Journal ArticleDOI
Guidelines for reporting the use of mass spectrometry in proteomics
Chris F. Taylor,Pierre-Alain Binz,Ruedi Aebersold,Michel Affolter,Robert Barkovich,Eric W. Deutsch,David M Horn,Andreas Huhmer,Martin Kussmann,Kathryn S. Lilley,Marcus Macht,Matthias Mann,Dieter Müller,Thomas A. Neubert,Janice Nickson,Scott D. Patterson,Roberto Raso,Kathryn Resing,Sean L. Seymour,Akira Tsugita,Ioannis Xenarios,Rong Zeng,Randall K. Julian +22 more
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This work presents a novel and scalable approach to regenerative medicine called “CellNet Initiative,” which aims to provide real-time information about the activity of individual cells in the “spatially aggregating” immune system.Abstract:
Joeri Borstlap1, Glyn Stacey2, Andreas Kurtz3, Anja Elstner3, Alexander Damaschun1, Begoña Arán4 & Anna Veiga4,5 1CellNet Initiative, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité– Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. 2The UK Stem Cell Bank, National Institute for Biological Standards and Control, Blanch Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK. 3Cell Therapy Group, BerlinBrandenburg Center for Regenerative Therapies (BCRT), Charité–Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. 4Banc de Linies Cellulars, Centre de Medicina Regenerativa de Barcelona (CMRB), C/Dr. Aiguader 88, 08003-Barcelona, Spain. 5Institut Universitari Dexeus, Passeig de la Bonanova 67, 08017-Barcelona, Spain. e-mail: joeri.borstlap@b-crt.deread more
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Journal ArticleDOI
mzML - a Community Standard for Mass Spectrometry Data
Lennart Martens,Matthew C. Chambers,Marc Sturm,Darren Kessner,Fredrik Levander,Jim Shofstahl,Wilfred H. Tang,Andreas Römpp,Steffen Neumann,Angel Pizarro,Luisa Montecchi-Palazzi,Natalie Tasman,Michael K. Coleman,Florian Reisinger,Puneet Souda,Henning Hermjakob,Pierre-Alain Binz,Eric W. Deutsch +17 more
TL;DR: The resulting standard data format, mzML, is a well tested open-source format formass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.
Journal ArticleDOI
The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
Andrew R. Jones,Martin Eisenacher,Gerhard Mayer,Oliver Kohlbacher,Jennifer A. Siepen,Simon J. Hubbard,Julian N. Selley,Brian C. Searle,James Shofstahl,Sean L. Seymour,Randall K. Julian,Pierre-Alain Binz,Eric W. Deutsch,Henning Hermjakob,Florian Reisinger,Johannes Griss,Juan Antonio Vizcaíno,Matthew C. Chambers,Angel Pizarro,David M. Creasy +19 more
TL;DR: The release of mzIdentML enables proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.
Journal ArticleDOI
Relation of completeness of reporting of health research to journals’ endorsement of reporting guidelines: systematic review
Adrienne Stevens,Larissa Shamseer,Larissa Shamseer,Erica G. Weinstein,F Yazdi,Lucy Turner,Justin Thielman,Douglas G. Altman,Allison Hirst,John Hoey,Anita Palepu,Anita Palepu,Kenneth F. Schulz,David Moher,David Moher +14 more
TL;DR: The completeness of reporting of only nine of 101 health research reporting guidelines (excluding CONSORT) has been evaluated in relation to journals’ endorsement, and insufficient evidence exists to determine the relation between journals' endorsement of reporting guidelines and the completenessOf reporting of published health research reports.
Journal ArticleDOI
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities.
TL;DR: The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information as discussed by the authors.
Journal ArticleDOI
Describing reporting guidelines for health research: a systematic review
David Moher,Laura Weeks,Mary Ocampo,Dugald Seely,Margaret Sampson,Douglas G. Altman,Kenneth F. Schulz,Donald R. Miller,Iveta Simera,Jeremy M. Grimshaw,John Hoey +10 more
TL;DR: Reporting-guideline developers need to endeavor to maximize the quality of their product and recently developed guidance is likely to facilitate more robust guideline development.
References
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Journal ArticleDOI
The minimum information about a proteomics experiment (MIAPE)
Chris F. Taylor,Chris F. Taylor,Norman W. Paton,Norman W. Paton,Kathryn S. Lilley,Kathryn S. Lilley,Pierre-Alain Binz,Pierre-Alain Binz,Randall K. Julian,Andrew R. Jones,Andrew R. Jones,Weimin Zhu,Weimin Zhu,Rolf Apweiler,Rolf Apweiler,Ruedi Aebersold,Ruedi Aebersold,Eric W. Deutsch,Eric W. Deutsch,Michael J. Dunn,Albert J. R. Heck,Alexander Leitner,Marcus Macht,Matthias Mann,Lennart Martens,Lennart Martens,Thomas A. Neubert,Scott D. Patterson,Peipei Ping,Sean L. Seymour,Sean L. Seymour,Puneet Souda,Akira Tsugita,Joël Vandekerckhove,Thomas M. Vondriska,Julian P. Whitelegge,Marc R. Wilkins,Ioannnis Xenarios,John R. Yates,Henning Hermjakob,Henning Hermjakob +40 more
TL;DR: The processes and principles underpinning the development of guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry are described and the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector are discussed.
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mzML - a Community Standard for Mass Spectrometry Data
Lennart Martens,Matthew C. Chambers,Marc Sturm,Darren Kessner,Fredrik Levander,Jim Shofstahl,Wilfred H. Tang,Andreas Römpp,Steffen Neumann,Angel Pizarro,Luisa Montecchi-Palazzi,Natalie Tasman,Michael K. Coleman,Florian Reisinger,Puneet Souda,Henning Hermjakob,Pierre-Alain Binz,Eric W. Deutsch +17 more
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Sandra Orchard,Lukasz Salwinski,Samuel Kerrien,Luisa Montecchi-Palazzi,Matthias Oesterheld,Volker Stümpflen,Arnaud Ceol,Andrew Chatr-aryamontri,John Armstrong,Peter Woollard,John J. Salama,Susan Moore,Jérôme Wojcik,Gary D. Bader,Marc Vidal,Michael E. Cusick,Mark Gerstein,Anne-Claude Gavin,Giulio Superti-Furga,Jack Greenblatt,Joel S. Bader,Peter Uetz,Mike Tyers,Pierre Legrain,Stanley Fields,Nicola Mulder,Michael K. Gilson,Michael Niepmann,Lyle D. Burgoon,Javier De Las Rivas,Carlos Prieto,Victoria M. Perreau,Christopher W. V. Hogue,Hans-Werner Mewes,Rolf Apweiler,Ioannis Xenarios,David Eisenberg,Gianni Cesareni,Henning Hermjakob +38 more