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 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/.
Note: Supplementary information is available on the Nature Biotechnology website.
SupplementaryTable 1, Guidelines