ProteinCenter is a web-based tool that enables scientists to compare and interpret proteomics data sets in minutes and overcomes the hurdle of proteins existing under different names and accession keys in different databases. Regularly updated from all major protein databases, ProteinCenter provides a consolidated, biologically annotated, protein sequence database to enable filtering, clustering and statistical bioinformatic analysis from single, combined or comparison data sets.
Based on user feedback, ProteinCenter is regularly updated with new and improved functions and features.  Listed below are some of the key features included in the most recent versions:
ProteinCenter 3.13
  • New lookup enables searching for all proteins with a particular taxonomy in the database.


ProteinCenter 3.12
  • It is now possible to select proteins in the similar proteins detail section of the ProteinCard. The selected proteins can subsequently be turned into a new dataset or used as selection throughout the application tools.

  • We have adopted the newest Blast executables (BLAST+) for improved sequence similarity and sequence alignment execution.
ProteinCenter 3.11
  • All CSV importers now support limiting input on taxonomy, i.e. each CSV line can specify a required Species.

  • Importers now have support for attaching generic supplementary data to peptides: GI#, GD#, GS# and L#. The number of generic supplementary data of any type for both proteins and peptides has been extended to 9, i.e. allowed values for the # above are in the range 1-9 (used to be 1-3).
  • The application will now automatically update itself whenever a new version is released.
ProteinCenter 3.10
  • CSV exporters supplemented with more gene and chromosome related information, including the possibility to output all alternative IDs for genes (EntrezGene official symbol, HGNC, ...)

ProteinCenter 3.9
  • A complete (Tapestry 5) rewrite of the user interface improves responsiveness, UI updating (Ajax), and general look and feel.

  • StatisticsCard presents better, more specific overview and detail sections; Gene Ontology statistics have been increased and split into several sections.

  • Interaction exporter now supports limiting output on (STRING) interaction scores.

ProteinCenter 3.8
  • STRING, a new source of more than 223 million protein-protein interactions has been added to the ProteinCenter database. This adds identifiers, links and interacting proteins to the ProteinCard extends the interaction source filters and enriches the new interaction exporter (see below).

  • Protein interactions (from IntAct, MIPS and STRING) can now be exported in Cytoscape .sif format, allowing for more detailed graph-oriented browsing and analysis of the protein networks.

  • (Genomics workflow) A new gene-based exporter has been introduced, which outputs data aggregated on genes

  • All exported rows are now ordered according to the current sorting on the Genes, Proteins and Experimental Data View respectively, enabling users to choose the preferred output order this way.

  • It is now possible to restrict imported proteins, by only loading proteins already represented in checked data folders of the workspace. This is particularly useful for importing proteins based on gene identifiers.

  • All importers have been optimized, resulting in dramatically reduced import times.

  • A new peptide modification filter revealing unannotated modifications has been added to the peptide, experimental data, protein and cluster view. This filter disregards modifications with the equivalent UniProt PTM feature already annotated to the corresponding protein.

  • Chromosome and chromosome map columns in the Genes View can now be sorted according to actual chromosome location, rather than the previous simple lexicographical order

ProteinCenter 3.7
  • To make it easier to find and navigate existing data, a Search Workspace functionality has been added, enabling the user to find categories and data sets by criteria like owner, creation date and annotations

  • Generic precursor and reporter ion based quantitation supported on peptides and proteins in Proteome Discoverer XML importer
  • A progress bar has been added to lengthy statistics calculations

ProteinCenter 3.6
  • (Genomics workflow) New gene view offers displaying, comparison and filtering of data in a gene-centric way

ProteinCenter 3.5
  • Peptide view has been optimized for much faster load of large data sets.

  • Possibility to filter on GO sources and GO evidence codes has been added to experimental, proteins and clusters view

  • New lookup enables searching for all proteins in the database with a particular annotation: GO, Enzyme Code, KEGG pathway, PFAM and InterPro domains

ProteinCenter 3.4
  • (Genomics workflow) New Genes CSV importer, which imports all proteins for each gene accession in a CSV file

  • All CSV importers now recognize peptide modifications given as UniMod standard names, or as delta/absolute masses

  • Direct support for 2- and 6-plex Tandem Mass Tag quantitation for both proteins and peptides

  • Support for generic quantitation has been extended to 20 ratios (including standard error, standard deviation, p-value and peptide count) for both proteins and peptides

ProteinCenter 3.3
  • Visualize quantitative proteomics data on pathways

  • Aggregate proteins according to chromosomal location

  • Clickable heat maps. Go from biological annotation to corresponding list of proteins

  • Perform profiling, heat mapping and statistics on entire data sets or on selected proteins only

  • Export heat map values directly to comma-separated files for post-processing

  • Added:

    Comprehensive Microbial Resource to the ProteinCenter database. See details on:

    New reference databases for enrichment analysis, including: Ensembl, NCBI (GI), TubercuList and Comprehensive Microbial Resource

    HUPO projects as reference data sets for enrichment analysis

ProteinCenter 3.2
  • Heatmaps to display quantitative data aggregated on protein or biological annotation level

  • Expression profiling at annotation level, e.g. match quantitative data on KEGG pathways

  • Export of statistics results directly into CSV files

  • Direct support of the Iprophet and Proteome Discoverer xml-formats

  • 'Most-used' modifications now recognized in Spectrum Mill

  • Encoded modifications in peptide sequences  included in CSV  format
  • Modification information can be imported from "evidence.txt" file in MaxQuant.
ProteinCenter 3.1
  • Customizable views in Exp. Data-, Peptides-, Proteins- and Cluster-view enables selection of columns for display

  • Perform expression profiling on groups of proteins.
  • Optimized export function

  • Report functionality includes Gene Ontology slim
  • Peptide Venn diagrams

ProteinCenter 3.0
  • Supports more data formats - import Mascot Distiller XML files and MaxQuant data

  • Separate view for working with peptide data includes sorting and filtering

  • Import data from user-defined quantitative methods in Mascot XML

  • 'Per-column' selection prevents export of unwanted data, resulting in better performance.

ProteinCenter 2.8
  • Profiling includes grouping by quantitative data on the peptide level and across data sets in a comparison

  • Display of basic protein sequence and annotation counts for current data release

  • Execute "Empty recycle bin" clean-up procedure from μLIMS page

ProteinCenter 2.7
  • Profiling - group proteins based on supplementary information such as quantitative data

  • Import files in the peptide summary format from ProteinPilot

ProteinCenter 2.6
  • Upload data from Phenyx software directly to ProteinCenter

  • Warning icon displayed when an application or license update is available

  • Import of more quantitative values such as iTRAQ8

  • Import files in protein summary format from ProteinPilot

  • Support for more quantitative methods in Mascot XML

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Description Part Number
Cloud-based subscription: 1 user license per 1 year
ProteinCenter subscription extension: 1 user license per 3 years
ProteinCenter subscription extension: 2 user licenses per 3 years
Product descriptions and specifications are subject to change without notice.