CPhos - Frequently Asked Questions (FAQ)

1. How do I add a new proteome database?

There is currently no option to add new proteome database for the online version. Please contact us if you are interested in adding a proteome database.

To add a new proteome database to the standalone desktop version, go to “Tools” -> “Update/Add Local Databases”. In the new dialog box, check “Add Database” and enter the name of the database (e.g. “yeast”). Browse to the location of the FASTA file (.fasta) of the proteome database. Click on “Add New Database”. A serialized version of the database (.sdb file) will be created and used by the software.

Please note the software only accepts FASTA format for the proteome, with the header similar to the following format below. The “ref” keyword is searched by the program to retrieve the refseq ID. >gi|77539434|ref|NP_037041.2| aquaporin-2 [Rattus norvegicus]

2. What does “no phosphosite found” in results mean?

Double check your input. The program cannot find symbols ('*'), which indicate sites of phosphorylation, in the input peptide sequences.

3. What does “multiple protein matches found” in results mean?

The input peptide is matched to multiple proteins in the input species database, and as such this peptide and the associated phosphosite(s) are omitted from further analysis.

4. What does “no protein match protein” in results mean?

This can be the result of several possible reasons:

The peptide sequence is not found in the protein database
The protein that is not found in the homologene database
There are multiple proteins from the same input species sharing the same HID. These proteins are omitted from further analysis
There is only one protein (i.e. the protein of input species) in the homologous group. As a result, there is no way we can do a sequence alignment and no conservation score is calculated.

5. I’m having trouble running the standalone version of CPhos on Mac OS. What do I do?

There has been some reported compatibility issues on the Mac OS platform. We tested CPhos on Mac OS X 10.5.8 (64-bit Intel Core 2 Duo, 2GB RAM, Java version 1.6.0_26) without any problems. We have not been able to replicate the problem and determine the cause. If you are having trouble running CPhos on Mac, let us know and please use a different OS platform or the online version in the meantime.