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A: You have three options:
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.
A: Yes, quantitative data can be imported from Mascot v.2.2, MSQuant, ProteinPilot or a spreadsheet.
A: Yes, ProteinCenter automatically removes redundancy, without removing your experimental data points.
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.
A: Yes, ProteinCenter can group proteins based on their respective peptides or sequence homology, separately or both at the same time.
A: Yes, ProteinCenter has a filter-functionality that can filter proteins based on their peptide modification.
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.
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
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: