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.
In order to allow the experimental proteomics community to use the mzIdentML standard, we developed a Graphical User Interface called ProteoIDViewer, an open source viewer, which simplifies the visualization and analysis of the identification data (See more in: https://github.com/fghali/mzidentml-viewer).
The laboratory scientists are the main users of ProteoIDViewer, which does not require bioinformatics expertise to get started. The viewer can be simply downloaded and installed with no complex setup procedures. The aims of this viewer are to provide an intuitive and useful views of peptides/proteins and the search of the corresponding metadata. Additionally, the software includes different functions embedded within the mzIdentML Library, comprising also exporters to spreadsheets.
The viewer provides several different methods for visualising data:
Protein-view: all proteins identified and the supporting peptide evidence for each identification
Spectrum-view: ranked identifications for each input spectrum and peptide fragmentation data.
Peptide-view: all peptides identified, and potential protein mappings for each peptide
Global-view: global statistics include total peptide-spectrum matches, FDR, in addition to plotting FDR data into graphs for better visualisation.
Protocols-view: spectrum identification protocol and protein detection protocol data
The viewer can be downloaded at the following address: http://www.proteoannotator.org/datasets/releases/ProteoIDViewer-1.4.1.zip