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\bibitem{anderson:new}
D.~C. Anderson, W.~Li, D.~G. Payan, and W.~S. Noble.
\newblock A new algorithm for the evaluation of shotgun peptide sequencing in
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\newblock {\em Journal of Proteome Research}, 2(2):137--146, 2003.

\bibitem{elias:intensity}
J.~E. Elias, F.~D. Gibbons, O.~D. King, F.~P. Roth, and S.~P. Gygi.
\newblock Intensity-based protein identification by machine learning from a
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\newblock {\em Nature Biotechnology}, 22:214--219, 2004.

\bibitem{eng:approach}
J.~K. Eng, A.~L. McCormack, and J.~R. {Yates, III}.
\newblock An approach to correlate tandem mass spectral data of peptides with
  amino acid sequences in a protein database.
\newblock {\em Journal of the American Society for Mass Spectrometry},
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\bibitem{field:radars}
H.~I. Field, D.~Fenyo, and R.~C. Beavis.
\newblock Radars, a bioinformatics solution that automates proteome mass
  spectral analysis, optimises protein identification, and archives data in a
  relational database.
\newblock {\em Proteomics}, 2:36--47, 2002.

\bibitem{keller:empirical}
A.~Keller, A.~I. Nezvizhskii, E.~Kolker, and R.~Aebersold.
\newblock Empirical statistical model to estimate the accuracy of peptide
  identification made by {MS/MS} and database search.
\newblock {\em Analytical Chemistry}, 74:5383--5392, 2002.

\bibitem{nesvizhskii:statistical}
A.~I. Nesvizhskii, A.~Keller, E.~Kolker, and R.~Aebersold.
\newblock A statistical model for identifying proteins by tandem mass
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\newblock {\em Analytical Chemistry}, 75:4646--4658, 2003.

\bibitem{perkins:probability}
D.~N. Perkins, D.~J.~C. Pappin, D.~M. Creasy, and J.~S. Cottrell.
\newblock Probability-based protein identification by searching sequence
  databases using mass spectrometry data.
\newblock {\em Electrophoresis}, 20:3551--3567, 1999.

\bibitem{tabb:influence}
D.~L. Tabb, Y.~Huang, V.~H. Wysocki, and J.~R. {Yates, III}.
\newblock Influence of basic residue content on fragment ion peak intensities
  in low-energy collision-induced dissociation spectra of peptides.
\newblock {\em Analytical Chemistry}, 76:1243--48, 2004.

\bibitem{tabb:similarity}
D.~L. Tabb, M.~J. MacCoss, C.~C. Wu, S.~D. Anderson, and J.~R. {Yates, III}.
\newblock Similarity among tandem mass spectra from proteomic experiments:
  detection, significance, and utility.
\newblock {\em Analytical Chemistry}, 75:2470--2477, 2003.

\bibitem{venable:impact}
J.~D. Venable and J.~R. {Yates, III}.
\newblock Impact of ion trap tandem mass spectra variability on the
  identification of peptides.
\newblock {\em Analytical Chemistry}, 76(10):2928--2937, 2004.

\bibitem{zhang:prediction}
Z.~Zhang.
\newblock Prediction of low-energy collision-induced dissociation spectra of
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\newblock {\em Analytical Chemistry}, 76:3908--3922, 2004.

\end{thebibliography}