Guidelines for reporting the use of gel image informatics in proteomics

To the Editor:

We present the gel informatics module (MIAPE-GI) of the minimum information about a proteomics experiment (MIAPE) guidelines¹. MIAPE-GI—a component of the MIAPE documentation system developed by the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/)—results from a coordinated effort by practitioners of gel informatics and representatives of appropriate software vendors, in consultation with the wider proteomics community. Previous MIAPE modules for mass spectrometry and gel electrophoresis have already been described in Nature Biotechnology^1,2,3.

The MIAPE-GI guidelines cover the processing of images derived from two-dimensional gel electrophoresis to detect and quantify features, for example, relating to distinct proteins. The guidelines describe the relationships between (sets of) features on different images established through analyses or known to exist prior to the experiment (such as standards), and the stable location at which data have been deposited (Box 1). These guidelines were developed with a view to supporting the sharing of best practice, validation of results, discovery of results and sharing of experimental data sets. For a full discussion of the principles underlying this specification, please refer to the MIAPE 'Principles' document¹.

For MIAPE modules to work well together, their scope must be tightly constrained. Therefore, the MIAPE-GI guidelines do not cover the preparation and running of a gel, nor do they cover image capture; those areas are the province of the MIAPE gel electrophoresis document (MIAPE-GE⁴). Items outside the scope of this module may be addressed in later versions or by complementary modules, such as MIAPE-GE, which can be obtained from the MIAPE web page (http://www.psidev.info/miape/). As is the case for all MIAPE modules, this specification does not recommend a particular format in which to transfer data nor the structure of any related repository or document.

These guidelines will evolve as circumstance dictates. The most recent version of MIAPE-GI is available from the HUPO-PSI website and the content is replicated here in 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-GI

The full MIAPE-GI document is divided into two parts: an introduction providing background and overview of the content and a full list of the items to be reported. The guidelines have been designed to cope with different types of workflows, as performed by particular software packages. As such, a number of items are optional if they refer to a specific procedure not employed by the software used. The MIAPE-GI guidelines themselves are subdivided as follows:

• General features describing the type of electrophoresis performed, the source images for analysis and the analysis software used.

• The gel analysis design with respect to replicates, groupings and standards used.

• Image preparation steps before bioinformatics analysis, such as scaling, resizing or crops.

• Image processing, such as image alignment, performed by bioinformatics software.

• Data extraction, including feature detection, feature matching and feature quantification (if performed).

• Data analyses performed, for example, extracting features with significant differential expression.

• Results of data analysis, including feature locations, matches and relative quantities where appropriate.