Box 1. The MIAPE modules

The various MIAPE modules are briefly described here, along with their status at the time of writing (in brackets). Recent versions of all modules that have progressed significantly are available from the MIAPE home page (http://www.psidev.info/miape).

• Study design and sample generation [to be developed collaboratively through MIBBI³⁵]
  Experimental motivation and design; factors of interest; origin and preprocessing of biological material; numbers of replicates; relationship to other studies; miscellaneous administrative detail.
• Separations and sample handling [to be developed collaboratively through MIBBI³⁵]
  The use of various techniques (excepting column chromatography, gel electrophoresis and capillary electrophoresis) to fractionate, deplete or otherwise manipulate a sample before analysis; also, sample storage and transport.
• Column chromatography [in the PSI document process]
  The use of columns, of all scales and flow rates.
• Capillary electrophoresis [drafting]
  The performance of any of the wide range of capillary electrophoresis protocols.
• Mass spectrometry [manuscript submitted for publication]
  The use of a mass spectrometer; the generation of peak lists from raw data; quantification based on the use of an isotopic or chemical label (the application of that label, though, is a form of 'sample handling', and is therefore captured elsewhere).
• Informatics for mass spectrometry [manuscript submitted for publication]
  The use of processing engines to analyze mass spectrometry data (both spectra and ion chromatograms). This includes search engines that assign peptides, proteins or biological class membership to spectra; the matching of assigned peptides, proteins or de novo sequences against a named database; quantification and the use of quality control measures.
• Gel electrophoresis [manuscript submitted for publication]
  The use of gel-based electrophoretic separation techniques, single- or multidimensional, native or denaturing; various visualization techniques, including 'electroblotting'; image acquisition.
• Gel image informatics [drafting]
  The processing, analysis and interrelation of gel images (to identify spots, measure relative intensities, or warp images to align them).
• Protein and peptide arrays [exploratory discussions]
  Array type, design and construction; experimental protocol; data collection and initial analysis.
• Statistical analysis of data [to be developed collaboratively through MIBBI³⁵]
  Applicable to qualitative, quantitative and comparative studies: the use of generic data transformation algorithms (for example, normalization); the calculation of descriptive statistics, such as confidence intervals; methods used to sum, average, cluster or otherwise compare datasets.
• Molecular interaction experiments [published in this issue⁴⁶, p. 894]
  The use of any of a range of techniques to determine a set of interacting molecules, within the context of a particular experiment. This includes such techniques as yeast two-hybrid and tandem affinity purification assays. This checklist is published separately under the title MIMIx ("minimum information about a molecular interaction experiment"), but is a MIAPE module.