The Human Proteome Standards Initiative (HUPO-PSI) released the mzIdentML standard format for peptide and protein identification, which can represent the output of the most popular search engines such as Mascot, The Open Mass Spectrometry Search Algorithm (OMSSA), X!Tandem and others (http://www.psidev.info/mzidentml). The mzIdentML file contains all the possible protein sequences. This standard is used to represent a peptide-spectrum match (PSM), which is linked to a peptide sequence and an identifier for the matching spectrum presented in an external file. This PSM is accompanied by a score, rank and the collection of all protein sequences that include the corresponding peptide.

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