Post-translational modifications and mass spectrometry detection.

In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.

[1]  L. Jensen,et al.  Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level* , 2010, Molecular & Cellular Proteomics.

[2]  J. Yates Mass spectrometry and the age of the proteome. , 1998, Journal of mass spectrometry : JMS.

[3]  Martin R Larsen,et al.  Selective enrichment of sialic acid–containing glycopeptides using titanium dioxide chromatography with analysis by HILIC and mass spectrometry , 2010, Nature Protocols.

[4]  Richard D. Smith,et al.  Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. , 2007, Genome research.

[5]  H. Forman,et al.  Redox signaling: thiol chemistry defines which reactive oxygen and nitrogen species can act as second messengers. , 2004, American journal of physiology. Cell physiology.

[6]  W. Hancock,et al.  Automated platform for fractionation of human plasma glycoproteome in clinical proteomics. , 2010, Analytical chemistry.

[7]  John R Yates,et al.  Proteomics by mass spectrometry: approaches, advances, and applications. , 2009, Annual review of biomedical engineering.

[8]  Organic mass spectrometry at the beginning of the 21st century , 2008 .

[9]  J. Strahler,et al.  Quantifying changes in the thiol redox proteome upon oxidative stress in vivo , 2008, Proceedings of the National Academy of Sciences.

[10]  N. Blom,et al.  Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence , 2004, Proteomics.

[11]  H. Schachter,et al.  The effect of a "bisecting" N-acetylglucosaminyl group on the binding of biantennary, complex oligosaccharides to concanavalin A, Phaseolus vulgaris erythroagglutinin (E-PHA), and Ricinus communis agglutinin (RCA-120) immobilized on agarose. , 1986, Carbohydrate research.

[12]  J. Celis,et al.  A search for differential polypeptide synthesis throughout the cell cycle of HeLa cells , 1980, The Journal of cell biology.

[13]  I. Blair,et al.  Liquid chromatography/tandem mass spectrometry characterization of oxidized amyloid beta peptides as potential biomarkers of Alzheimer's disease. , 2006, Rapid communications in mass spectrometry : RCM.

[14]  N. Blom,et al.  Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry. , 2004, Journal of proteome research.

[15]  E. Meucci,et al.  Metal-catalyzed oxidation of human serum albumin: conformational and functional changes. Implications in protein aging. , 1991, The Journal of biological chemistry.

[16]  Adelina Rogowska-Wrzesinska,et al.  Protein carbonylation and metal-catalyzed protein oxidation in a cellular perspective. , 2011, Journal of proteomics.

[17]  P. Kebarle,et al.  From ions in solution to ions in the gas phase - the mechanism of electrospray mass spectrometry , 1993 .

[18]  S. A. McLuckey,et al.  Implementation of ion/ion reactions in a quadrupole/time-of-flight tandem mass spectrometer. , 2006, Analytical chemistry.

[19]  Richard D. LeDuc,et al.  Mapping Intact Protein Isoforms in Discovery Mode Using Top Down Proteomics , 2011, Nature.

[20]  W. Lehmann,et al.  Improving the precision of quantitative bottom-up proteomics based on stable isotope-labeled proteins , 2012, Analytical and Bioanalytical Chemistry.

[21]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[22]  F. McLafferty,et al.  Electrospray mass spectra from protein electroeluted from sodium dodecylsulfate polyacrylamide gel electrophoresis gels , 1999, Journal of the American Society for Mass Spectrometry.

[23]  Phillip C. Wright,et al.  An insight into iTRAQ: where do we stand now? , 2012, Analytical and Bioanalytical Chemistry.

[24]  F. Tan,et al.  Differential histone modification and protein expression associated with cell wall removal and regeneration in rice (Oryza sativa). , 2011, Journal of proteome research.

[25]  Kate S Carroll,et al.  Chemical 'omics' approaches for understanding protein cysteine oxidation in biology. , 2011, Current opinion in chemical biology.

