Applications of Targeted Proteomics in Systems Biology and Translational Medicine, Proteomics, vol.2015, issue.118, pp.15-3193 ,
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
High Resolution Two-Dimensional Electrophoresis of Proteins, J. Biol. Chem, issue.310, pp.250-4007, 1975. ,
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. ,
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
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
Ultraviolet photofragmentation of biomolecular ions, Mass Spectrometry Reviews, vol.120, issue.102, pp.425-447, 2009. ,
DOI : 10.1002/jms.703
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
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
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
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
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
What are biomarkers?, Current Opinion in HIV and AIDS, vol.5, issue.6, pp.463-466, 2010. ,
DOI : 10.1097/COH.0b013e32833ed177
Urinary Sugars???A Biomarker of Total Sugars Intake, Nutrients, vol.142, issue.7, pp.5816-5833 ,
DOI : 10.3945/ajcn.114.095604
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
Stimulus-dependent dynamics of p53 in single cells, Molecular Systems Biology, vol.58, issue.1, 2011. ,
DOI : 10.1101/GAD.827700
Sickle Cell Anemia, a Molecular Disease, Science, vol.110, issue.2865, pp.543-548, 1949. ,
DOI : 10.1126/science.110.2865.543
PRODUCTION OF EMBRYONAL ??-GLOBULIN BY TRANSPLANTABLE MOUSE HEPATOMAS, Transplantation, vol.1, issue.2, pp.174-180, 1963. ,
DOI : 10.1097/00007890-196301020-00004
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
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
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
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
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
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
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
The Enzymatic Phosphorylation of Proteins, J. Biol. Chem, vol.211, issue.2, pp.969-980, 1954. ,
The origins of protein phosphorylation, Nature Cell Biology, vol.1, issue.5, pp.127-130, 2002. ,
DOI : 10.1038/nrd773
The Protein Kinase Complement of the Human Genome, Science, vol.298, issue.5600, pp.298-1912, 2002. ,
DOI : 10.1126/science.1075762
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
Cell Cycle: Principles of Control, Yale J. Biol. Med, vol.80, issue.3, pp.141-142, 2007. ,
Phospholamban: A Key Determinant of Cardiac Function and Dysfunction, Arch. Mal. Coeur Vaiss, issue.12, pp.98-1239, 2005. ,
Rising behind NO: cGMP-Dependent Protein Kinases, J. Cell Sci, vol.113, pp.1671-1676, 2000. ,
CASEIN KINASE I: ANOTHER COG IN THE CIRCADIAN CLOCKWORKS, Chronobiology International, vol.291, issue.3, pp.389-398, 2001. ,
DOI : 10.1126/science.1057499
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
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
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
Kinetic and Catalytic Mechanisms of Protein Kinases, Chemical Reviews, vol.101, issue.8, pp.2271-2290, 2001. ,
DOI : 10.1021/cr000230w
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
Regulation of Protein Kinases, Molecular Cell, vol.15, issue.5, pp.661-675, 2004. ,
DOI : 10.1016/j.molcel.2004.08.024
MAP kinase signalling pathways in cancer, Oncogene, vol.4, issue.22, pp.3279-3290 ,
DOI : 10.1158/0008-5472.CAN-05-0115
A census of amplified and overexpressed human cancer genes, Nature Reviews Cancer, vol.68, issue.1, pp.59-64, 2010. ,
DOI : 10.1038/nrc2771
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
Mitogen-Activated Protein Kinases in Heart Development and Diseases, Circulation, vol.116, issue.12, pp.1413-1423, 2007. ,
DOI : 10.1161/CIRCULATIONAHA.106.679589
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
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
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
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
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
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
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
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
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
Immunoaffinity profiling of tyrosine phosphorylation in cancer cells, Nature Biotechnology, vol.100, issue.1, pp.94-101, 2005. ,
DOI : 10.1073/pnas.0832254100
Intérêts Des Marqueurs Bilogiques Dans Les Essais Cliniques, 2011. ,
The Human Plasma Proteome, Molecular & Cellular Proteomics, vol.39, issue.11, pp.845-867, 2002. ,
DOI : 10.1515/CCLM.2001.139
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
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
Ion Activation Methods for Peptides and Proteins, Analytical Chemistry, vol.88, issue.1, pp.30-51 ,
DOI : 10.1021/acs.analchem.5b04563
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
Top-down Proteomics, Anal. Chem, vol.76, issue.11, pp.197-203, 2004. ,
Toward an Optimized Workflow for Middle-Down Proteomics, Analytical Chemistry, vol.89, issue.6, pp.89-3318 ,
DOI : 10.1021/acs.analchem.6b03756
Proteoform: A Single Term Describing Protein Complexity. Nature methods. United States, pp.186-187, 2013. ,
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
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
Mass Spectrometry: Bottom-up or Top-Down? Science, pp.314-65, 2006. ,
Technical advances in proteomics: new developments in data-independent acquisition, F1000Research, vol.5, 2005. ,
DOI : 10.12688/f1000research.7042.1
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. ,
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
Rapid empirical discovery of optimal peptides for targeted proteomics, Nature Methods, vol.13, issue.12, pp.1041-1043, 2011. ,
DOI : 10.1021/ac060279n
Targeted Quantitation of Proteins by Mass Spectrometry, Biochemistry, vol.52, issue.22, pp.52-3797 ,
DOI : 10.1021/bi400110b
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
Advances in targeted proteomics and applications to biomedical research, PROTEOMICS, vol.13, issue.15-16, pp.15-16 ,
DOI : 10.1021/pr400876p
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
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
Aebersold, R. Selected Reaction Monitoring for Quantitative Proteomics: A Tutorial, Mol. Syst. Biol, 2008. ,
Systematic quantification of peptides/proteins in urine using selected reaction monitoring, PROTEOMICS, vol.8, issue.6, pp.1135-1147, 2011. ,
DOI : 10.1021/pr800401m
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
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
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
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
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
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
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
Mass spectrometry-based proteomics, Nature, vol.12, issue.6928, pp.198-207, 2003. ,
DOI : 10.1016/S0960-9822(01)00632-7
A Fast SEQUEST Cross Correlation Algorithm, Journal of Proteome Research, vol.7, issue.10, pp.7-4598, 2008. ,
DOI : 10.1021/pr800420s
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
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
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
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
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
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
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
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
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
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
