SILVER: intensity-based scoring and visualization of tandem mass spectra

Introduction to SILVER

SILVER allows you to upload spectrum (DTA) files, and view them in the light of a LOD-based scoring scheme, indicating which peaks are surprising, either by their presence or by their absence.
Upload a spectrum (.DTA) file
Upload a peptide-list (.OUT) file

To refer to the algorithm implemented on this website, please cite these two publications: one for the algorithm, one for its implementation in this site:

  1. Elias, J.E., Gibbons, F.D., King, O.D., Roth, F.P., and Gygi, S.P. (2004) Intensity-based protein identifiation by machine learning from a library of tandem mass spectra., Nat. Biotech. vol. 22, pp214-219
  2. Gibbons, F.D., Elias, J.E., Gygi, S.P., and Roth, F.P. (2004) SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. J. Am. Soc. Mass Spectrom. (accepted)

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<type 'exceptions.IOError'>		Python 2.7.5: /usr/bin/python
Wed Dec 6 16:16:50 2023

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /srv/www/llama.mshri.on.ca/cgi/SILVER/silver.cgi in ()
   1364 
   1365 if __name__ == "__main__":
=> 1366     main()
   1367 
   1368 
main = <function main>
 /srv/www/llama.mshri.on.ca/cgi/SILVER/silver.cgi in main()
   1361         Actions['Start'](form, state, session_key, Config)
   1362     footer()
=> 1363     save_state(form, state, session_key)
   1364 
   1365 if __name__ == "__main__":
global save_state = <function save_state>, form = FieldStorage(None, None, [MiniFieldStorage('id', '665224')]), state = {'LOD_labels': '1', 'OUT_data': '', 'action': 'Show me a demo', 'data': '', 'id': '665224'}, session_key = '665224'
 /srv/www/llama.mshri.on.ca/cgi/SILVER/silver.cgi in save_state(form=FieldStorage(None, None, [MiniFieldStorage('id', '665224')]), state={'LOD_labels': '1', 'OUT_data': '', 'action': 'Show me a demo', 'data': '', 'id': '665224'}, session_key='665224')
   1244     if (valid(session_key)):
   1245         state_session_key = os.path.join(STATE_DIR, session_key)
=> 1246         f = open(state_session_key, "w")
   1247         if verbose: print "<br>Opened %s<br>" % state_session_key
   1248         if not f:
f undefined, builtin open = <built-in function open>, state_session_key = '/srv/bundler/Staging/SILVER/DOCROOT/tmp/665224'

<type 'exceptions.IOError'>: [Errno 13] Permission denied: '/srv/bundler/Staging/SILVER/DOCROOT/tmp/665224'
      args = (13, 'Permission denied')
      errno = 13
      filename = '/srv/bundler/Staging/SILVER/DOCROOT/tmp/665224'
      message = ''
      strerror = 'Permission denied'