[26]  Jay J Thelen,et al.  Modulation of Protein Phosphorylation, N-Glycosylation and Lys-Acetylation in Grape (Vitis vinifera) Mesocarp and Exocarp Owing to Lobesia botrana Infection* , 2012, Molecular & Cellular Proteomics.

[27]  Yuan Tian,et al.  Altered Expression of Sialylated Glycoproteins in Breast Cancer Using Hydrazide Chemistry and Mass Spectrometry* , 2012, Molecular & Cellular Proteomics.

[28]  K. Davies,et al.  The proteasomal system and HNE-modified proteins. , 2003, Molecular aspects of medicine.

[29]  Dietrich A. Volmer,et al.  Ion suppression: A major concern in mass spectrometry , 2006 .

[30]  J. Silberg,et al.  A transposase strategy for creating libraries of circularly permuted proteins , 2012, Nucleic acids research.

[31]  O. Jensen,et al.  Analytical strategies in mass spectrometry-based phosphoproteomics. , 2011, Methods in molecular biology.

[32]  F. Regnier,et al.  Differential carbonylation of proteins as a function of in vivo oxidative stress. , 2011, Journal of proteome research.

[33]  J. F. Nemeth-Cawley,et al.  Identification and sequencing analysis of intact proteins via collision-induced dissociation and quadrupole time-of-flight mass spectrometry. , 2002, Journal of mass spectrometry : JMS.

[34]  G. McAlister,et al.  Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry*S , 2007, Molecular & Cellular Proteomics.

[35]  O. Schilling,et al.  Glycocapture‐based proteomics for secretome analysis , 2013, Proteomics.

[36]  Leonor David,et al.  Alterations in glycosylation as biomarkers for cancer detection , 2010, Journal of Clinical Pathology.

[37]  Jürgen Cox,et al.  A systematic investigation into the nature of tryptic HCD spectra. , 2012, Journal of proteome research.

[38]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[39]  D. Desiderio,et al.  Identification and characterization of phosphorylated proteins in the human pituitary , 2004, Proteomics.

[40]  W. Vermaak,et al.  Spontaneous oxidation of methionine: effect on the quantification of plasma methionine levels. , 1997, Analytical biochemistry.

[41]  Xiaoxia Tang,et al.  Protein Adducts Generated from Products of Lipid Oxidation: Focus on HNE and ONE , 2006, Drug metabolism reviews.

[42]  T. Thannhauser,et al.  A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics. , 2007, Journal of biomolecular techniques : JBT.

[43]  Tabiwang N. Arrey,et al.  Elastase Digests , 2009, Molecular & Cellular Proteomics.

[44]  S. Gaskell,et al.  Matrix-assisted laser desorption/ionisation mass spectrometric response factors of peptides generated using different proteolytic enzymes. , 2011, Journal of mass spectrometry : JMS.

[45]  C. Deng,et al.  Concanavalin A‐immobilized magnetic nanoparticles for selective enrichment of glycoproteins and application to glycoproteomics in hepatocelluar carcinoma cell line , 2010, Proteomics.

[46]  Martin R Larsen,et al.  Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques. , 2007, Rapid communications in mass spectrometry : RCM.

[47]  F. McLafferty,et al.  Metastable-ion characteristics: characterization of isomeric molecules , 1967 .

[48]  Rainer Bischoff,et al.  Glycopeptide enrichment and separation for protein glycosylation analysis. , 2012, Journal of separation science.

[49]  M. Buse,et al.  Identification of the Major Site of O-Linked β-N-Acetylglucosamine Modification in the C Terminus of Insulin Receptor Substrate-1 *S , 2006, Molecular & Cellular Proteomics.

[50]  Guozhong Xu,et al.  Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. , 2007, Chemical reviews.

[51]  Steven P Gygi,et al.  A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.

[52]  T. Annesley Ion suppression in mass spectrometry. , 2003, Clinical chemistry.

