, Andrew R. ^{[1
]}

机构：

[1] Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England

[2] Univ Liverpool, Inst Infect & Global Hlth, Liverpool L69 7ZB, Merseyside, England

来源：

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY | 2012年 / 16卷 / 09期

基金：

英国生物技术与生命科学研究理事会;

关键词：

D O I：

10.1089/omi.2012.0042

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Numerous software packages exist to provide support for quantifying peptides and proteins from mass spectrometry (MS) data. However, many support only a subset of experimental methods or instrument types, meaning that laboratories often have to use multiple software packages. The Progenesis LC-MS software package from Nonlinear Dynamics is a software solution for label-free quantitation. However, many laboratories using Progenesis also wish to employ stable isotope-based methods that are not natively supported in Progenesis. We have developed a Java programming interface that can use the output files produced by Progenesis, allowing the basic MS features quantified across replicates to be used in a range of different experimental methods. We have developed post-processing software (the Progenesis Post-Processor) to embed Progenesis in the analysis of stable isotope labeling data and top3 pseudo-absolute quantitation. We have also created export ability to the new data standard, mzQuantML, produced by the Proteomics Standards Initiative to facilitate the development and standardization process. The software is provided to users with a simple graphical user interface for accessing the different features. The underlying programming interface may also be used by Java developers to develop other routines for analyzing data produced by Progenesis.

引用

页码：489 / 495

页数：7

共 11 条

[1] Absolute Quantification of the Glycolytic Pathway in Yeast: DEPLOYMENT OF A COMPLETE QconCAT APPROACH [J].

Carroll, Kathleen M. ;

Simpson, Deborah M. ;

Eyers, Claire E. ;

Knight, Christopher G. ;

Brownridge, Philip ;

Dunn, Warwick B. ;

Winder, Catherine L. ;

Lanthaler, Karin ;

Pir, Pinar ;

Malys, Naglis ;

Kell, Douglas B. ;

Oliver, Stephen G. ;

Gaskell, Simon J. ;

Beynon, Robert J. .

MOLECULAR & CELLULAR PROTEOMICS, 2011, 10 (12)

[2] MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification [J].

Cox, Juergen ;

Mann, Matthias .

NATURE BIOTECHNOLOGY, 2008, 26 (12) :1367-1372

[3] 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

[4] The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results [J].

Jones, Andrew R. ;

Eisenacher, Martin ;

Mayer, Gerhard ;

Kohlbacher, Oliver ;

Siepen, Jennifer ;

Hubbard, Simon J. ;

Selley, Julian N. ;

Searle, Brian C. ;

Shofstahl, James ;

Seymour, Sean L. ;

Julian, Randall ;

Binz, Pierre-Alain ;

Deutsch, Eric W. ;

Hermjakob, Henning ;

Reisinger, Florian ;

Griss, Johannes ;

Vizcaino, Juan Antonio ;

Chambers, Matthew ;

Pizarro, Angel ;

Creasy, David .

MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (07)

[5] mzML-a Community Standard for Mass Spectrometry Data [J].

Martens, Lennart ;

Chambers, Matthew ;

Sturm, Marc ;

Kessner, Darren ;

Levander, Fredrik ;

Shofstahl, Jim ;

Tang, Wilfred H. ;

Roempp, Andreas ;

Neumann, Steffen ;

Pizarro, Angel D. ;

Montecchi-Palazzi, Luisa ;

Tasman, Natalie ;

Coleman, Mike ;

Reisinger, Florian ;

Souda, Puneet ;

Hermjakob, Henning ;

Binz, Pierre-Alain ;

Deutsch, Eric W. .

MOLECULAR & CELLULAR PROTEOMICS, 2011, 10 (01)

[6] Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics [J].

Ong, SE ;

Blagoev, B ;

Kratchmarova, I ;

Kristensen, DB ;

Steen, H ;

Pandey, A ;

Mann, M .

MOLECULAR & CELLULAR PROTEOMICS, 2002, 1 (05) :376-386

[7] iTRAQ Underestimation in Simple and Complex Mixtures: "The Good, the Bad and the Ugly" [J].

Ow, Saw Yen ;

Salim, Malinda ;

Noirel, Josselin ;

Evans, Caroline ;

Rehman, Ishtiaq ;

Wright, Phillip C. .

JOURNAL OF PROTEOME RESEARCH, 2009, 8 (11) :5347-5355

[8] Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance [J].

Paulovich, Amanda G. ;

Billheimer, Dean ;

Ham, Amy-Joan L. ;

Vega-Montoto, Lorenzo ;

Rudnick, Paul A. ;

Tabb, David L. ;

Wang, Pei ;

Blackman, Ronald K. ;

Bunk, David M. ;

Cardasis, Helene L. ;

Clauser, Karl R. ;

Kinsinger, Christopher R. ;

Schilling, Birgit ;

Tegeler, Tony J. ;

Variyath, Asokan Mulayath ;

Wang, Mu ;

Whiteaker, Jeffrey R. ;

Zimmerman, Lisa J. ;

Fenyo, David ;

Carr, Steven A. ;

Fisher, Susan J. ;

Gibson, Bradford W. ;

Mesri, Mehdi ;

Neubert, Thomas A. ;

Regnier, Fred E. ;

Rodriguez, Henry ;

Spiegelman, Cliff ;

Stein, Stephen E. ;

Tempst, Paul ;

Liebler, Daniel C. .

MOLECULAR & CELLULAR PROTEOMICS, 2010, 9 (02) :242-254

[9] Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents [J].

Ross, PL ;

Huang, YLN ;

Marchese, JN ;

Williamson, B ;

Parker, K ;

Hattan, S ;

Khainovski, N ;

Pillai, S ;

Dey, S ;

Daniels, S ;

Purkayastha, S ;

Juhasz, P ;

Martin, S ;

Bartlet-Jones, M ;

He, F ;

Jacobson, A ;

Pappin, DJ .

MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (12) :1154-1169

[10] Absolute quantification of proteins by LCMSE -: A virtue of parallel MS acquisition [J].

Silva, JC ;

Gorenstein, MV ;

Li, GZ ;

Vissers, JPC ;

Geromanos, SJ .

MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (01) :144-156

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