Literature DB >> 24972168

CPTAC Assay Portal: a repository of targeted proteomic assays.

Jeffrey R Whiteaker1, Goran N Halusa2, Andrew N Hoofnagle3, Vagisha Sharma4, Brendan MacLean4, Ping Yan1, John A Wrobel5, Jacob Kennedy1, D R Mani6, Lisa J Zimmerman7, Matthew R Meyer8, Mehdi Mesri9, Henry Rodriguez9, Amanda G Paulovich1.   

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Year:  2014        PMID： 24972168      PMCID： PMC4113142          DOI： 10.1038/nmeth.3002

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  13 in total

1.  Open source system for analyzing, validating, and storing protein identification data.

Authors:  Robertson Craig; John P Cortens; Ronald C Beavis
Journal:  J Proteome Res       Date:  2004 Nov-Dec       Impact factor: 4.466

2.  Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.

Authors:  Terri A Addona; Susan E Abbatiello; Birgit Schilling; Steven J Skates; D R Mani; David M Bunk; Clifford H Spiegelman; Lisa J Zimmerman; Amy-Joan L Ham; Hasmik Keshishian; Steven C Hall; Simon Allen; Ronald K Blackman; Christoph H Borchers; Charles Buck; Helene L Cardasis; Michael P Cusack; Nathan G Dodder; Bradford W Gibson; Jason M Held; Tara Hiltke; Angela Jackson; Eric B Johansen; Christopher R Kinsinger; Jing Li; Mehdi Mesri; Thomas A Neubert; Richard K Niles; Trenton C Pulsipher; David Ransohoff; Henry Rodriguez; Paul A Rudnick; Derek Smith; David L Tabb; Tony J Tegeler; Asokan M Variyath; Lorenzo J Vega-Montoto; Asa Wahlander; Sofia Waldemarson; Mu Wang; Jeffrey R Whiteaker; Lei Zhao; N Leigh Anderson; Susan J Fisher; Daniel C Liebler; Amanda G Paulovich; Fred E Regnier; Paul Tempst; Steven A Carr
Journal:  Nat Biotechnol       Date:  2009-06-28       Impact factor: 54.908

3.  Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

Authors:  Brendan MacLean; Daniela M Tomazela; Nicholas Shulman; Matthew Chambers; Gregory L Finney; Barbara Frewen; Randall Kern; David L Tabb; Daniel C Liebler; Michael J MacCoss
Journal:  Bioinformatics       Date:  2010-02-09       Impact factor: 6.937

4.  Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer.

Authors:  Sebastien Gallien; Elodie Duriez; Catharina Crone; Markus Kellmann; Thomas Moehring; Bruno Domon
Journal:  Mol Cell Proteomics       Date:  2012-09-07       Impact factor: 5.911

5.  Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics.

Authors:  Amelia C Peterson; Jason D Russell; Derek J Bailey; Michael S Westphall; Joshua J Coon
Journal:  Mol Cell Proteomics       Date:  2012-08-03       Impact factor: 5.911

6.  A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer.

Authors:  Elizabeth R Remily-Wood; Richard Z Liu; Yun Xiang; Yi Chen; C Eric Thomas; Neal Rajyaguru; Laura M Kaufman; Joana E Ochoa; Lori Hazlehurst; Javier Pinilla-Ibarz; Jeffrey Lancet; Guolin Zhang; Eric Haura; David Shibata; Timothy Yeatman; Keiran S M Smalley; William S Dalton; Emina Huang; Ed Scott; Gregory C Bloom; Steven A Eschrich; John M Koomen
Journal:  Proteomics Clin Appl       Date:  2011-06-08       Impact factor: 3.494

7.  A database of mass spectrometric assays for the yeast proteome.

Authors:  Paola Picotti; Henry Lam; David Campbell; Eric W Deutsch; Hamid Mirzaei; Jeff Ranish; Bruno Domon; Ruedi Aebersold
Journal:  Nat Methods       Date:  2008-11       Impact factor: 28.547

8.  Using iRT, a normalized retention time for more targeted measurement of peptides.

Authors:  Claudia Escher; Lukas Reiter; Brendan MacLean; Reto Ossola; Franz Herzog; John Chilton; Michael J MacCoss; Oliver Rinner
Journal:  Proteomics       Date:  2012-04       Impact factor: 3.984

9.  Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Authors:  Steven A Carr; Susan E Abbatiello; Bradley L Ackermann; Christoph Borchers; Bruno Domon; Eric W Deutsch; Russell P Grant; Andrew N Hoofnagle; Ruth Hüttenhain; John M Koomen; Daniel C Liebler; Tao Liu; Brendan MacLean; D R Mani; Elizabeth Mansfield; Hendrik Neubert; Amanda G Paulovich; Lukas Reiter; Olga Vitek; Ruedi Aebersold; Leigh Anderson; Robert Bethem; Josip Blonder; Emily Boja; Julianne Botelho; Michael Boyne; Ralph A Bradshaw; Alma L Burlingame; Daniel Chan; Hasmik Keshishian; Eric Kuhn; Christopher Kinsinger; Jerry S H Lee; Sang-Won Lee; Robert Moritz; Juan Oses-Prieto; Nader Rifai; James Ritchie; Henry Rodriguez; Pothur R Srinivas; R Reid Townsend; Jennifer Van Eyk; Gordon Whiteley; Arun Wiita; Susan Weintraub
Journal:  Mol Cell Proteomics       Date:  2014-01-17       Impact factor: 5.911

10.  MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides.

Authors:  Xu Yang; Iulia M Lazar
Journal:  BMC Cancer       Date:  2009-03-27       Impact factor: 4.430
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  64 in total

1.  Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry.

