B. Bibliographie, H. A. Ebhardt, A. Root, C. Sander, and R. Aebersold, Applications of Targeted Proteomics in Systems Biology and Translational Medicine, Proteomics, vol.2015, issue.118, pp.15-3193

E. Engvall and P. Perlmann, Enzyme-linked immunosorbent assay (ELISA) quantitative assay of immunoglobulin G, Immunochemistry, vol.8, issue.9, pp.871-874, 1971.
DOI : 10.1016/0019-2791(71)90454-X

). Farrell and P. H. , High Resolution Two-Dimensional Electrophoresis of Proteins, J. Biol. Chem, issue.310, pp.250-4007, 1975.

R. E. Gerszten and S. A. Carr, Developing Multiplexed Assays for Troponin I and Interleukin- 33 in Plasma by Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry, Clin. Chem, issue.6, pp.55-1108, 2009.

A. N. Hoofnagle, J. O. Becker, M. H. Wener, and J. W. Heinecke, Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry, Clinical Chemistry, vol.54, issue.11, pp.54-1796, 2008.
DOI : 10.1373/clinchem.2008.109652

M. Girod, J. Biarc, Q. Enjalbert, A. Salvador, R. Antoine et al., Implementing visible 473 nm photodissociation in a Q-Exactive mass spectrometer: towards specific detection of cysteine-containing peptides, The Analyst, vol.12, issue.21, pp.139-5523
DOI : 10.1002/pmic.201100463

URL : https://hal.archives-ouvertes.fr/hal-01234356

J. P. Reilly, Ultraviolet photofragmentation of biomolecular ions, Mass Spectrometry Reviews, vol.120, issue.102, pp.425-447, 2009.
DOI : 10.1002/jms.703

R. Antoine and P. Dugourd, Visible and ultraviolet spectroscopy of gas phase protein ions, Physical Chemistry Chemical Physics, vol.130, issue.462, pp.13-37, 2011.
DOI : 10.1021/ja805257v

URL : https://hal.archives-ouvertes.fr/hal-00676501

E. R. Williams, J. J. Furlong, and F. W. Mclafferty, Efficiency of collisionally-activated dissociation and 193-nm photodissociation of peptide ions in fourier transform mass spectrometry, Journal of the American Society for Mass Spectrometry, vol.2, issue.4, pp.288-294, 1990.
DOI : 10.1021/bk-1987-0359.ch002

J. S. Brodbelt, Photodissociation mass spectrometry: new tools for characterization of biological molecules, Chem. Soc. Rev., vol.51, issue.8, pp.43-2757
DOI : 10.1140/epjd/e2008-00085-3

Q. Enjalbert, M. Girod, R. Simon, J. Jeudy, F. Chirot et al., Improved detection specificity for plasma proteins by targeting cysteine-containing peptides with photo-SRM, Analytical and Bioanalytical Chemistry, vol.9, issue.12, pp.405-2321
DOI : 10.1021/pr100821m

URL : https://hal.archives-ouvertes.fr/hal-00960559

S. Wang, X. Zhang, and F. Regnier, Quantitative proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates, Journal of Chromatography A, vol.949, issue.1-2, pp.153-162, 2002.
DOI : 10.1016/S0021-9673(01)01509-6

K. Strimbu and J. A. Tavel, What are biomarkers?, Current Opinion in HIV and AIDS, vol.5, issue.6, pp.463-466, 2010.
DOI : 10.1097/COH.0b013e32833ed177

N. Tasevska, Urinary Sugars???A Biomarker of Total Sugars Intake, Nutrients, vol.142, issue.7, pp.5816-5833
DOI : 10.3945/ajcn.114.095604

Y. Zhao, X. Cheng, and R. Lin, Lipidomics Applications for Discovering Biomarkers of Diseases in Clinical Chemistry, Int. Rev. Cell Mol. Biol, vol.313, pp.1-26, 2014.
DOI : 10.1016/B978-0-12-800177-6.00001-3

E. Batchelor, A. Loewer, C. Mock, and G. Lahav, Stimulus-dependent dynamics of p53 in single cells, Molecular Systems Biology, vol.58, issue.1, 2011.
DOI : 10.1101/GAD.827700

L. Pauling and H. A. Itano, Sickle Cell Anemia, a Molecular Disease, Science, vol.110, issue.2865, pp.543-548, 1949.
DOI : 10.1126/science.110.2865.543

G. I. Abelev, S. D. Perova, N. I. Khramkova, and Z. Postnikova, PRODUCTION OF EMBRYONAL ??-GLOBULIN BY TRANSPLANTABLE MOUSE HEPATOMAS, Transplantation, vol.1, issue.2, pp.174-180, 1963.
DOI : 10.1097/00007890-196301020-00004

R. C. Bast-jr, M. Feeney, H. Lazarus, L. M. Nadler, R. B. Colvin et al., Reactivity of a monoclonal antibody with human ovarian carcinoma., Journal of Clinical Investigation, vol.68, issue.5, pp.68-1331, 1981.
DOI : 10.1172/JCI110380

J. E. Mcdermott, J. Wang, H. Mitchell, B. Webb-robertson, R. Hafen et al., Challenges in biomarker discovery: combining expert insights with statistical analysis of complex omics data, Expert Opinion on Medical Diagnostics, vol.36, issue.1, pp.37-51
DOI : 10.1067/mcp.2001.113989

D. S. Marks, L. J. Colwell, R. Sheridan, T. A. Hopf, A. Pagnani et al., Protein 3D Structure Computed from Evolutionary Sequence Variation, Protein 3D Structure Computed from Evolutionary Sequence Variation, p.28766, 2011.
DOI : 10.1371/journal.pone.0028766.s022

URL : https://doi.org/10.1371/journal.pone.0028766

H. Towbin, T. Staehelin, and J. Gordon, Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications., Proc. Natl. Acad. Sci, pp.76-4350, 1979.
DOI : 10.1073/pnas.76.9.4350

S. X. Leng, J. E. Mcelhaney, J. D. Walston, D. Xie, N. S. Fedarko et al., ELISA and Multiplex Technologies for Cytokine Measurement in Inflammation and Aging Research, The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, vol.63, issue.2, pp.63-879, 2008.
DOI : 10.1093/gerona/63.2.184

N. Rifai, M. A. Gillette, and S. A. Carr, Protein biomarker discovery and validation: the long and uncertain path to clinical utility, Nature Biotechnology, vol.33, issue.8, pp.24-971, 2006.
DOI : 10.1515/CCLM.2003.196

J. Cummings, T. H. Ward, A. Greystoke, M. Ranson, and C. Dive, Biomarker method validation in anticancer drug development, British Journal of Pharmacology, vol.26, issue.Suppl 1, pp.646-656, 2008.
DOI : 10.1155/2002/929274

G. Burnett and E. P. Kennedy, The Enzymatic Phosphorylation of Proteins, J. Biol. Chem, vol.211, issue.2, pp.969-980, 1954.

