F. Cliquet, G. Fertin, I. Rusu, and D. Tessier, Comparison of Spectra in Unsequenced Species, Proc. 4th Brazilian Symposium on Bioinformatics, pp.24-35, 2009.
DOI : 10.1021/pr060271u

URL : https://hal.archives-ouvertes.fr/hal-00416462

P. A. Pevzner, V. Dancik, and C. L. Tang, Mutation-Tolerant Protein Identification by Mass Spectrometry, Journal of Computational Biology, vol.7, issue.6, pp.777-787, 2000.
DOI : 10.1089/10665270050514927

J. Klimek, J. Eddes, L. Hohmann, J. Jackson, A. Peterson et al., The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools, Journal of Proteome Research, vol.7, issue.1, pp.96-103, 2008.
DOI : 10.1021/pr070244j

Y. Chen, J. Zhang, G. Xing, and Y. Zhao, Mascot-Derived False Positive Peptide Identifications Revealed by Manual Analysis of Tandem Mass Spectra, Journal of Proteome Research, vol.8, issue.6, pp.3141-3147, 2009.
DOI : 10.1021/pr900172v

D. N. Perkins, D. J. Pappin, D. M. Creasy, and J. S. Cottrell, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, vol.447, issue.18, pp.3551-3567, 1999.
DOI : 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

J. Eng, A. Mccormack, and J. R. Yates, An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, Journal of the American Society for Mass Spectrometry, vol.7, issue.11, pp.976-989, 1994.
DOI : 10.1016/1044-0305(94)80016-2

R. Craig and R. Beavis, TANDEM: matching proteins with tandem mass spectra, Bioinformatics, vol.20, issue.9, pp.1466-1467, 2004.
DOI : 10.1093/bioinformatics/bth092

S. Tanner, H. Shu, A. M. Frank, L. Wang, E. Zandi et al., InsPecT:?? Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra, Analytical Chemistry, vol.77, issue.14, pp.4626-4639, 2005.
DOI : 10.1021/ac050102d

J. R. Yates, J. Eng, A. Mccormack, and D. Schieltz, Method to Correlate Tandem Mass Spectra of Modified Peptides to Amino Acid Sequences in the Protein Database, Analytical Chemistry, vol.67, issue.8, pp.1426-1436, 1995.
DOI : 10.1021/ac00104a020

P. A. Pevzner, Z. Mulyukov, V. Dancik, and C. L. Tang, Efficiency of Database Search for Identification of Mutated and Modified Proteins via Mass Spectrometry, Genome Research, vol.11, issue.2, pp.290-299, 2001.
DOI : 10.1101/gr.154101

D. Tsur, S. Tanner, E. Zandi, V. Bafna, and P. A. Pevzner, Identification of post-translational modifications by blind search of mass spectra, Nature Biotechnology, vol.3, issue.12, pp.1562-1567, 2005.
DOI : 10.1038/nbt1168

P. Roepstorff and J. Fohlman, Proposal for a common nomenclature for sequence ions in mass spectra of peptides, Biomedical mass spectrometry, vol.11, issue.11, 1984.

V. Dancik, T. Addona, K. R. Clauser, J. Vath, and P. A. Pevzner, De novo peptide sequencing via tandem mass spectrometry, Journal of Computational Biology, vol.6, pp.3-4, 1999.

A. M. Frank, M. M. Savitski, M. L. Nielsen, R. A. Zubarev, and P. A. Pevzner, De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry, Journal of Proteome Research, vol.6, issue.1, pp.114-123, 2007.
DOI : 10.1021/pr060271u

T. Sing, O. Sander, N. Beerenwinkel, and T. Lengauer, ROCR: visualizing classifier performance in R, Bioinformatics, vol.21, issue.20, pp.3940-3941, 2005.
DOI : 10.1093/bioinformatics/bti623

T. Fawcett, An introduction to ROC analysis, Pattern Recognition Letters, vol.27, issue.8, pp.861-874, 2006.
DOI : 10.1016/j.patrec.2005.10.010

M. Dayhoff, R. Schwartz, and B. Orcutt, A model of evolutionary change in proteins Atlas of protein sequence and structure, pp.345-352, 1978.

S. Needleman and C. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-453, 1970.
DOI : 10.1016/0022-2836(70)90057-4