[53]  A. Guttman,et al.  Boronic acid–lectin affinity chromatography. 1. Simultaneous glycoprotein binding with selective or combined elution , 2007, Analytical and bioanalytical chemistry.

[54]  M. Zeng,et al.  A metabolic enzyme for S-nitrosothiol conserved from bacteria to humans , 2001, Nature.

[55]  K. Abbott,et al.  Lectin-based glycoproteomic techniques for the enrichment and identification of potential biomarkers. , 2010, Methods in enzymology.

[56]  M. Mann,et al.  Higher-energy C-trap dissociation for peptide modification analysis , 2007, Nature Methods.

[57]  J. Thelen,et al.  The proteomic future: where mass spectrometry should be taking us. , 2012, The Biochemical journal.

[58]  P. James,et al.  Protein identification in the post-genome era: the rapid rise of proteomics , 1997, Quarterly Reviews of Biophysics.

[59]  J. Porath,et al.  Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. , 1986, Analytical biochemistry.

[60]  M. Chance,et al.  Radiolytic modification of sulfur-containing amino acid residues in model peptides: fundamental studies for protein footprinting. , 2005, Analytical chemistry.

[61]  David Fenyö,et al.  Protein quantitation using mass spectrometry. , 2010, Methods in molecular biology.

[62]  J R Yates,et al.  Protein sequencing by tandem mass spectrometry. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[63]  S. Shirran,et al.  A comparison of the accuracy of iTRAQ quantification by nLC-ESI MSMS and nLC-MALDI MSMS methods , 2010, Journal of proteomics.

[64]  Mingzi M. Zhang,et al.  Emerging roles for protein S-palmitoylation in immunity from chemical proteomics. , 2013, Current opinion in chemical biology.

[65]  Sebastian A. Wagner,et al.  A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles* , 2011, Molecular & Cellular Proteomics.

[66]  N. Kelleher,et al.  Toward efficient analysis of <70 kDa proteins with 100% sequence coverage , 2001 .

[67]  Bermseok Oh,et al.  Prediction of phosphorylation sites using SVMs , 2004, Bioinform..

[68]  C. Watanabe,et al.  Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[69]  M. Larsen,et al.  SIMAC (Sequential Elution from IMAC), a Phosphoproteomics Strategy for the Rapid Separation of Monophosphorylated from Multiply Phosphorylated Peptides*S , 2008, Molecular & Cellular Proteomics.

[70]  Lennart Martens,et al.  Chromatographic Isolation of Methionine-containing Peptides for Gel-free Proteome Analysis , 2002, Molecular & Cellular Proteomics.

[71]  F. McLafferty,et al.  Top down versus bottom up protein characterization by tandem high- resolution mass spectrometry , 1999 .

[72]  Manisha N. Patel,et al.  Post-Translational Oxidative Modification and Inactivation of Mitochondrial Complex I in Epileptogenesis , 2012, The Journal of Neuroscience.

[73]  M. Mann,et al.  Precision proteomics: The case for high resolution and high mass accuracy , 2008, Proceedings of the National Academy of Sciences.

[74]  G. Lubec,et al.  Differential protein levels and post-translational modifications in spinal cord injury of the rat. , 2010, Journal of proteome research.

[75]  J. Garrels Changes in protein synthesis during myogenesis in a clonal cell line. , 1979, Developmental biology.

[76]  Jennifer M. Campbell,et al.  Intact protein analysis by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[77]  M. Mann,et al.  Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation* , 2011, Molecular & Cellular Proteomics.

[78]  Pedro Domingues,et al.  Glycation and oxidation of histones H2B and H1: in vitro study and characterization by mass spectrometry , 2011, Analytical and bioanalytical chemistry.

[79]  F W McLafferty,et al.  Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. , 1994, Analytical chemistry.

[80]  A. Pitt,et al.  Protein oxidation: role in signalling and detection by mass spectrometry , 2010, Amino Acids.