P. Cohen, The origins of protein phosphorylation, Nature Cell Biology, vol.1, issue.5, pp.127-130, 2002.
DOI : 10.1038/nrd773

G. Manning, D. B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam, The Protein Kinase Complement of the Human Genome, Science, vol.298, issue.5600, pp.298-1912, 2002.
DOI : 10.1126/science.1075762

E. G. Krebs and E. H. Fischer, The phosphorylase b to a converting enzyme of rabbit skeletal muscle, Biochimica et Biophysica Acta, vol.20, issue.1, pp.150-157, 1956.
DOI : 10.1016/0006-3002(56)90273-6

M. E. Crosby, Cell Cycle: Principles of Control, Yale J. Biol. Med, vol.80, issue.3, pp.141-142, 2007.

P. Rodriguez and E. G. Kranias, Phospholamban: A Key Determinant of Cardiac Function and Dysfunction, Arch. Mal. Coeur Vaiss, issue.12, pp.98-1239, 2005.

F. Hofmann, A. Ammendola, and J. Schlossmann, Rising behind NO: cGMP-Dependent Protein Kinases, J. Cell Sci, vol.113, pp.1671-1676, 2000.

E. J. Eide and D. M. Virshup, CASEIN KINASE I: ANOTHER COG IN THE CIRCADIAN CLOCKWORKS, Chronobiology International, vol.291, issue.3, pp.389-398, 2001.
DOI : 10.1126/science.1057499

H. Wang, J. Brown, and M. Martin, Glycogen synthase kinase 3: A point of convergence for the host inflammatory response, Cytokine, vol.53, issue.2, pp.130-140, 2011.
DOI : 10.1016/j.cyto.2010.10.009

L. K. Chico, L. J. Van-eldik, and D. M. Watterson, Targeting protein kinases in central nervous system disorders, Nature Reviews Drug Discovery, vol.9, issue.11, pp.892-909, 2009.
DOI : 10.4049/jimmunol.175.1.566

URL : http://europepmc.org/articles/pmc2825114?pdf=render

L. N. Johnson, M. E. Noble, and D. J. Owen, Active and Inactive Protein Kinases: Structural Basis for Regulation, Cell, vol.85, issue.2, pp.149-158, 1996.
DOI : 10.1016/S0092-8674(00)81092-2

J. A. Adams, Kinetic and Catalytic Mechanisms of Protein Kinases, Chemical Reviews, vol.101, issue.8, pp.2271-2290, 2001.
DOI : 10.1021/cr000230w

S. S. Taylor and E. Radzio-andzelm, Protein kinase inhibition: natural and synthetic variations on a theme, Current Opinion in Chemical Biology, vol.1, issue.2, pp.219-226, 1997.
DOI : 10.1016/S1367-5931(97)80013-0

B. Nolen, S. Taylor, and G. Ghosh, Regulation of Protein Kinases, Molecular Cell, vol.15, issue.5, pp.661-675, 2004.
DOI : 10.1016/j.molcel.2004.08.024

A. S. Dhillon, S. Hagan, O. Rath, and W. Kolch, MAP kinase signalling pathways in cancer, Oncogene, vol.4, issue.22, pp.3279-3290
DOI : 10.1158/0008-5472.CAN-05-0115

T. Santarius, J. Shipley, D. Brewer, M. R. Stratton, and C. S. Cooper, A census of amplified and overexpressed human cancer genes, Nature Reviews Cancer, vol.68, issue.1, pp.59-64, 2010.
DOI : 10.1038/nrc2771

B. L. Bennett, c-Jun N-terminal kinase-dependent mechanisms in respiratory disease, European Respiratory Journal, vol.28, issue.3, pp.651-661, 2006.
DOI : 10.1183/09031936.06.00012106

Y. Wang, Mitogen-Activated Protein Kinases in Heart Development and Diseases, Circulation, vol.116, issue.12, pp.1413-1423, 2007.
DOI : 10.1161/CIRCULATIONAHA.106.679589

N. Pandya, D. Santani, and S. Jain, Role of Mitogen-Activated Protein (MAP) Kinases in Cardiovascular Diseases, Cardiovascular Drug Reviews, vol.301, issue.3, pp.247-254, 2005.
DOI : 10.1161/01.RES.82.1.7

M. Sevecka and G. Macbeath, State-based discovery: a multidimensional screen for small-molecule modulators of EGF signaling, Nature Methods, vol.20, issue.10, pp.825-831, 2006.
DOI : 10.1042/bj2960297

H. Daub, K. Specht, and A. Ullrich, Strategies to overcome resistance to targeted protein kinase inhibitors, Nature Reviews Drug Discovery, vol.410, issue.Suppl. 1, pp.1001-1010, 2004.
DOI : 10.1038/35073673

F. E. Mcallister, M. Niepel, W. Haas, E. Huttlin, P. K. Sorger et al., Mass Spectrometry Based Method to Increase Throughput for Kinome Analyses Using ATP Probes, Analytical Chemistry, vol.85, issue.9, pp.85-4666
DOI : 10.1021/ac303478g

L. Zhang, I. P. Holmes, F. Hochgräfe, S. R. Walker, N. A. Ali et al., Characterization of the Novel Broad-Spectrum Kinase Inhibitor CTx-0294885 As an Affinity Reagent for Mass Spectrometry-Based Kinome Profiling, Journal of Proteome Research, vol.12, issue.7, pp.12-3104, 2013.
DOI : 10.1021/pr3008495

A. Stensballe, S. Andersen, and O. N. Jensen, Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off-line mass spectrometry analysis, PROTEOMICS, vol.1, issue.2, pp.207-222, 2001.
DOI : 10.1002/1615-9861(200102)1:2<207::AID-PROT207>3.0.CO;2-3

M. Kokubu, Y. Ishihama, T. Sato, T. Nagasu, and Y. Oda, Specificity of Immobilized Metal Affinity-Based IMAC/C18 Tip Enrichment of Phosphopeptides for Protein Phosphorylation Analysis, Analytical Chemistry, vol.77, issue.16, pp.77-5144, 2005.
DOI : 10.1021/ac050404f

M. Mazanek, G. Mituloviae, F. Herzog, C. Stingl, J. R. Hutchins et al., Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS/MS analysis, Nature Protocols, vol.398, issue.3, pp.1059-1069, 2007.
DOI : 10.1074/mcp.M400219-MCP200

N. Sugiyama, T. Masuda, K. Shinoda, A. Nakamura, M. Tomita et al., Phosphopeptide Enrichment by Aliphatic Hydroxy Acid-modified Metal Oxide Chromatography for Nano-LC-MS/MS in Proteomics Applications, Molecular & Cellular Proteomics, vol.24, issue.6, pp.1103-1109, 2007.
DOI : 10.1073/pnas.0609836104

J. Rush, A. Moritz, K. A. Lee, A. Guo, V. L. Goss et al., Immunoaffinity profiling of tyrosine phosphorylation in cancer cells, Nature Biotechnology, vol.100, issue.1, pp.94-101, 2005.
DOI : 10.1073/pnas.0832254100

R. Julien, Intérêts Des Marqueurs Bilogiques Dans Les Essais Cliniques, 2011.

N. L. Anderson and N. G. Anderson, The Human Plasma Proteome, Molecular & Cellular Proteomics, vol.39, issue.11, pp.845-867, 2002.
DOI : 10.1515/CCLM.2001.139

