Frequently Asked Questions

Q: How do I import my data into ProteinCenter?
A: You have three options:
  1. Import database search results from Mascot, ProteinPilot, Bioworks, SpectrumMill, MSQuant and X!Tandem.

  2. Import proteins and peptides from a spreadsheet as a csv-file
  3. Import proteins and peptides from ProtXML or PRIDE
Q: How can I purchase ProteinCenter?
A: You purchase ProteinCenter as an Application Service Provider (ASP) solution. ProteinCenter will be run through Thermo and you do not have to be concerned about maintenance. You will access the application through a standard web browser.
Q: Does ProteinCenter support quantitative proteomics data?

A: Yes, quantitative data can be imported from Mascot v.2.2, MSQuant, ProteinPilot or a spreadsheet.

Q: When I look carefully at the data I see redundancy - several protein accession keys point to the same protein. Does ProteinCenter handle that?
A: Yes, ProteinCenter automatically removes redundancy, without removing your experimental data points.
Q: How does ProteinCenter handle annotation?
A: ProteinCenter uses annotation from all the major protein sequence databases. So you have access to all the knowledge that exists about a specific protein. If there is no annotation for a protein, you can perform a ‘similarity search’ to see how other similar proteins are annotated.
Q: Can ProteinCenter group proteins based on their identified peptides?
A: Yes, ProteinCenter can group proteins based on their respective peptides or sequence homology, separately or both at the same time.
Q: Is it possible to filter on modifications? We are only interested in phosphorylation.
A: Yes, ProteinCenter has a filter-functionality that can filter proteins based on their peptide modification.
Q: I have 10 bands for which I have individual search results files. I use a script and excel now to combine them, but it is not that easy. How do you work with that in ProteinCenter?
A: You import each of the 10 files individually. Then you create a comparison. Now you can visually see if a protein is found in more than one band. You can also apply the comparison filters to automatically detect proteins found in more than one band. Depending on the application you might want to merge the files into one large dataset instead. ProteinCenter can do this thus automatically handling redundancy for you.
Q: Is it possible to customize the names in the pie-chart showing the Gene Ontology distribution on the statistics page in ProteinCenter?
A: No, the text on the pie-charts of Gene Ontology in ProteinCenter is static. However you can copy the table format of the Gene Ontology distribution
Q: Why are my protein records rejected by the ProteinCenter importer?
A: Protein records are rejected by ProteinCenter if the protein accession key is not present in the database. There can be several reasons for that:
  • Your protein accession key is not from one of the protein data sources supported by ProteinCenter (perhaps list the sources or link to list of sources)
  • Your protein accession key is out of date. ProteinCenter keeps historical data from various protein data sources, but does not include certain protein accession keys that have been outdated for a long time.
  • ProteinCenter does not include synthetic constructs.
  • Your protein accession key is new. The ProteinCenter database is updated every weekend, so if you protein accession key is brand new, it will be rejected.
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