Guidelines for reporting the use of capillary electrophoresis in proteomics

To the Editor:

We wish to announce the capillary electrophoresis module (MIAPE-CE) of the minimum information about a proteomics experiment (MIAPE) guidelines¹, specifying the minimum information that should be provided when reporting the use of capillary electrophoresis in a proteomics experiment (Box 1). The MIAPE-CE module is the result of a coordinated effort by a consortium of capillary electrophoresis researchers working in the proteomics field and constitutes an additional part of the MIAPE documentation system established by the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/). MIAPE modules for mass spectrometry and gel electrophoresis have already been described in previous issues of Nature Biotechnology^2,3,4.

Capillary electrophoresis comprises a broad family of techniques, for all of which the subtleties of operation are the key to obtaining robust and reliable results. Therefore, it is necessary to specify that a significant degree of descriptive detail be captured, for the equipment deployed, its manner of use, the sample analyzed and the data processing performed. The MIAPE-CE guidelines provide a checklist of the information that should be provided when describing a capillary electrophoresis experiment (Supplementary Table 1). Providing the information requested by MIAPE-CE enables improved corroboration of results by enhancing the comparability of data, whether they are to be submitted to a public repository or reported in a scientific publication (e.g., in a 'materials and methods' section). MIAPE-CE does not specify the format in which to transfer data, or the structure of any repository or document. Nor does it require a description of the preparation of the sample (excepting directl assay-related preparation) or the 'fate' of the analyzed sample beyond the process of detection. Items falling outside the scope of this module may be captured in complementary modules.

These guidelines will evolve as circumstances dictate. The most recent version of MIAPE-CE is now available (http://www.psidev.info/miape/ce/) and the content is replicated here as supplementary information (Supplementary Table 1). To contribute or to track progress to remain 'MIAPE compliant', browse the HUPO-PSI website (http://www.psidev.info/miape/).

Box 1: Contents snapshot for MIAPE-CE

The full MIAPE-CE document is divided into two parts: an introduction, providing background and an overview of the content, and the full list of items to be reported.

The MIAPE-CE guidelines themselves are subdivided as follows:

• 1 General features: the overall type and aim of the experiment.

• 2 Sample details and method-specific sample preparation.

• 3 Equipment used, in terms of the instrumentation, software and capillary; with a description of type and manufacturer along with any subsequent modifications.

• 4 Run process: the steps followed in each experiment and all the parameters that are associated with this. For example, capillary and sample temperatures, auxiliary data channels, time of data collection, step name/purpose, step length/order, pressures, voltages, geometries, flush solution and electrolyte compositions.

• 5 Detection: type, wavelengths/mass range, data collection rate, whether direct or indirect and detector calibration requirements.

• 6 Electropherogram data processing.