J. Graumann, N. C. Hubner, J. B. Kim, K. Ko, M. Moser et al., Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins, Molecular & Cellular Proteomics, vol.113, issue.4, pp.672-683, 2008.
DOI : 10.1091/mbc.E06-07-0624

E. I. Chen, D. Mcclatchy, S. K. Park, and J. R. Yates, Comparisons of Mass Spectrometry Compatible Surfactants for Global Analysis of the Mammalian Brain Proteome, Analytical Chemistry, vol.80, issue.22, pp.80-8694, 2008.
DOI : 10.1021/ac800606w

J. S. Brodbelt, Ion Activation Methods for Peptides and Proteins, Analytical Chemistry, vol.88, issue.1, pp.30-51
DOI : 10.1021/acs.analchem.5b04563

C. D. Kelstrup, C. Young, R. Lavallee, M. L. Nielsen, and J. Olsen, Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer, Journal of Proteome Research, vol.11, issue.6, pp.11-3487
DOI : 10.1021/pr3000249

N. L. Kelleher, Top-down Proteomics, Anal. Chem, vol.76, issue.11, pp.197-203, 2004.

A. Cristobal, F. Marino, H. Post, H. W. Van-den-toorn, S. Mohammed et al., Toward an Optimized Workflow for Middle-Down Proteomics, Analytical Chemistry, vol.89, issue.6, pp.89-3318
DOI : 10.1021/acs.analchem.6b03756

L. M. Smith and N. L. Kelleher, Proteoform: A Single Term Describing Protein Complexity. Nature methods. United States, pp.186-187, 2013.

A. D. Catherman, O. S. Skinner, and N. L. Kelleher, Top Down proteomics: Facts and perspectives, Biochemical and Biophysical Research Communications, vol.445, issue.4, pp.683-693
DOI : 10.1016/j.bbrc.2014.02.041

J. D. Worboys, J. Sinclair, Y. Yuan, and C. Jorgensen, Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome, Nature Methods, vol.11, issue.10, pp.11-1041
DOI : 10.1002/pmic.201100463

B. T. Chait and . Chemistry, Mass Spectrometry: Bottom-up or Top-Down? Science, pp.314-65, 2006.

A. Hu, W. S. Noble, and A. Wolf-yadlin, Technical advances in proteomics: new developments in data-independent acquisition, F1000Research, vol.5, 2005.
DOI : 10.12688/f1000research.7042.1

S. J. Fisher, D. C. Liebler, A. G. Paulovich, F. E. Regnier, P. Tempst et al., Multi-Site Assessment of the Precision and Reproducibility of Multiple Reaction Monitoring-Based Measurements of Proteins in Plasma, Nat Biotech, issue.7, pp.27-633, 2009.

E. Kuhn, J. R. Whiteaker, D. R. Mani, A. M. Jackson, L. Zhao et al., Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma, Molecular & Cellular Proteomics, vol.6, issue.6
DOI : 10.1016/j.jim.2004.06.002

A. B. Stergachis, B. Maclean, K. Lee, J. A. Stamatoyannopoulos, and M. J. Maccoss, Rapid empirical discovery of optimal peptides for targeted proteomics, Nature Methods, vol.13, issue.12, pp.1041-1043, 2011.
DOI : 10.1021/ac060279n

D. C. Liebler and L. J. Zimmerman, Targeted Quantitation of Proteins by Mass Spectrometry, Biochemistry, vol.52, issue.22, pp.52-3797
DOI : 10.1021/bi400110b

V. Vidova and Z. Spacil, A review on mass spectrometry-based quantitative proteomics: Targeted and data independent acquisition, Analytica Chimica Acta, vol.964, pp.7-23, 2017.
DOI : 10.1016/j.aca.2017.01.059

T. Shi, E. Song, S. Nie, K. D. Rodland, T. Liu et al., Advances in targeted proteomics and applications to biomedical research, PROTEOMICS, vol.13, issue.15-16, pp.15-16
DOI : 10.1021/pr400876p

B. Rougemont, S. Gallo, S. Ayciriex, R. Carrière, H. Hondermarck et al., Proteomic Analysis during Plant Infection, Analytical Chemistry, vol.89, issue.3, pp.89-1421
DOI : 10.1021/acs.analchem.6b03201

URL : https://hal.archives-ouvertes.fr/hal-01518912

C. A. Mueller, W. Weinmann, S. Dresen, A. Schreiber, and M. Gergov, Development of a multi-target screening analysis for 301 drugs using a QTrap liquid chromatography/tandem mass spectrometry system and automated library searching, Rapid Communications in Mass Spectrometry, vol.773, issue.10, pp.19-1332, 2005.
DOI : 10.1093/jat/16.6.351

V. Lange, P. Picotti, and B. Domon, Aebersold, R. Selected Reaction Monitoring for Quantitative Proteomics: A Tutorial, Mol. Syst. Biol, 2008.

N. Selevsek, M. Matondo, M. Sanchez-carbayo, R. Aebersold, and B. Domon, Systematic quantification of peptides/proteins in urine using selected reaction monitoring, PROTEOMICS, vol.8, issue.6, pp.1135-1147, 2011.
DOI : 10.1021/pr800401m

A. N. Hoofnagle, J. O. Becker, M. N. Oda, G. Cavigiolio, P. Mayer et al., Multiple-Reaction Monitoring-Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures, Clinical Chemistry, vol.58, issue.4, pp.777-781
DOI : 10.1373/clinchem.2011.173856

A. C. Peterson, J. D. Russell, D. J. Bailey, M. S. Westphall, and J. J. Coon, Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics, Molecular & Cellular Proteomics, vol.4, issue.11, pp.11-1475
DOI : 10.1073/pnas.1205292109

S. Gallien, E. Duriez, K. Demeure, and B. Domon, Selectivity of LC-MS/MS analysis: Implication for proteomics experiments, Journal of Proteomics, vol.81, pp.148-158, 2013.
DOI : 10.1016/j.jprot.2012.11.005

G. E. Ronsein, N. Pamir, P. D. Von-haller, D. S. Kim, M. N. Oda et al., Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics, Journal of Proteomics, vol.113, pp.388-399, 2015.
DOI : 10.1016/j.jprot.2014.10.017

URL : http://europepmc.org/articles/pmc4259393?pdf=render

P. Majovsky, C. Naumann, C. Lee, I. Lassowskat, M. Trujillo et al., Targeted Proteomics Analysis of Protein Degradation in Plant Signaling on an LTQ-Orbitrap Mass Spectrometer, Journal of Proteome Research, vol.13, issue.10, pp.13-4246
DOI : 10.1021/pr500164j

L. Morin, J. Mess, and F. Garofolo, Large-molecule quantification: sensitivity and selectivity head-to-head comparison of triple quadrupole with Q-TOF, Bioanalysis, vol.17, issue.10, pp.1181-1193
DOI : 10.1016/j.jpba.2011.11.007

N. Rauniyar, Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry, International Journal of Molecular Sciences, vol.604, issue.12, pp.16-28566
DOI : 10.1016/j.ymeth.2011.05.005