[81]  M. L. Nielsen,et al.  Advances in characterizing ubiquitylation sites by mass spectrometry. , 2013, Current opinion in chemical biology.

[82]  P. O’Farrell High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[83]  Benno Schwikowski,et al.  Automated phosphopeptide identification using multiple MS/MS fragmentation modes. , 2012, Journal of proteome research.

[84]  D. Petersen,et al.  Covalent modification of amino acid nucleophiles by the lipid peroxidation products 4-hydroxy-2-nonenal and 4-oxo-2-nonenal. , 2002, Chemical research in toxicology.

[85]  W. Kolch,et al.  Proteomic analysis of phosphorylation, oxidation and nitrosylation in signal transduction. , 2006, Biochimica et biophysica acta.

[86]  Daniel Kolarich,et al.  Determination of site-specific glycan heterogeneity on glycoproteins , 2012, Nature Protocols.

[87]  John R Yates,et al.  The revolution and evolution of shotgun proteomics for large-scale proteome analysis. , 2013, Journal of the American Chemical Society.

[88]  A. Heck,et al.  Next-generation proteomics: towards an integrative view of proteome dynamics , 2012, Nature Reviews Genetics.

[89]  Trong Khoa Pham,et al.  Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ). , 2007, Journal of proteome research.

[90]  M. Mann,et al.  Global and site-specific quantitative phosphoproteomics: principles and applications. , 2009, Annual review of pharmacology and toxicology.

[91]  K. Biemann,et al.  Amino Acid Sequencing of Proteins , 1994 .

[92]  J. Shabanowitz,et al.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[93]  S. Mohammed,et al.  Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. , 2009, Journal of proteome research.

[94]  L. Huc,et al.  Chemistry and biochemistry of lipid peroxidation products , 2010, Free radical research.

[95]  S. Elledge,et al.  A quantitative atlas of mitotic phosphorylation , 2008, Proceedings of the National Academy of Sciences.

[96]  S. Brunak,et al.  Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. , 2005, Glycobiology.

[97]  Subhadip Basu,et al.  AMS 4.0: consensus prediction of post-translational modifications in protein sequences , 2012, Amino Acids.

[98]  Henrik Molina,et al.  The oxidized thiol proteome in fission yeast--optimization of an ICAT-based method to identify H2O2-oxidized proteins. , 2011, Journal of proteomics.

[99]  L. Deterding,et al.  Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: Chemical artifact or post-translational modification? , 2010, Journal of the American Society for Mass Spectrometry.

[100]  M. Hill,et al.  Lectin magnetic bead array for biomarker discovery. , 2010, Journal of proteome research.

[101]  L. Deterding,et al.  Comparison of metal and metal oxide media for phosphopeptide enrichment prior to mass spectrometric analyses , 2010, Journal of the American Society for Mass Spectrometry.

[102]  R. Vitorino,et al.  Synthesis and optimization of lectin functionalized nanoprobes for the selective recovery of glycoproteins from human body fluids. , 2011, Analytical chemistry.

[103]  L. Prokai,et al.  Detection and identification of 4‐hydroxy‐2‐nonenal Schiff‐base adducts along with products of Michael addition using data‐dependent neutral loss‐driven MS3 acquisition: Method evaluation through an in vitro study on cytochrome c oxidase modifications , 2009, Proteomics.

[104]  S. Brunak,et al.  Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis , 2010, Science Signaling.

[105]  The UniProt Consortium,et al.  Reorganizing the protein space at the Universal Protein Resource (UniProt) , 2011, Nucleic Acids Res..

[106]  K. Jennings Collision-induced decompositions of aromatic molecular ions , 1968 .

[107]  Koichi Kato [Structural biology of post-translational modifications of proteins]. , 2012, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan.

[108]  Dylan J. Sorensen,et al.  A lectin affinity workflow targeting glycosite-specific, cancer-related carbohydrate structures in trypsin-digested human plasma. , 2011, Analytical biochemistry.

