Guidelines for reporting the use of mass spectrometry in proteomics
2
860 VOLUME 26 NUMBER 8 AUGUST 2008 NATURE BIOTECHNOLOGY will be possible for the community to make changes only on request. We intend to provide a more extensive evaluation of hESCreg’s data at the end of this year. Joeri Borstlap 1 , Glyn Stacey 2 , Andreas Kurtz 3 , Anja Elstner 3, Alexander Damaschun 1 , Begoña Arán 4 & Anna Veiga 4,5 1 CellNet Initiative, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité– Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. 2 The UK Stem Cell Bank, National Institute for Biological Standards and Control, Blanch Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK. 3 Cell Therapy Group, Berlin- Brandenburg Center for Regenerative Therapies (BCRT), Charité–Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. 4 Banc de Linies Cellulars, Centre de Medicina Regenerativa de Barcelona (CMRB), C/Dr. Aiguader 88, 08003-Barcelona, Spain. 5 Institut Universitari Dexeus, Passeig de la Bonanova 67, 08017-Barcelona, Spain. e-mail: [email protected] 1. 1st European Human Embryonic Stem Cell Registry Symposium, January 18–19, 2008, Magnus-Haus, Berlin, Germany. <http://www.hescreg.eu/typo3/ index.php?id=28> 2. Borstlap, J. Nature Reports Stem Cells published online, doi: 10.1038/stemcells.2008.46 (6 March 2008). 3. Sipp, D. Nat. Med. 14, 234 (2008). 4. http://www.hescreg.eu/typo3/index.php?id=12 5. Andrews, P.W. et al. Nat. Biotechnol. 25, 803-816 (2007). 6. Avilion, A.A. et al. Genes Dev. 17, 126-140 (2003). 7. Decision No 1982/2006/EC of the European Parliament and of the Council. Off. J. Eur. Union, L412, 42-43 (2006). cell lines, 58 have been characterized with the ‘core set’ of ISCI markers. Thus far, 49 of all available cell lines display information on cell culture conditions, together with at least four of the proposed hESCreg standard markers or complete ISCI ‘core set’ of markers. The ‘additional information’ category is not yet complete for various hES cell lines in the database, although many providers are entering information on 285 cell lines in this category, mostly about culture conditions and publications. Forty nine of all listed lines were entered by the UK Stem Cell Bank (London), which is in the process of independently characterizing them. These cells are listed as ‘subsets’ and have been indicated with the ‘original’ name of the cell line following a code provided by the UK Stem Cell Bank. For example, RH-1/R-06-029 is a subset of the hES cell line RH-1 derived at Roslin Cells/ University of Edinburgh (Edinburgh, UK). Subtracting subset lines from all the listed hES cell lines leaves a total of 258 original listed cell lines in hESCreg. The hESCreg database is still under development and publicly available for review and data entry until the end of this September. We would welcome any feedback from the community as to recommendations for improving the hESCreg interface before that time. After this deadline, the project’s Scientific Advisory Board system will evaluate hESCreg’s content and subsequently it Guidelines for reporting the use of mass spectrometry in proteomics that should be provided when reporting the use of mass spectrometry in a proteomics experiment (Box 1). Developed through a joint effort between the Mass Spectrometry working group of the Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/) and the wider proteomics community, MIAPE-MS constitutes one part of the MIAPE documentation system. It comprises a checklist of information that should be provided about mass spectrometry performed in the course of generating a data set that is submitted to a public repository or when such an experimental step is reported in a scientific publication (for instance, in the materials and methods section). MIAPE-MS specifies neither the format in which information should be transferred nor the structure of any repository or document. However, HUPO-PSI is not developing the MIAPE modules in isolation; several compatible data exchange standards are now well established and supported both by public databases and by data processing software in proteomics. The modern mass spectrometer is a rather complex instrument with many operational parameters; the data sets generated are similarly complex and often rather voluminous. Therefore, MIAPE-MS does not prescribe that all of that information be captured; and given the diversity of instruments currently available, the utility of such detail is clearly open to question. However, it is possible to specify parameters that are representative of the way in which the mass spectrometer was used, to contextualize the data generated and thereby enable a better-informed process of assessment and interpretation. The guidelines (see Supplementary Guidelines and Supplementary Table 1 online) cover both the operation of a mass spectrometer and the generation of mass spectra from the ‘raw’ data. They do not cover the delivery of sample to the mass spectrometer or the interpretation of spectra by search engines; those details are captured in separate MIAPE modules, the latest versions of which can be obtained from the MIAPE home page. Note also that MIAPE-MS does not cover all the available components of a mass spectrometer (e.g., some of the less frequently used ion sources); subsequent versions may have expanded coverage, as will almost certainly be the case for all MIAPE modules. These guidelines will evolve as circumstances dictate. The most recent version of MIAPE-MS is available at http:// www.psidev.info/miape/ms/ and the content is replicated here as supplementary information (Supplementary Guidelines and Supplementary Table 1). To contribute, or to track the process to remain ‘MIAPE compliant’, browse to the website at http://www.psidev.info/miape/. To the editor: A paper in last August’s issue presented the overall Minimum Information about a Proteomics Experiment (MIAPE) reporting guidelines for the field of proteomics 1 . We would like to draw the community’s attention to the MIAPE Mass Spectrometry (MIAPE-MS) module, which specifies the minimum information CORRESPONDENCE © 2008 Nature Publishing Group http://www.nature.com/naturebiotechnology
Transcript of Guidelines for reporting the use of mass spectrometry in proteomics
860 volume 26 number 8 august 2008 nature biotechnology
will be possible for the community to make changes only on request. We intend to provide a more extensive evaluation of hESCreg’s data at the end of this year.