R. Aebersold and M. Mann, Mass spectrometry-based proteomics, Nature, vol.12, issue.6928, pp.198-207, 2003.
DOI : 10.1016/S0960-9822(01)00632-7

J. K. Eng, B. Fischer, J. Grossmann, and M. J. Maccoss, A Fast SEQUEST Cross Correlation Algorithm, Journal of Proteome Research, vol.7, issue.10, pp.7-4598, 2008.
DOI : 10.1021/pr800420s

T. Koenig, B. H. Menze, M. Kirchner, F. Monigatti, K. C. Parker et al., Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics, Journal of Proteome Research, vol.7, issue.9, pp.3708-3717, 2008.
DOI : 10.1021/pr700859x

J. Cox and M. Mann, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nature Biotechnology, vol.7, issue.12, pp.26-1367, 2008.
DOI : 10.1038/nprot.2007.261

N. Nagaraj, N. A. Kulak, J. Cox, N. Neuhauser, K. Mayr et al., System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap, Molecular & Cellular Proteomics, vol.83, issue.3, pp.111-013722
DOI : 10.1016/j.molcel.2010.09.024

S. Ong and M. Mann, A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC), Nature Protocols, vol.3, issue.6, pp.2650-2660, 2006.
DOI : 10.1074/mcp.M500178-MCP200

S. Wiese, K. A. Reidegeld, H. E. Meyer, and B. Warscheid, Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research, PROTEOMICS, vol.39, issue.3, pp.340-350, 2007.
DOI : 10.1002/pmic.200600422

J. Villén, S. A. Beausoleil, S. A. Gerber, and S. P. Gygi, Large-scale phosphorylation analysis of mouse liver, Proceedings of the National Academy of Sciences, vol.14, issue.6, pp.1488-1493, 2007.
DOI : 10.1101/gr.849004

A. Gavin, K. Maeda, and S. Kuhner, Recent advances in charting protein???protein interaction: mass spectrometry-based approaches, Current Opinion in Biotechnology, vol.22, issue.1, pp.42-49, 2011.
DOI : 10.1016/j.copbio.2010.09.007

J. D. Venable, M. Dong, J. Wohlschlegel, A. Dillin, and J. R. Yates, Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra, Nature Methods, vol.3, issue.1, pp.39-45, 2004.
DOI : 10.1038/nmeth705

S. Purvine, *. Eppel, J. Yi, E. C. Goodlett, and D. R. , Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer, PROTEOMICS, vol.3, issue.6, pp.847-850, 2003.
DOI : 10.1002/pmic.200300362

Y. Liu, R. Huttenhain, B. Collins, and R. Aebersold, Mass spectrometric protein maps for biomarker discovery and clinical research, Expert Review of Molecular Diagnostics, vol.20, issue.13, pp.13-811
DOI : 10.1002/rcm.2550

URL : http://www.tandfonline.com/doi/pdf/10.1586/14737159.2013.845089?needAccess=true

T. Sajic, Y. Liu, and R. Aebersold, Using data-independent, high-resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications, PROTEOMICS - Clinical Applications, vol.19, issue.3-4, pp.3-4
DOI : 10.1016/j.drudis.2013.07.008

C. Tsou, D. Avtonomov, B. Larsen, M. Tucholska, H. Choi et al., DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics, Nature Methods, vol.12, issue.3, pp.258-64
DOI : 10.1038/nbt.2839

M. Bern, G. Finney, M. R. Hoopmann, G. Merrihew, M. J. Toth et al., Deconvolution of Mixture Spectra from Ion-Trap Data-Independent-Acquisition Tandem Mass Spectrometry, Analytical Chemistry, vol.82, issue.3, pp.82-833, 2010.
DOI : 10.1021/ac901801b

Y. S. Ting, J. D. Egertson, S. H. Payne, S. Kim, B. Maclean et al., Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data, Molecular & Cellular Proteomics, vol.14, issue.9, pp.2301-2307
DOI : 10.1021/ac400476w

L. C. Gillet, P. Navarro, S. Tate, H. Rost, N. Selevsek et al., Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis, Molecular & Cellular Proteomics, vol.83, issue.6, pp.11-111
DOI : 10.1074/mcp.M111.013045

H. L. Rost, G. Rosenberger, P. Navarro, L. Gillet, S. M. Miladinovic et al., Targeted Analysis of Data-Independent Acquisition MS Data. Nature biotechnology. United States, Aebersold, R. OpenSWATH Enables Automated, issue.118, pp.219-223, 2014.

R. Bruderer, O. M. Bernhardt, T. Gandhi, S. M. Miladinovic, L. Cheng et al., Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues, Molecular & Cellular Proteomics, vol.3, issue.5, pp.1400-1410
DOI : 10.1007/s12079-014-0231-0

B. Maclean, D. M. Tomazela, N. Shulman, M. Chambers, G. L. Finney et al., Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, vol.8, issue.7, pp.26-966, 2010.
DOI : 10.1021/pr801028b

J. C. Silva, R. Denny, C. Dorschel, M. V. Gorenstein, G. Li et al., Proteome, Molecular & Cellular Proteomics, vol.116, issue.4, pp.589-607, 2006.
DOI : 10.1093/oxfordjournals.jbchem.a124616

URL : https://hal.archives-ouvertes.fr/hal-00131503

T. Geiger, J. Cox, and M. Mann, Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation, Molecular & Cellular Proteomics, vol.75, issue.10, pp.2252-2261
DOI : 10.1016/0092-8674(79)90368-4

C. R. Weisbrod, J. K. Eng, M. R. Hoopmann, T. Baker, and J. Bruce, Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification, Journal of Proteome Research, vol.11, issue.3
DOI : 10.1021/pr2008175

URL : http://europepmc.org/articles/pmc3319072?pdf=render

J. D. Egertson, A. Kuehn, G. E. Merrihew, N. W. Bateman, B. X. Maclean et al., Multiplexed MS/MS for improved data-independent acquisition, Nature Methods, vol.30, issue.8, pp.10-744
DOI : 10.1038/nbt.2377

A. Prakash, S. Peterman, S. Ahmad, D. Sarracino, B. Frewen et al., Hybrid Data Acquisition and Processing Strategies with Increased Throughput and Selectivity: pSMART Analysis for Global Qualitative and Quantitative Analysis, Journal of Proteome Research, vol.13, issue.12, pp.13-5415
DOI : 10.1021/pr5003017

Y. Liu, A. Buil, B. C. Collins, L. C. Gillet, L. C. Blum et al., Quantitative variability of 342 plasma proteins in a human twin population, Molecular Systems Biology, vol.11, issue.2, p.786
DOI : 10.15252/msb.20145728

J. Lambert, G. Ivosev, A. L. Couzens, B. Larsen, M. Taipale et al., Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition, Nature Methods, vol.10, issue.12, pp.10-1239
DOI : 10.1093/bioinformatics/19.2.185

A. Bilbao, E. Varesio, J. Luban, C. Strambio-de-castillia, G. Hopfgartner et al., Processing strategies and software solutions for data-independent acquisition in mass spectrometry, PROTEOMICS, vol.82, issue.5-6, pp.5-6
DOI : 10.1021/ac901801b

E. Nilsson, B. Pratt, B. Prazen, J. K. Eng, D. B. Martin et al., Aebersold, R. A Guided Tour of the Trans-Proteomic Pipeline, Proteomics, vol.10, issue.6, pp.1150-1159, 2010.

