Skip to content
This repository has been archived by the owner on Jun 23, 2024. It is now read-only.

1. PRIDE Inspector feature list

Jump to bottom
Yasset Perez-Riverol edited this page Aug 23, 2015 · 1 revision

  1. Key Features:

    1.1. Rapid loading of Peaks files: mzML, mgf, pkl, ms2, dta, apl, mzData, mzXML

    1.2. Rapid loading of identification and quantitation files: PRIDE XML, mzIdentML, mzTab

    1.3. Search, access and download PRIDE Archive ‘complete’ public experiments through web-services, with search capabilities for modifications, species, disease, tissue, etc

    1.4. Distinct views on mass spectra, chromatograms, proteins, peptide-spectrum-matches, peptides, protein-groups, quantification and experiment details:

    • Visualize all spectra and chromatograms with their fragment annotations

      • Automatic annotation of Fragment Ion information

    • Automatic annotation for spectra using MS/MS fragment ions (if ion assignments are not included) Support for various ion types, including co-eluting and immonium ions and amino acid annotation for different fragment ion series within a spectrum

      • Filtering based on types of fragment ions and amino acid annotations
      • Ability to show/hide mass differences for amino acid annotations
      • Configurable fragment ion mass error tolerance for performing the amino acid annotations
      • Visualization of Mass Table to see the differences between assigned ions and spectrum peaks
      • Visualization of the delta mass at Fragment Ion level
      • Save a spectrum or chromatogram as an image. Supported formats include SVG, PNG, JPEG, GIF and PDF file.
      • Highlight peaks with m/z and intensity values in a spectrum.
      • Export spectra data to mgf
      • Show mass differences for selected peaks and annotated fragment ions, showing the sequence of the assigned peptide
      • Automatic suggestion on possible amino acids and charges based on mass differences of the selected peaks
      • Highlight peak with its m/z and intensity value
      • Show categorized metadata for each spectrum or chromatogram and annotated precursor ions
      • Batch loading for experiments containing large number of spectra
      • Easy adjustment on the display size of spectra and chromatogram
      • Show MS level and precursor details for each spectrum

    • Visualization of Quantitation Results by supporting study variables and abundances for Quantitation Experiments at protein and peptide levels

    • Visualize original information from PSM/Peptide/Protein search engines, scores, p-values, thresholds and annotations

      • Show all protein identifications, together with the peptide-spectrum-matches and the spectra used for identification.
      • Show general details about protein identifications (such as search engine, search database, search parameters, number of PSMs, number of unique peptides) from original data
      • Automatic correction of poorly formatted protein accessions by using web services to retrieve protein names, protein status and protein sequences from different protein databases (for UniProt, UniParc, Ensembl)
      • Show Protein sequence information for those files that contains sequences such as mzIdentML and mzTab
      • Calculate the theoretical pI for both protein and peptide identifications
      • Show the protein group for those files that contains Protein Group information
      • Calculate delta m/z for each peptide (difference between the theoretical and the experimental m/z). Highlighting is also done according to the chosen threshold (4 Da)
      • Show for each peptide the list of PSM with the corresponding information of protein modifications, scores, etc
      • Hyperlink all valid protein accessions and protein modifications accessions.
      • Possibility to filter by PSM ranks

    • Visualization of protein group information in tree tables from original files and also visualization of Protein Inference information using graph representation

    • Display short summary of key measurements on experiment quality like delta masses, protein modification annotations

    1.5 Download additional protein details, such as the protein name and the most up-to-date protein sequence (for the following protein sequence databases: UniProt, UniParc, Ensembl).

    1.6 Protein inference algorithm to those experiments without protein group information.

    • Display Protein group information and the relation between protein-peptides-PSMs
    • Select different topologies to visualize the protein group information
    • Collapse and un-collapse peptide and PSMs information
    • Highlight the differences between peptides and PSMs
    • Filter the data by PSMs scores
    • Compute the number of shared peptides and PSMs by protein
    • Highlight the overlapping peptides and the protein groups

    1.7 Ability to perform an initial data quality assessment using a statistical view with different charts for four different categories: all spectra, identified spectra, decoy identifications and target identifications.

    1.8 User-friendly download facility for private PRIDE experiments (suitable for journal reviewers and editors)

    1.9 Experiment Detail Related Features

    • Display experiment details, including sample, protocol and instrument configurations. The overview tab is split in three different views: ‘Experiment General’, ‘Sample and Protocol’, and ‘Instrument and Processing’
    • Information about the peptide/protein identification protocols: databases, software, search parameters, etc
    • Possibility to export the peptide/protein identifications to mzTab files 1.10 Quantification Related Features
    • Show the quantification method that has been used and the current study variables and abundances for each variable
    • Show a summary of sample study variables and the abundances details for each quantification reagent
    • Show quantification ratios for both proteins and peptides based on a selected for all the study variables or for abundances depending of the selection of (abundances or study variables)
    • Possibility to multi-select peptide isoforms for the same Protein
    • Display bar charts based on quantification ratios
    • Map filtered proteins identifications to the Ensembl web Karyotype Viewer
    • Save/Print the protein quantification data to a file 1.11 Summary Chart Related Features
    • ‘Delta m/z’ distribution for all peptides, including all spectra, identified, non-identified, target and decoy identifications
    • Histogram on number of peptides per protein identification (percentage of controversial identifications)
    • Histogram on the distribution of missed tryptic cleavages for all peptides including all spectra, identified, non-identified, target and decoy identifications
    • Average MS/MS spectrum (for all spectra, or filtering between identified and unidentified spectra)
    • Histogram on the distribution of precursor ion charge for identified spectra including all spectra, identified, non-identified, target and decoy identifications
    • Precursor ion masses distribution for all spectra including all spectra, identified, non-identified, target and decoy identifications. It is also possible to visualize a human, mouse and PRIDE reference curves
    • Histogram on number of peaks per spectrum including all spectra, identified, non-identified, target and decoy identifications
    • Histogram on peak intensity for all spectra (for all, or filtering between identified and unidentified spectra) including all spectra, identified, non-identified, target and decoy identifications
    • Histogram on number of peaks per spectrum including all spectra, identified, non-identified, target and decoy identifications
    • Distribution of Peptide per Ratio showing all the quantitation study variables and abundances
    • Save/Print all charts as images
    • Zoom in/out ability for all the charts
    • Easy navigation between charts
Clone this wiki locally