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, Berlin-Brandenburg 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: [email protected]
1. 1st European Human Embryonic Stem Cell Registry Symposium, January 18–19, 2008, Magnus-Haus, Berlin, Germany. <http://www.hescreg.eu/typo3/index.php?id=28>
2. Borstlap, J. Nature Reports Stem Cells published online, doi: 10.1038/stemcells.2008.46 (6 March 2008).
3. Sipp, D. Nat. Med. 14, 234 (2008).4. http://www.hescreg.eu/typo3/index.php?id=125. Andrews, P.W. et al. Nat. Biotechnol. 25, 803-816
(2007).6. Avilion, A.A. et al. Genes Dev. 17, 126-140
(2003).7. Decision no 1982/2006/EC of the European
Parliament and of the Council. Off. J. Eur. Union, L412, 42-43 (2006).
cell lines, 58 have been characterized with the ‘core set’ of ISCI markers. Thus far, 49 of all available cell lines display information on cell culture conditions, together with at least four of the proposed hESCreg standard markers or complete ISCI ‘core set’ of markers. The ‘additional information’ category is not yet complete for various hES cell lines in the database, although many providers are entering information on 285 cell lines in this category, mostly about culture conditions and publications. Forty nine of all listed lines were entered by the UK Stem Cell Bank (London), which is in the process of independently characterizing them. These cells are listed as ‘subsets’ and have been indicated with the ‘original’ name of the cell line following a code provided by the UK Stem Cell Bank. For example, RH-1/R-06-029 is a subset of the hES cell line RH-1 derived at Roslin Cells/University of Edinburgh (Edinburgh, UK). Subtracting subset lines from all the listed hES cell lines leaves a total of 258 original listed cell lines in hESCreg.
The hESCreg database is still under development and publicly available for review and data entry until the end of this September. We would welcome any feedback from the community as to recommendations for improving the hESCreg interface before that time. After this deadline, the project’s Scientific Advisory Board system will evaluate hESCreg’s content and subsequently it
Guidelines for reporting the use of mass spectrometry in proteomics
that should be provided when reporting the use of mass spectrometry in a proteomics experiment (Box 1). Developed through a joint effort between the Mass Spectrometry working group of the Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/) and the wider proteomics
community, MIAPE-MS constitutes one part of the MIAPE documentation system. It comprises a checklist of information that should be provided about mass spectrometry performed in the course of generating a data set that is submitted to a public repository or when such an experimental step is reported in a scientific publication (for instance, in the materials and methods section). MIAPE-MS specifies neither the format in which information should be transferred nor the structure of any repository or document. However, HUPO-PSI is not developing the MIAPE modules in isolation; several compatible data exchange standards are now well established and supported both by public databases and by data processing software in proteomics.
The modern mass spectrometer is a rather complex instrument with many operational parameters; the data sets generated are similarly complex and often rather voluminous. Therefore, MIAPE-MS does not prescribe that all of that information be captured; and given the diversity of instruments currently available, the utility of such detail is clearly open to question. However, it is possible to specify parameters that are representative of the way in which the mass spectrometer was used, to contextualize the data generated and thereby enable a better-informed process of assessment and interpretation.
