Literature DB >> 17687369

The minimum information about a proteomics experiment (MIAPE).

Chris F Taylor1, Norman W Paton, Kathryn S Lilley, Pierre-Alain Binz, Randall K Julian, Andrew R Jones, Weimin Zhu, Rolf Apweiler, Ruedi Aebersold, Eric W Deutsch, Michael J Dunn, Albert J R Heck, Alexander Leitner, Marcus Macht, Matthias Mann, Lennart Martens, Thomas A Neubert, Scott D Patterson, Peipei Ping, Sean L Seymour, Puneet Souda, Akira Tsugita, Joel Vandekerckhove, Thomas M Vondriska, Julian P Whitelegge, Marc R Wilkins, Ioannnis Xenarios, John R Yates, Henning Hermjakob.   

Abstract

Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry. This paper describes the processes and principles underpinning the development of these modules; discusses the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector; addresses the issue of overlap with other reporting guidelines; and highlights the criticality of appropriate tools and resources in enabling 'MIAPE-compliant' reporting.

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Year:  2007        PMID: 17687369     DOI: 10.1038/nbt1329

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  221 in total

Review 1.  Software for systems biology: from tools to integrated platforms.

Authors:  Samik Ghosh; Yukiko Matsuoka; Yoshiyuki Asai; Kun-Yi Hsin; Hiroaki Kitano
Journal:  Nat Rev Genet       Date:  2011-11-03       Impact factor: 53.242

2.  Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Authors:  Christopher R Kinsinger; James Apffel; Mark Baker; Xiaopeng Bian; Christoph H Borchers; Ralph Bradshaw; Mi-Youn Brusniak; Daniel W Chan; Eric W Deutsch; Bruno Domon; Jeff Gorman; Rudolf Grimm; William Hancock; Henning Hermjakob; David Horn; Christie Hunter; Patrik Kolar; Hans-Joachim Kraus; Hanno Langen; Rune Linding; Robert L Moritz; Gilbert S Omenn; Ron Orlando; Akhilesh Pandey; Peipei Ping; Amir Rahbar; Robert Rivers; Sean L Seymour; Richard J Simpson; Douglas Slotta; Richard D Smith; Stephen E Stein; David L Tabb; Danilo Tagle; John R Yates; Henry Rodriguez
Journal:  Mol Cell Proteomics       Date:  2011-11-03       Impact factor: 5.911

Review 3.  Cancer biomarkers.

Authors:  N Lynn Henry; Daniel F Hayes
Journal:  Mol Oncol       Date:  2012-02-06       Impact factor: 6.603

4.  A formal mathematical framework for physiological observations, experiments and analyses.

Authors:  Thomas A Nielsen; Henrik Nilsson; Tom Matheson
Journal:  J R Soc Interface       Date:  2011-10-05       Impact factor: 4.118

5.  Guidelines for reporting the use of column chromatography in proteomics.

Authors:  Andrew R Jones; Kathleen Carroll; David Knight; Kirsty Maclellan; Paula J Domann; Cristina Legido-Quigley; Lihua Huang; Lance Smallshaw; Hamid Mirzaei; James Shofstahl; Norman W Paton
Journal:  Nat Biotechnol       Date:  2010-07       Impact factor: 54.908

6.  Guidelines for reporting the use of capillary electrophoresis in proteomics.

Authors:  Paula J Domann; Satoko Akashi; Coral Barbas; Lihua Huang; Wendy Lau; Cristina Legido-Quigley; Stephen McClean; Christian Neusüss; David Perrett; Milena Quaglia; Erdmann Rapp; Lance Smallshaw; Norman W Smith; W Franklin Smyth; Chris F Taylor
Journal:  Nat Biotechnol       Date:  2010-07       Impact factor: 54.908

7.  Guidelines for reporting the use of gel image informatics in proteomics.

Authors:  Christine Hoogland; Martin O'Gorman; Philippe Bogard; Frank Gibson; Matthias Berth; Simon J Cockell; Andreas Ekefjärd; Ola Forsstrom-Olsson; Anna Kapferer; Mattias Nilsson; Salvador Martínez-Bartolomé; Juan Pablo Albar; Sira Echevarría-Zomeño; Montserrat Martínez-Gomariz; Johann Joets; Pierre-Alain Binz; Chris F Taylor; Andrew Dowsey; Andrew R Jones
Journal:  Nat Biotechnol       Date:  2010-07       Impact factor: 54.908

8.  Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant.

Authors:  Kenneth R Williams; Christopher M Colangelo; Lin Hou; Lisa Chung; Justin M Belcher; Thomas Abbott; Isaac E Hall; Hongyu Zhao; Lloyd G Cantley; Chirag R Parikh
Journal:  Proteomics Clin Appl       Date:  2017-03-31       Impact factor: 3.494

9.  Proteomic landscape of bronchoalveolar lavage fluid in human immunodeficiency virus infection.

Authors:  Elizabeth V Nguyen; Sina A Gharib; Kristina Crothers; Yu-Hua Chow; David R Park; David R Goodlett; Lynn M Schnapp
Journal:  Am J Physiol Lung Cell Mol Physiol       Date:  2013-11-08       Impact factor: 5.464

Review 10.  Plasmodium Parasites Viewed through Proteomics.

Authors:  Kristian E Swearingen; Scott E Lindner
Journal:  Trends Parasitol       Date:  2018-08-23
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