H. Lam and R. Aebersold, Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics, Methods, vol.54, issue.4, pp.424-431, 2011.
DOI : 10.1016/j.ymeth.2011.01.007

R. Aebersold, A Stress Test for Mass Spectrometry-Based Proteomics. Nature methods. United States, pp.411-412, 2009.

F. Kryuchkov, T. Verano-braga, T. A. Hansen, R. R. Sprenger, and F. Kjeldsen, Deconvolution of Mixture Spectra and Increased Throughput of Peptide Identification by Utilization of Intensified Complementary Ions Formed in Tandem Mass Spectrometry, Journal of Proteome Research, vol.12, issue.7, pp.12-3362, 2013.
DOI : 10.1021/pr400210m

Y. Liu, J. Chen, A. Sethi, Q. K. Li, L. Chen et al., Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness, Molecular & Cellular Proteomics, vol.33, issue.7, pp.1753-1768
DOI : 10.1200/JCO.2004.04.109

B. L. Parker, G. Yang, S. J. Humphrey, R. Chaudhuri, X. Ma et al., Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry, Science Signaling, vol.13, issue.380, pp.6-6
DOI : 10.1021/pr5006636

P. Roepstorff and J. Fohlman, Letter to the editors, 601. (139) Biemann, K. Contributions of Mass Spectrometry to Peptide and Protein Structure, pp.1-12, 1984.
DOI : 10.1042/bj2010105

R. J. Waugh and J. H. Bowie, A review of the collision-induced dissociations of deprotonated dipeptides and tripeptides. An aid to structure determination, Rapid Communications in Mass Spectrometry, vol.118, issue.119, pp.169-173, 1994.
DOI : 10.1002/rcm.1290080209

J. H. Bowie, C. S. Brinkworth, and S. Dua, Collision-induced fragmentations of the (M-H)? parent anions of underivatized peptides: An aid to structure determination and some unusual negative ion cleavages, Mass Spectrometry Reviews, vol.35, issue.2, pp.87-107, 2002.
DOI : 10.1002/1096-9888(200012)35:12<1399::AID-JMS86>3.0.CO;2-R

B. Paizs and S. Suhai, Fragmentation pathways of protonated peptides, Mass Spectrometry Reviews, vol.65, issue.191, pp.508-548, 2005.
DOI : 10.1016/S1387-3806(02)00961-2

J. Mitchell-wells and S. A. Mcluckey, Collision???Induced Dissociation (CID) of Peptides and Proteins, In Biological Mass, vol.402, issue.143, pp.148-185, 2005.
DOI : 10.1016/S0076-6879(05)02005-7

C. Cunningham, G. L. Glish, and D. J. Burinsky, High amplitude short time excitation: A method to form and detect low mass product ions in a quadrupole ion trap mass spectrometer, Journal of the American Society for Mass Spectrometry, vol.13, issue.1, pp.81-84, 2006.
DOI : 10.1002/(SICI)1097-0231(19990430)13:8<663::AID-RCM538>3.0.CO;2-H

R. A. Zubarev, A. R. Zubarev, and M. M. Savitski, Electron Capture/Transfer versus Collisionally Activated/Induced Dissociations: Solo or Duet?, Journal of the American Society for Mass Spectrometry, vol.19, issue.6, pp.753-761, 2008.
DOI : 10.1016/j.jasms.2008.03.007

S. A. Mcluckey, G. J. Van-berkel, and G. L. Glish, Tandem Mass Spectrometry of Small, Multiply Charged Oligonucleotides, Journal of the American Society for Mass Spectrometry, vol.106, issue.1, pp.60-70, 1992.
DOI : 10.1016/0168-1176(91)85020-M

A. R. Dongré, J. L. Jones, Á. Somogyi, and V. H. Wysocki, Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency:?? Evidence for the Mobile Proton Model, Journal of the American Chemical Society, vol.118, issue.35, pp.118-8365, 1996.
DOI : 10.1021/ja9542193

V. H. Wysocki, G. Tsaprailis, L. L. Smith, and L. A. Breci, Mobile and localized protons: a framework for understanding peptide dissociation, Journal of Mass Spectrometry, vol.13, issue.12, pp.35-1399, 2000.
DOI : 10.1002/(SICI)1097-0231(19991030)13:20<2040::AID-RCM754>3.0.CO;2-W

J. V. Olsen, B. Macek, O. Lange, A. Makarov, S. Horning et al., Higher-energy C-trap dissociation for peptide modification analysis, Nature Methods, vol.66, issue.9, pp.709-712, 2007.
DOI : 10.1038/nmeth1060

F. Ichou, A. Schwarzenberg, D. Lesage, S. Alves, C. Junot et al., Comparison of the activation time effects and the internal energy distributions for the CID, PQD and HCD excitation modes, Journal of Mass Spectrometry, vol.74, issue.183, pp.49-498
DOI : 10.1021/ac020547r

URL : https://hal.archives-ouvertes.fr/hal-01664188

B. A. Budnik, K. F. Haselmann, and R. A. Zubarev, Electron detachment dissociation of peptide di-anions: an electron???hole recombination phenomenon, Chemical Physics Letters, vol.342, issue.3-4, pp.342-299, 2001.
DOI : 10.1016/S0009-2614(01)00501-2

J. J. Coon, J. Shabanowitz, D. F. Hunt, and J. E. Syka, Electron transfer dissociation of peptide anions, Journal of the American Society for Mass Spectrometry, vol.73, issue.6, pp.16-880, 2005.
DOI : 10.1021/ac001130t

R. A. Zubarev, Reactions of polypeptide ions with electrons in the gas phase, Mass Spectrometry Reviews, vol.8, issue.183, pp.57-77, 2003.
DOI : 10.1255/ejms.517

K. O. Zhurov, L. Fornelli, M. D. Wodrich, U. A. Laskay, and Y. Tsybin, Principles of Electron Capture and Transfer Dissociation Mass Spectrometry Applied to Peptide and Protein Structure Analysis, Chem. Soc. Rev, vol.2013, issue.15512, pp.42-5014

R. A. Zubarev, Electron-capture dissociation tandem mass spectrometry, Current Opinion in Biotechnology, vol.15, issue.1, pp.12-16, 2004.
DOI : 10.1016/j.copbio.2003.12.002

J. E. Syka, J. J. Coon, M. J. Schroeder, J. Shabanowitz, and D. Hunt, Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry, Proc. Natl. Acad
DOI : 10.1021/pr034054u

. Sci, United States Am, pp.9528-9533, 2004.

F. Ture?ek, NC? Bond Dissociation Energies and Kinetics in Amide and Peptide Radicals. Is the Dissociation a Non-Ergodic Process?, J. Am. Chem. Soc, issue.15919, pp.125-5954, 2003.