The guidelines (see Supplementary Guidelines and Supplementary Table 1 online) cover both the operation of a mass spectrometer and the generation of mass spectra from the ‘raw’ data. They do not cover the delivery of sample to the mass spectrometer or the interpretation of spectra by search engines; those details are captured in separate MIAPE modules, the latest versions of which can be obtained from the MIAPE home page. Note also that MIAPE-MS does not cover all the available components of a mass spectrometer (e.g., some of the less frequently used ion sources); subsequent versions may have expanded coverage, as will almost certainly be the case for all MIAPE modules.
These guidelines will evolve as circumstances dictate. The most recent version of MIAPE-MS is available at http://www.psidev.info/miape/ms/ and the content is replicated here as supplementary information (Supplementary Guidelines and Supplementary Table 1). To contribute, or to track the process to remain ‘MIAPE compliant’, browse to the website at http://www.psidev.info/miape/.
To the editor:A paper in last August’s issue presented the overall Minimum Information about a Proteomics Experiment (MIAPE) reporting guidelines for the field of proteomics1. We would like to draw the community’s attention to the MIAPE Mass Spectrometry (MIAPE-MS) module, which specifies the minimum information
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nature biotechnology volume 26 number 8 august 2008 861
Box 1 Content snapshot for MIAPE-MS
The full MIAPE-MS document is divided into three parts: An introduction providing background and context; a summary list of the items to be reported; and a glossary with definitions and examples.
The MIAPE-MS guidelines themselves are subdivided as follows:
1. General features. Summary information such as instrument manufacturer, the software used to run the machine and the parameters applied to it.
2. Ion source. For example, electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI).
3. All major components after the ion source. For example, ion traps, collision cells, time-of-flight tubes and detectors. note that if a collision cell is also an ion trap (e.g., Fourier Transform Ion Cyclotron Resonance, or FT-ICR, cells), the guidelines for the relevant components should be combined.
4. The data resulting from the procedure, the method of generation of peak lists and the location of the raw data from which they were generated, the method by which quantification was performed (where appropriate) and the resulting quantitative data set.
Note: Supplementary information is available on the Nature Biotechnology website.
Chris F Taylor1,2, Pierre-Alain Binz3,4, Ruedi Aebersold5, Michel Affolter6, Robert Barkovich7, Eric W Deutsch8, David M Horn9, Andreas Hühmer10, Martin Kussmann6, Kathryn Lilley11, Marcus Macht12, Matthias Mann13, Dieter Müller14, Thomas A Neubert15, Janice Nickson16, Scott D Patterson17, Roberto Raso18, Kathryn Resing19, Sean L Seymour20, Akira Tsugita21, Ioannis Xenarios22, Rong Zeng23 & Randall K Julian, Jr24
1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. 2NERC Environmental Bioinformatics Centre, Mansfield Road, Oxford, OX1 3SR, UK. 3Swiss Institute of Bioinformatics, Proteome Informatics Group, Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland. 4GeneBio SA, 25 Av. de Champel, CH-1206 Geneva, Switzerland. 5Institute for Molecular Systems Biology, ETH Zurich, HPT E 78, Wolfgang-Pauli-Str. 16, 8093 Zürich, Switzerland. 6Nestlé Research Center, Nestec Ltd., Vers-chez-Les-Blanc, 1000 Lausanne 26, Switzerland. 7Affimetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA. 8Institute for Systems Biology, 1441 N. 34th Street, Seattle, Washington 98103, USA. 9Agilent Technologies, 5301 Stevens Creek Blvd., Santa Clara, California 95051, USA. 10Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, USA. 11Cambridge Centre for Proteomics, University of Cambridge,
Cambridge, Cambridgeshire, CB2 1QW, UK. 12Bruker Daltonik GmbH, Bremen, Germany. 13Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany. 14Novartis Institutes for BioMedical Research, Developmental and Molecular Pathways, Pathway Profiling, WSJ-088.702, CH-4056 Basel, Switzerland. 15Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA. 16Pathways, DECS, AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TF, UK. 17Amgen Inc., Molecular Sciences, One Amgen Center Drive MS 38-3-A, Thousand Oaks, California 91320-1799, USA. 18Kratos Analytical (Shimadzu), Wharfside, Trafford Wharf Road, Manchester, M17 1GP UK. 19Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA. 20Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA. 21Proteomics Research Laboratory, Tokyo Rikakikai Co., Tsukuba, Japan. 22Swiss Institute of Bioinformatics, Vital-IT group, Quartier Sorge – Bâtiment Génopole, CH-1015 Lausanne, Switzerland. 23Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China. 24Indigo BioSystems, Inc., 111 Congressional Blvd., Suite 160, Carmel, Indiana 46032, USA.e-mail: [email protected]
1. Taylor, C.F. et al. Nat. Biotechnol. 25, 887–893 (2007).
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