Advances
in high-throughput proteomics have led to a rapid increase
in the number, size, and complexity of the associated data sets. Managing
and extracting reliable information from such large series of data
sets require the use of dedicated software organized in a consistent
pipeline to reduce, validate, exploit, and ultimately export data.
The compilation of multiple mass-spectrometry-based identification
and quantification results obtained in the context of a large-scale
project represents a real challenge for developers of bioinformatics
solutions. In response to this challenge, we developed a dedicated
software suite called hEIDI to manage and combine both identifications
and semiquantitative data related to multiple LC–MS/MS analyses.
This paper describes how, through a user-friendly interface, hEIDI
can be used to compile analyses and retrieve lists of nonredundant
protein groups. Moreover, hEIDI allows direct comparison of series
of analyses, on the basis of protein groups, while ensuring consistent
protein inference and also computing spectral counts. hEIDI ensures
that validated results are compliant with MIAPE guidelines as all
information related to samples and results is stored in appropriate
databases. Thanks to the database structure, validated results generated
within hEIDI can be easily exported in the PRIDE XML format for subsequent
publication. hEIDI can be downloaded from http://biodev.extra.cea.fr/docs/heidi.