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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Python 2.4.6: /usr/bin/python2.4
Sat Jan 21 18:34:47 2017

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 1361 if __name__ == "__main__":
 1362     main()
main = <function main>
 /www/ in main()
 1357         Actions['Start'](form, state, session_key, Config)
 1358     footer()
 1359     save_state(form, state, session_key)
 1361 if __name__ == "__main__":
global save_state = <function save_state>, form = FieldStorage(None, None, [MiniFieldStorage('id', '916487')]), state = {'id': '916487'}, session_key = '916487'
 /www/ in save_state(form=FieldStorage(None, None, [MiniFieldStorage('id', '916487')]), state={'id': '916487'}, session_key='916487')
 1240     if (valid(session_key)):
 1241         state_session_key = os.path.join(STATE_DIR, session_key)
 1242         f = open(state_session_key, "w")
 1243         if verbose: print "<br>Opened %s<br>" % state_session_key
 1244         if not f:
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IOError: [Errno 13] Permission denied: '/www/'
      args = (13, 'Permission denied')
      errno = 13
      filename = '/www/'
      strerror = 'Permission denied'