N. Leymarie, C. E. Costello, and P. O-'connor, Electron Capture Dissociation Initiates a Free Radical Reaction Cascade, Journal of the American Chemical Society, vol.125, issue.29, pp.125-8949, 2003.
DOI : 10.1021/ja028831n

A. R. Ledvina, G. C. Mcalister, M. W. Gardner, S. I. Smith, J. A. Madsen et al., Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration Following ETD Tandem Mass Spectrometry, Angew. Chem. Int. Ed. Engl, issue.16145, pp.48-8526, 2009.
DOI : 10.1002/anie.200903557

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788484

D. M. Horn, Y. Ge, and F. W. Mclafferty, Activated Ion Electron Capture Dissociation for Mass Spectral Sequencing of Larger (42 kDa) Proteins, Analytical Chemistry, vol.72, issue.20, pp.72-4778, 2000.
DOI : 10.1021/ac000494i

T. W. Chung, C. L. Moss, M. Zimnicka, R. S. Johnson, R. L. Moritz et al., Electron-Capture and -Transfer Dissociation of Peptides Tagged with Tunable Fixed-Charge Groups: Structures and Dissociation Energetics, Journal of The American Society for Mass Spectrometry, vol.130, issue.1, pp.13-30, 2011.
DOI : 10.1021/ja805257v

B. M. Ueberheide, D. Fenyo, P. F. Alewood, and B. Chait, Rapid sensitive analysis of cysteine rich peptide venom components, Proceedings of the National Academy of Sciences, vol.17, issue.9, pp.106-6910, 2009.
DOI : 10.1016/j.jasms.2006.05.017

H. J. Cooper, K. Hakansson, and A. G. Marshall, The role of electron capture dissociation in biomolecular analysis, Mass Spectrometry Reviews, vol.8, issue.187, pp.201-222, 2005.
DOI : 10.1255/ejms.517

Y. O. Tsybin, J. P. Quinn, O. Y. Tsybin, C. L. Hendrickson, and A. G. Marshall, Electron Capture Dissociation Implementation Progress in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Journal of the American Society for Mass Spectrometry, vol.19, issue.6, pp.762-771, 2008.
DOI : 10.1016/j.jasms.2008.02.007

Y. Ge, I. N. Rybakova, Q. Xu, and R. L. Moss, Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state, Proc. Natl. Acad. Sci, pp.106-12658, 2009.
DOI : 10.1021/ac051691q

D. M. Good, M. Wirtala, G. C. Mcalister, and J. J. Coon, Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry, Molecular & Cellular Proteomics, vol.70, issue.11, pp.1942-1951, 2007.
DOI : 10.1016/S1044-0305(02)00384-7

L. Fornelli, E. Damoc, P. M. Thomas, N. L. Kelleher, K. Aizikov et al., Analysis of Intact Monoclonal Antibody IgG1 by Electron Transfer Dissociation Orbitrap FTMS, Molecular & Cellular Proteomics, vol.82, issue.12, pp.11-1758
DOI : 10.1021/ac203391z

Y. O. Tsybin, L. Fornelli, C. Stoermer, M. Luebeck, J. Parra et al., Structural Analysis of Intact Monoclonal Antibodies by Electron Transfer Dissociation Mass Spectrometry, Analytical Chemistry, vol.83, issue.23, pp.83-8919, 2011.
DOI : 10.1021/ac201293m

J. S. Brodbelt and J. J. Wilson, Infrared multiphoton dissociation in quadrupole ion traps, Mass Spectrometry Reviews, vol.15, issue.250, pp.390-424, 2009.
DOI : 10.2174/0929867023371085

W. Zhou and K. Håkansson, Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry, Current Proteomics, vol.8, issue.4, pp.297-308, 2011.
DOI : 10.2174/157016411798220826

G. C. Stafford, P. E. Kelley, J. E. Syka, W. E. Reynolds, and J. F. Todd, Recent improvements in and analytical applications of advanced ion trap technology, International Journal of Mass Spectrometry and Ion Processes, vol.60, issue.1, pp.85-98, 1984.
DOI : 10.1016/0168-1176(84)80077-4

A. H. Payne and G. L. Glish, Thermally Assisted Infrared Multiphoton Photodissociation in a Quadrupole Ion Trap, Analytical Chemistry, vol.73, issue.15, pp.73-3542, 2001.
DOI : 10.1021/ac010245+

G. A. Newsome and G. L. Glish, Improving IRMPD in a quadrupole ion trap, Journal of the American Society for Mass Spectrometry, vol.177, issue.6, pp.1127-1131, 2009.
DOI : 10.1016/S1387-3806(98)14043-5

P. M. Remes and G. L. Glish, Collisional cooling in a quadrupole ion trap at sub-ambient temperatures, International Journal of Mass Spectrometry, vol.265, issue.2-3, pp.2-3, 2007.
DOI : 10.1016/j.ijms.2007.02.004

V. H. Vartanian, B. Goolsby, and J. S. Brodbelt, Identification of tetracycline antibiotics by electrospray ionization in a quadrupole ion trap, Journal of the American Society for Mass Spectrometry, vol.109, issue.10, pp.9-1089, 1998.
DOI : 10.3181/00379727-109-27339

B. J. Goolsby and J. S. Brodbelt, Tandem Infrared Multiphoton Dissociation and Collisionally Activated Dissociation Techniques in a Quadrupole Ion Trap, Analytical Chemistry, vol.73, issue.6, pp.73-1270, 2001.
DOI : 10.1021/ac001161o

T. Doussineau, R. Antoine, M. Santacreu, and P. Dugourd, Pushing the Limit of Infrared Multiphoton Dissociation to Megadalton-Size DNA Ions, The Journal of Physical Chemistry Letters, vol.3, issue.16, pp.3-2141
DOI : 10.1021/jz300844e

C. L. Mazzitelli and J. S. Brodbelt, Probing Ligand Binding to Duplex DNA Using KMnO4 Reactions and Electrospray Ionization Tandem Mass Spectrometry, Anal. Chem, issue.12, pp.79-4636, 2007.

Y. Hashimoto, H. Hasegawa, and I. Waki, High sensitivity and broad dynamic range infrared multiphoton dissociation for a quadrupole ion trap, Rapid Communications in Mass Spectrometry, vol.14, issue.19, pp.18-2255, 2004.
DOI : 10.1002/rcm.1619

M. S. Thompson, W. Cui, and J. P. Reilly, Fragmentation of Singly Charged Peptide Ions by Photodissociation at Lambda = 157 Nm, Angew. Chem. Int. Ed. Engl, issue.36, pp.43-4791, 2004.