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
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics, Nature Methods, vol.12, issue.3, pp.258-64 ,
DOI : 10.1038/nbt.2839
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
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
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
Targeted Analysis of Data-Independent Acquisition MS Data. Nature biotechnology. United States, Aebersold, R. OpenSWATH Enables Automated, issue.118, pp.219-223, 2014. ,
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
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
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
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
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
Multiplexed MS/MS for improved data-independent acquisition, Nature Methods, vol.30, issue.8, pp.10-744 ,
DOI : 10.1038/nbt.2377
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
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
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
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
Aebersold, R. A Guided Tour of the Trans-Proteomic Pipeline, Proteomics, vol.10, issue.6, pp.1150-1159, 2010. ,
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
A Stress Test for Mass Spectrometry-Based Proteomics. Nature methods. United States, pp.411-412, 2009. ,
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
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
Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry, Science Signaling, vol.13, issue.380, pp.6-6 ,
DOI : 10.1021/pr5006636
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
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
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
Fragmentation pathways of protonated peptides, Mass Spectrometry Reviews, vol.65, issue.191, pp.508-548, 2005. ,
DOI : 10.1016/S1387-3806(02)00961-2
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
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
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
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
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
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
Higher-energy C-trap dissociation for peptide modification analysis, Nature Methods, vol.66, issue.9, pp.709-712, 2007. ,
DOI : 10.1038/nmeth1060
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
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
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
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
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 ,
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
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry, Proc. Natl. Acad ,
DOI : 10.1021/pr034054u
United States Am, pp.9528-9533, 2004. ,
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. ,
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
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
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
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
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
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
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
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
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
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
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
Infrared multiphoton dissociation in quadrupole ion traps, Mass Spectrometry Reviews, vol.15, issue.250, pp.390-424, 2009. ,
DOI : 10.2174/0929867023371085
Structural Characterization of Carbohydrates by Fourier Transform Tandem Mass Spectrometry, Current Proteomics, vol.8, issue.4, pp.297-308, 2011. ,
DOI : 10.2174/157016411798220826
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
Thermally Assisted Infrared Multiphoton Photodissociation in a Quadrupole Ion Trap, Analytical Chemistry, vol.73, issue.15, pp.73-3542, 2001. ,
DOI : 10.1021/ac010245+
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
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
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
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
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
Probing Ligand Binding to Duplex DNA Using KMnO4 Reactions and Electrospray Ionization Tandem Mass Spectrometry, Anal. Chem, issue.12, pp.79-4636, 2007. ,
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
Fragmentation of Singly Charged Peptide Ions by Photodissociation at Lambda = 157 Nm, Angew. Chem. Int. Ed. Engl, issue.36, pp.43-4791, 2004. ,
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
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
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
Chromogenic Chemical Probe for Protein Structural Characterization via Ultraviolet Photodissociation Mass Spectrometry, Anal. Chem, vol.2013, issue.15, pp.85-7391 ,
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
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
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
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 ,
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
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
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
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
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
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
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
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
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
-Amino Acid-Containing Peptide Epimers by Radical-Directed Dissociation Mass Spectrometry, Analytical Chemistry, vol.84, issue.15, pp.6814-6820 ,
DOI : 10.1021/ac3013434
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
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
High Performance Liquid Chromatography Mass Spectrometry ,
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
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
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
Interfacing the Orbitrap Mass Analyzer to an Electrospray Ion Source, Analytical Chemistry, vol.75, issue.7, pp.75-1699, 2003. ,
DOI : 10.1021/ac0258047
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
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
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
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
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. ,
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
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 Systematic Investigation into the Nature of Tryptic HCD Spectra, Journal of Proteome Research, vol.11, issue.11, pp.11-5479 ,
DOI : 10.1021/pr3007045
Chemie Int, pp.55-12417, 2016. ,
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 ,
SPS1-related proline-alanine-rich protein kinase EATVPCSATGR Tyrosine-protein kinase-like 7 ,
threonine-protein kinase PAK 1 ECVYIIPSSK Transient receptor potential cation channel subfamily M member 7 EEAFEIIVEFPETNCDVK Alpha-protein kinase 1 ,
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 ,
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 ,
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 ,
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 ,
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 ,
threonine-protein kinase H1 TTSVGPSNSGGSLCAMSGR Serine/threonine-protein kinase ULK2 TVAACDLLQSLLHK Serine/threonine-protein kinase Sgk2 VCYGLGMEHLR Receptor tyrosine-protein kinase erbB ,