Validation. This step consists of the assignment of MS/MS spectra to a database search using one of several engines available (e.g., Sequest, Mascot, Comet, X!tandem, etc.). One of the difficulties related to the use of sequest for peptide identifications is the lack of methods to globally evaluate the quality of data and the lack of methods to access global changes created by filtering schemes and/or database changes [186] . Most approaches are matching and scoring large sets of experimental spectra with predicted masses of fragment ions of peptide sequences derived from a protein database. Results are scored according to a scheme specific to each search engine that also depends on the database used for the search. Usually tools are linked to one specific platform or were optimized for one instrument type. The various search engines do not yield identical results as they are based on different algorithms and scoring functions, making comparison and integration of results from different studies or experiments tedious [187, 188] . Peptide identification via database searches is very computationally intensive and time-demanding. High quality data allow more effective searches due to tighter constrains, that is, tolerance on precursor ion mass and charge state assignment, which will drastically reduce the search time in case of an indexed database. In addition, accurate mass measurements of fragment ions further simplify the database searches and add confidence to the results. The association of identified peptides with their precursor proteins is a very critical and difficult step in shotgun proteomics strategies as many peptides are common to several proteins, thus leading to ambiguous protein assignments. Therefore it becomes critical to have an appropriate tool that is able to assess the validity of the protein inference and associate a probability to it. Protein Prophet database tool combines probabilities assigned to peptides identified by MS/MS to compute accurate probabilities for the proteins present [189] . 5:1921-1926, 2006. impossible. The lack of common standards and protocols has led to this situation and often resulted in duplication of efforts. Results were usually reported as a set of identified proteins (i.e., list of peptides identified and associated proteins) with minimal supporting data. Obviously the large volume of such data sets has made publication of detailed results using classical mechanisms very challenging. Sharing and exchange of data and results requires the definition of standard formats for the data at all levels (including raw mass spectrometric data, processed data, and search results) as well as a better definition (and/or standardization) of the parameters used for the data processing or the database searches.