J. A. Madsen, D. R. Boutz, and J. S. Brodbelt, Ultrafast Ultraviolet Photodissociation at 193 nm and its Applicability to Proteomic Workflows, Journal of Proteome Research, vol.9, issue.8, pp.9-4205
DOI : 10.1021/pr100515x

M. A. Halim, M. Girod, L. Macaleese, J. Lemoine, R. Antoine et al., Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization, Journal of The American Society for Mass Spectrometry, vol.9, issue.332, pp.27-1435
DOI : 10.1021/pr901206j

URL : https://hal.archives-ouvertes.fr/hal-01344631

G. K. Yeh, Q. Sun, C. Meneses, and R. R. Julian, Rapid peptide fragmentation without electrons, collisions, infrared radiation, or native chromophores, Journal of the American Society for Mass Spectrometry, vol.130, issue.10, pp.385-393, 2009.
DOI : 10.1021/ja077690s

URL : https://link.springer.com/content/pdf/10.1016%2Fj.jasms.2008.10.019.pdf

J. P. Brien, J. M. Pruet, and J. S. Brodbelt, Chromogenic Chemical Probe for Protein Structural Characterization via Ultraviolet Photodissociation Mass Spectrometry, Anal. Chem, vol.2013, issue.15, pp.85-7391

R. Parthasarathi, Y. He, J. P. Reilly, and K. Raghavachari, New Insights into the Vacuum UV Photodissociation of Peptides, Journal of the American Chemical Society, vol.132, issue.5, pp.1606-1610, 2010.
DOI : 10.1021/ja907975v

N. Webber, Y. He, and J. P. Reilly, 157 nm Photodissociation of Dipeptide Ions Containing N-Terminal Arginine, Journal of The American Society for Mass Spectrometry, vol.31, issue.1, pp.196-203
DOI : 10.1002/(SICI)1096-9888(199605)31:5<500::AID-JMS327>3.0.CO;2-Q

L. Zhang and J. P. Reilly, Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer, Analytical Chemistry, vol.82, issue.3, pp.898-908, 2010.
DOI : 10.1021/ac902050y

L. Zhang and J. P. Reilly, De Novo Sequencing of Tryptic Peptides Derived from Deinococcus Radiodurans Ribosomal Proteins Using 157 Nm Photodissociation MALDI TOF/TOF Mass Spectrometry, J. Proteome Res, vol.2010, issue.96, pp.3025-3034

J. H. Moon, S. H. Yoon, and M. S. Kim, Photodissociation of singly protonated peptides at 193 nm investigated with tandem time-of-flight mass spectrometry, Rapid Communications in Mass Spectrometry, vol.101, issue.102, pp.19-3248, 2005.
DOI : 10.1002/rcm.2184

J. H. Moon, Y. S. Shin, H. J. Cha, and M. S. Kim, Photodissociation at 193???nm of some singly protonated peptides and proteins withm/z 2000???9000 using a tandem time-of-flight mass spectrometer equipped with a second source for delayed extraction/post-acceleration of product ions, Rapid Communications in Mass Spectrometry, vol.16, issue.158, pp.359-368, 2007.
DOI : 10.1002/rcm.2855

J. H. Moon, S. H. Yoon, Y. J. Bae, and M. S. Kim, Dissociation kinetics of singly protonated leucine enkephalin investigated by time-resolved photodissociation tandem mass spectrometry, Journal of the American Society for Mass Spectrometry, vol.74, issue.7, pp.1151-1158, 2010.
DOI : 10.1063/1.441385

K. M. Choi, S. H. Yoon, M. Sun, J. Y. Oh, J. H. Moon et al., Characteristics of photodissociation at 193 nm of singly protonated peptides generated by matrix-assisted laser desorption ionization (MALDI), Journal of the American Society for Mass Spectrometry, vol.19, issue.12, pp.17-1643, 2006.
DOI : 10.1002/rcm.2184

A. Racaud, R. Antoine, P. Dugourd, and J. Lemoine, Photoinduced Dissociation of Heparin-Derived Oligosaccharides Controlled by Charge Location, Journal of the American Society for Mass Spectrometry, vol.21, issue.12, pp.2077-2084, 2010.
DOI : 10.1016/j.jasms.2010.08.021

A. Agarwal, J. K. Diedrich, and R. R. Julian, Direct Elucidation of Disulfide Bond Partners Using Ultraviolet Photodissociation Mass Spectrometry, Analytical Chemistry, vol.83, issue.17, pp.83-6455, 2011.
DOI : 10.1021/ac201650v

X. Zhang, H. Li, B. Moore, P. Wongkongkathep, R. R. Ogorzalek-loo et al., Radical-directed dissociation of peptides and proteins by infrared multiphoton dissociation and sustained off-resonance irradiation collision-induced dissociation with Fourier transform ion cyclotron resonance mass spectrometry, Rapid Communications in Mass Spectrometry, vol.125, issue.24, pp.28-2729
DOI : 10.1021/ja028831n

B. Moore, Q. Sun, J. C. Hsu, A. H. Lee, G. C. Yoo et al., Dissociation Chemistry of Hydrogen-Deficient Radical Peptide Anions, Journal of The American Society for Mass Spectrometry, vol.108, issue.45, pp.460-468
DOI : 10.1021/jp040355v

J. K. Diedrich and R. R. Julian, Facile Identification of Phosphorylation Sites in Peptides by Radical Directed Dissociation, Analytical Chemistry, vol.83, issue.17, pp.83-6818, 2011.
DOI : 10.1021/ac201647w

Y. Tao, N. R. Quebbemann, and R. R. Julian, -Amino Acid-Containing Peptide Epimers by Radical-Directed Dissociation Mass Spectrometry, Analytical Chemistry, vol.84, issue.15, pp.6814-6820
DOI : 10.1021/ac3013434

J. R. Aponte, L. Vasicek, J. Swaminathan, H. Xu, M. C. Koag et al., Streamlining Bottom-Up Protein Identification Based on Selective Ultraviolet Photodissociation (UVPD) of Chromophore-Tagged Histidine- and Tyrosine-Containing Peptides, Analytical Chemistry, vol.86, issue.13, pp.86-6237
DOI : 10.1021/ac403654m

V. C. Cotham, Y. Wine, and J. S. Brodbelt, Selective 351 nm Photodissociation of Cysteine-Containing Peptides for Discrimination of Antigen-Binding Regions of IgG Fragments in Bottom-Up Liquid Chromatography???Tandem Mass Spectrometry Workflows, Analytical Chemistry, vol.85, issue.11, pp.85-5577
DOI : 10.1021/ac400851x

). Gates, High Performance Liquid Chromatography Mass Spectrometry

J. V. Iribarne and B. A. Thomson, On the evaporation of small ions from charged droplets, The Journal of Chemical Physics, vol.64, issue.6, pp.2287-2294, 1976.
DOI : 10.1063/1.432536

B. A. Thomson and J. Iribarne, Field induced ion evaporation from liquid surfaces at atmospheric pressure, The Journal of Chemical Physics, vol.61, issue.11, pp.71-4451, 1979.
DOI : 10.1007/BF01881023

A. Makarov, Electrostatic Axially Harmonic Orbital Trapping:?? A High-Performance Technique of Mass Analysis, Analytical Chemistry, vol.72, issue.6, pp.72-1156, 2000.
DOI : 10.1021/ac991131p

M. Hardman and A. A. Makarov, Interfacing the Orbitrap Mass Analyzer to an Electrospray Ion Source, Analytical Chemistry, vol.75, issue.7, pp.75-1699, 2003.
DOI : 10.1021/ac0258047

