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Is SILVER restricted to use with any particular software?
SILVER requires only a list of candidate peptides.
How you generate that list is up to you. If you're using SEQUEST,
then the .OUT file will do nicely as your candidate-peptide list.
If you're using Mascot, we've written
this Python module to help
generate a list from the output results.
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Can I use SILVER on results obtained from the Mascot website?
No. We offer a Python script
for parsing the results file produced by the command-line
version of Mascot.
The web pages produced by Mascot running in
CGI mode are difficult to parse.
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How can I use SILVER with Mascot results?
Assuming you have a complete results file produced by Mascot
running in command-line mode (not the results obtained from the website),
you can download this Python module
to help parse it. The output produced consists of one line for
each spectrum, and lists all peptides that matched that spectrum.
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What are the allowed formats for the candidate-peptide list?
- One option is to use a SEQUEST .OUT file. You can upload it as is.
Since the format is well known, it can be interprted by SILVER.
Only the most relevant data will be shown.
- If that is not available (for example, if you're not using SEQUEST),
you can use the 'generic format', as specified in the following:
- Each line consists of an arbitrary number of elements, separated by whitespace (e.g., tabs, blanks).
- The first element on each line is assumed to be the peptide name.
- There can be only one peptide per line.
- Lines beginning with '#' will be ignored.
- All elements will be displayed in a table,
but elements other than the peptide name will not be interpreted
in any way.