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.

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:

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
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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IOError

Python 2.4.6: /usr/bin/python2.4
Sat May 25 15:20:09 2013

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

/www/llama.mshri.on.ca/cgi/SILVER/silver.cgi

1360

1361 if __name__ == "__main__":

1362 main()

1363

1364

main = <function main>

/www/llama.mshri.on.ca/cgi/SILVER/silver.cgi in main()

1357 Actions['Start'](form, state, session_key, Config)

1358 footer()

1359 save_state(form, state, session_key)

1360

1361 if __name__ == "__main__":

global save_state = <function save_state>, form = FieldStorage(None, None, [MiniFieldStorage('id', '916487')]), state = {'id': '916487'}, session_key = '916487'

/www/llama.mshri.on.ca/cgi/SILVER/silver.cgi 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:

f undefined, builtin open = <type 'file'>, state_session_key = '/www/llama.med.harvard.edu/docroot/SILVER/tmp/916487'

IOError: [Errno 13] Permission denied: '/www/llama.med.harvard.edu/docroot/SILVER/tmp/916487'
      args = (13, 'Permission denied')
      errno = 13
      filename = '/www/llama.med.harvard.edu/docroot/SILVER/tmp/916487'
      strerror = 'Permission denied'

Upload a spectrum (.DTA) file
Upload a peptide-list (.OUT) file