R. H. Perry, R. G. Cooks, and R. J. Noll, Orbitrap mass spectrometry: Instrumentation, ion motion and applications, Mass Spectrometry Reviews, vol.22, issue.57, pp.27-661, 2008.
DOI : 10.1103/PhysRevA.50.177

Q. Hu, R. J. Noll, H. Li, A. Makarov, M. Hardman et al., The Orbitrap: a new mass spectrometer, Journal of Mass Spectrometry, vol.15, issue.57, pp.430-443, 2005.
DOI : 10.1021/bk-2003-0849.ch003

A. Makarov, E. Denisov, A. Kholomeev, W. Balschun, O. Lange et al., Performance Evaluation of a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer, Analytical Chemistry, vol.78, issue.7, pp.78-2113, 2006.
DOI : 10.1021/ac0518811

A. Makarov, E. Denisov, and O. Lange, Performance evaluation of a high-field orbitrap mass analyzer, Journal of the American Society for Mass Spectrometry, vol.54, issue.14, pp.1391-1396, 2009.
DOI : 10.1016/0168-1176(83)85016-2

O. Lange, S. Horning, and M. Mann, Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-Trap, Mol. Cell. Proteomics, vol.4, issue.12, pp.2010-2021, 2005.

A. Bilbao, Y. Zhang, E. Varesio, J. Luban, C. Strambio-de-castillia et al., Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC???MS/MS, Journal of Proteome Research, vol.14, issue.11, pp.14-4581
DOI : 10.1021/acs.jproteome.5b00394

C. Shao, Y. Zhang, and W. Sun, Statistical characterization of HCD fragmentation patterns of tryptic peptides on an LTQ Orbitrap Velos mass spectrometer, Journal of Proteomics, vol.109, pp.26-37, 2014.
DOI : 10.1016/j.jprot.2014.06.012

A. Michalski, N. Neuhauser, J. Cox, and M. Mann, A Systematic Investigation into the Nature of Tryptic HCD Spectra, Journal of Proteome Research, vol.11, issue.11, pp.11-5479
DOI : 10.1021/pr3007045

. Angew, Chemie Int, pp.55-12417, 2016.

C. Serine, /. Threonine-protein-kinase, and S. Cvsahpgllqtlagplqtpr, Putative uncharacterized serine/threonine-protein kinase SgK110 CVSGSTAISTYPK Serine/threonine-protein kinase Nek11 CYEATDTETGSAYAVK Serine/threonine-protein kinase PLK3 DALDELGCFQLELR Atrial natriuretic peptide receptor B DCANVNDFFMR Serine/threonine-protein kinase RIO1 DDEYNPCQGSK Proto-oncogene tyrosine-protein kinase FGR DEQTCLMWAYEK Serine/threonine-protein kinase TNNI3K DFICHLLEK Calcium/calmodulin-dependent protein kinase type 1G DGAPQVCPIPPEQSK Serine/threonine-protein kinase MRCK beta DGVCAQIEK CaM kinase-like vesicle

E. Ste20, SPS1-related proline-alanine-rich protein kinase EATVPCSATGR Tyrosine-protein kinase-like 7

E. Serine, threonine-protein kinase PAK 1 ECVYIIPSSK Transient receptor potential cation channel subfamily M member 7 EEAFEIIVEFPETNCDVK Alpha-protein kinase 1

E. Traf2, N. Protein, and . Mast, stem cell growth factor receptor EGFCLQNVDK Ribosomal protein S6 kinase alpha-5 EGIDSECGPFIK Tyrosine-protein kinase JAK1 EIEEFLSEAACMK Proto-oncogene tyrosine-protein kinase MER EIGQCAIQISDYLK Transient receptor potential cation channel subfamily M member 6

L. Serine, threonine-protein kinase 10 LSPDLSVCGQPR Serine/threonine-protein kinase haspin LSQNACILESVSEK STE20-like serine/threonine-protein kinase LTLPIPSTCPEPFAK Mitogen-activated protein kinase kinase kinase LTLPIPSTCPEPFAR Mitogen

L. Proto-oncogene-tyrosine-protein-kinase-receptor and . Serine, threonine-protein kinase 32B LYLAENYCFDSIPK Cytoplasmic tyrosine-protein kinase BMX MCHLPEPELNK Protein kinase C theta type MEQPEGCPPK Tyrosine-protein kinase ABL2 MGGSFLICSK Chaperone activity of bc1 complex-like, mitochondrial MLCDQYYLSSPELK [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial MSPDTCATILEK Myosin IIIA MYLVMELCEDGELK Serine/threonine-protein kinase 33 NACLQTSSLAVR SCY1-like protein 2 NCLVGENLLVK BDNF/NT-3 growth factors receptor NCLVGENNVLK Proto-oncogene tyrosine-protein kinase FER NCMVAEDFTVK Insulin-like growth factor 1 receptor NCVIDDTLQVK Tyrosine-protein kinase RYK NDDGVIPCQNK Tyrosine-protein kinase Tec NDIEQLCYVLR Cell cycle

N. Serine, /. Threonine-protein-kinase-kist, and N. Tyrosine, protein kinase transmembrane receptor ROR2 NQGSELSGVISSACDK Mitotic checkpoint serine/threonine-protein kinase BUB1 NSDCVGSYTLIPYVVTATGR Mitogen-activated protein kinase kinase kinase 6 NTGIICTIGPASR Pyruvate kinase PKM NTMECSGPQDSK Serine/threonine-protein kinase ULK4 NVLVDDGLACK Tyrosine-protein kinase Srms SAESCATWK Serine/threonine-protein kinase VRK2 SAPTSPCDQEIK Protein kinase C epsilon type SCVPLSVQPTEPR SPS1/STE20-related protein kinase YSK4 SDIQDSLCYK Hormonally up-regulated neu tumor-associated kinase SDISIPCHYK Tyrosine-protein kinase ITK/TSK SDSSADCQWLDTLR Mitogen-activated protein kinase kinase kinase MLT SEPSVIIVSCK Striated muscle preferentially expressed protein kinase SEQYDLDSLCAGMEQSLR Serine

T. Serine, Serine/threonine-protein kinase 40 TCVFFEAPGVR Anti-Muellerian hormone type-2 receptor TDDLSNDVCAVLK Serine/threonine-protein kinase N2 TEPFQDGYSLCPGR Serine/threonine-protein kinase 17A TFSFCGTIEYMAPEIIR Ribosomal protein S6 kinase alpha-4 TFSPHFHHFVEQCLQR STE20-related kinase adapter protein alpha TICGTPNYLSPEVLNK Serine/threonine-protein kinase PLK2 TLCGTPEYIAPEVLLR Serine/threonine-protein kinase H2 TLGIGAFGEVCLAR Serine/threonine-protein kinase LATS1 TLGSGACGEVK Serine

T. Serine, threonine-protein kinase H1 TTSVGPSNSGGSLCAMSGR Serine/threonine-protein kinase ULK2 TVAACDLLQSLLHK Serine/threonine-protein kinase Sgk2 VCYGLGMEHLR Receptor tyrosine-protein kinase erbB