Authors:  Eric Vallabh Minikel; Eric Kuhn; Alexandra R Cocco; Sonia M Vallabh; Christina R Hartigan; Andrew G Reidenbach; Jiri G Safar; Gregory J Raymond; Michael D McCarthy; Rhonda O'Keefe; Franc Llorens; Inga Zerr; Sabina Capellari; Piero Parchi; Stuart L Schreiber; Steven A Carr
Journal:  Mol Cell Proteomics       Date:  2019-09-26       Impact factor: 5.911

2.  Toward a Consensus on Applying Quantitative Liquid Chromatography-Tandem Mass Spectrometry Proteomics in Translational Pharmacology Research: A White Paper.

Authors:  Bhagwat Prasad; Brahim Achour; Per Artursson; Cornelis E C A Hop; Yurong Lai; Philip C Smith; Jill Barber; Jacek R Wisniewski; Daniel Spellman; Yasuo Uchida; Michael A Zientek; Jashvant D Unadkat; Amin Rostami-Hodjegan
Journal:  Clin Pharmacol Ther       Date:  2019-07-26       Impact factor: 6.875

3.  Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-Up Plasma Proteomics.

Authors:  Andrew J Percy; Christoph H Borchers
Journal:  Methods Mol Biol       Date:  2021

4.  Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain.

Authors:  Stefani N Thomas; Austin J Yang
Journal:  Methods Mol Biol       Date:  2017

Review 5.  Psoriatic arthritis under a proteomic spotlight: application of novel technologies to advance diagnosis and management.

Authors:  Aisha Q Butt; Angela McArdle; David S Gibson; Oliver FitzGerald; Stephen R Pennington
Journal:  Curr Rheumatol Rep       Date:  2015-05       Impact factor: 4.592

6.  Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.

Authors:  Andrew N Hoofnagle; Jeffrey R Whiteaker; Steven A Carr; Eric Kuhn; Tao Liu; Sam A Massoni; Stefani N Thomas; R Reid Townsend; Lisa J Zimmerman; Emily Boja; Jing Chen; Daniel L Crimmins; Sherri R Davies; Yuqian Gao; Tara R Hiltke; Karen A Ketchum; Christopher R Kinsinger; Mehdi Mesri; Matthew R Meyer; Wei-Jun Qian; Regine M Schoenherr; Mitchell G Scott; Tujin Shi; Gordon R Whiteley; John A Wrobel; Chaochao Wu; Brad L Ackermann; Ruedi Aebersold; David R Barnidge; David M Bunk; Nigel Clarke; Jordan B Fishman; Russ P Grant; Ulrike Kusebauch; Mark M Kushnir; Mark S Lowenthal; Robert L Moritz; Hendrik Neubert; Scott D Patterson; Alan L Rockwood; John Rogers; Ravinder J Singh; Jennifer E Van Eyk; Steven H Wong; Shucha Zhang; Daniel W Chan; Xian Chen; Matthew J Ellis; Daniel C Liebler; Karin D Rodland; Henry Rodriguez; Richard D Smith; Zhen Zhang; Hui Zhang; Amanda G Paulovich
Journal:  Clin Chem       Date:  2016-01       Impact factor: 8.327

7.  Immobilized Metal Affinity Chromatography Coupled to Multiple Reaction Monitoring Enables Reproducible Quantification of Phospho-signaling.

Authors:  Jacob J Kennedy; Ping Yan; Lei Zhao; Richard G Ivey; Uliana J Voytovich; Heather D Moore; Chenwei Lin; Era L Pogosova-Agadjanyan; Derek L Stirewalt; Kerryn W Reding; Jeffrey R Whiteaker; Amanda G Paulovich
Journal:  Mol Cell Proteomics       Date:  2015-11-30       Impact factor: 5.911

8.  Targeted Proteomic Analyses of Histone H4 Acetylation Changes Associated with Homologous-Recombination-Deficient High-Grade Serous Ovarian Carcinomas.

Authors:  Stefani N Thomas; Lijun Chen; Yang Liu; Naseruddin Höti; Hui Zhang
Journal:  J Proteome Res       Date:  2017-09-14       Impact factor: 4.466

Review 9.  Clinical potential of mass spectrometry-based proteogenomics.

Authors:  Bing Zhang; Jeffrey R Whiteaker; Andrew N Hoofnagle; Geoffrey S Baird; Karin D Rodland; Amanda G Paulovich
Journal:  Nat Rev Clin Oncol       Date:  2019-04       Impact factor: 66.675

10.  Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic Alignment.

Authors:  Philip M Remes; Ping Yip; Michael J MacCoss
Journal:  Anal Chem       Date:  2020-08-12       Impact factor: 6.986
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