Why we developed ProteinCenter

Wasting time?

At Proxeon we realized that, despite the excellent performance of modern mass spectrometers and the use of various software options for preliminary protein identification and validation, proteomics scientists still faced the time-consuming task of using multiple data sources and other analytical tools to interpret large data sets into meaningful biological information. Redundancy, different accession numbers, poorly annotated proteins, fragments, splice variants and isoforms, multiple databases all contributed to the complexity of interpretation. Biologists were spending months on bioinformatic analysis.

The solution!

We based ProteinCenter on a consolidated, biologically annotated, protein sequence database derived from all major protein databases allows filtering, clustering and statistical bioinformatic analysis from single, combined or comparison datasets - in other words, faster, more confident data interpretation using only one unique analytical tool.
Using ProteinCenter, biologists can now confidently interpret large data sets to produce meaningful biological information within minutes. A bioinformatic analysis that could take months to finalize using conventional tools is performed in four simple steps:

Step 1. Integrate experimental data

  • Import from sources such as Mascot, BioWorks, Pride, Trans-Proteomic Pipeline or Excel CSV files
  • Import data such as protein accession numbers, peptide sequences, search engine scores, MS3 score, quantitation data and other parameters.

Step 2. Remove redundancy using up-to-date protein databases

  • Work with the latest data - ProteinCenter integrates sequence information and annotation from all major public sequence databases including: GenBank, RefSeq, EMBL, UniProt, Swiss-Prot, Trembl, PIR, IPI, Ensembl and more

  • Access more than 7 million protein sequences derived from 30 million accession codes from past and present versions of the public databases.

  • ProteinCenter handles all bookkeeping - sequences referred to by multiple accession codes are merged to non-redundant ones

Step 3. Compare data sets

  • Compare multiple data sets of thousands of proteins and get the true overlap, independent of the original database source e.g. compare lists of IPI to SwissProt accession keys regardless of their age

  • Compare experimental data sets with results from other scientific studies to see data in a new context.

  • Compare datasets with accessions from different protein databases

Step 4. Produce an instant biological overview

  • Obtain comprehensive biological annotation to large sets of proteins
  • Obtain a wealth of extra information for each sequence based on state-of-the-art bioinformatics tools
  • ProteinCenter automatically adds annotations, such as GO, protein description and PFAM to experimental data - no important details are missed
  • ProteinCenter consolidates and categorizes all sequence and annotation data to optimize the interpretation of experimental data
  • Quickly and easily filter lists of proteins based on biologically relevant parameters and experimental observations simultaneously to find the proteins relevant to the project