[109]  M. Mann,et al.  Oxidation of peptides during electrospray ionization. , 1993, Rapid communications in mass spectrometry : RCM.

[110]  T. Griffin,et al.  Proteomic mapping of 4-hydroxynonenal protein modification sites by solid-phase hydrazide chemistry and mass spectrometry. , 2007, Analytical chemistry.

[111]  R. Vachet,et al.  Transition metal-peptide binding studied by metal-catalyzed oxidation reactions and mass spectrometry. , 2006, Analytical chemistry.

[112]  Simon J. Gaskell,et al.  The promotion of d-type ions during the low energy collision-induced dissociation of some cysteic acid-containing peptides , 1997 .

[113]  M. Karas,et al.  Influence of the wavelength in high-irradiance ultraviolet laser desorption mass spectrometry of organic molecules , 1985 .

[114]  A. Saurin,et al.  Widespread sulfenic acid formation in tissues in response to hydrogen peroxide , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[115]  T. Squier,et al.  Oxidation of Met144 and Met145 in calmodulin blocks calmodulin dependent activation of the plasma membrane Ca-ATPase. , 2003, Biochemistry.

[116]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[117]  L. F. Waanders,et al.  Top-down Protein Sequencing and MS3 on a Hybrid Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer*S , 2006, Molecular & Cellular Proteomics.

[118]  M. Bedair,et al.  Affinity chromatography with monolithic capillary columns I. Polymethacrylate monoliths with immobilized mannan for the separation of mannose-binding proteins by capillary electrochromatography and nano-scale liquid chromatography. , 2004, Journal of chromatography. A.

[119]  F. McLafferty,et al.  Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. , 2002, Journal of the American Chemical Society.

[120]  K. Gevaert,et al.  A review of COFRADIC techniques targeting protein N-terminal acetylation , 2009, BMC proceedings.

[121]  Roberto Colombo,et al.  Protein carbonylation in human diseases. , 2003, Trends in molecular medicine.

[122]  A. Pandey,et al.  Electron transfer dissociation mass spectrometry in proteomics , 2012, Proteomics.

[123]  F W McLafferty,et al.  Biomolecule Mass Spectrometry , 1999, Science.

[124]  T. Squier,et al.  Redox modulation of cellular signaling and metabolism through reversible oxidation of methionine sensors in calcium regulatory proteins. , 2005, Biochimica et biophysica acta.

[125]  A. Makarov,et al.  Interfacing the orbitrap mass analyzer to an electrospray ion source. , 2003, Analytical chemistry.

[126]  Yehia Mechref,et al.  Efficacy of glycoprotein enrichment by microscale lectin affinity chromatography. , 2008, Journal of separation science.

[127]  D L Buhrman,et al.  Quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry: A study of ion suppression , 1996, Journal of the American Society for Mass Spectrometry.

[128]  P. Domingues,et al.  Reactivity of Tyr-Leu and Leu-Tyr dipeptides: identification of oxidation products by liquid chromatography-tandem mass spectrometry. , 2009, Journal of mass spectrometry : JMS.

[129]  B. Gould,et al.  m-Aminophenylboronate affinity ligands distinguish between nonenzymically glycosylated proteins and glycoproteins. , 1987, Clinica chimica acta; international journal of clinical chemistry.

[130]  N. Yates,et al.  Detection and characterization of methionine oxidation in peptides by collision-induced dissociation and electron capture dissociation , 2003, Journal of the American Society for Mass Spectrometry.

[131]  J. Klose Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues , 1975, Humangenetik.

[132]  K. Davies,et al.  Selective degradation of oxidatively modified protein substrates by the proteasome. , 2003, Biochemical and biophysical research communications.

[133]  F. Pociot,et al.  TiSH--a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC. , 2012, Journal of proteomics.

[134]  S. Fields,et al.  Proteomics. Proteomics in genomeland. , 2001, Science.

[135]  U. Jakob,et al.  The redoxome: Proteomic analysis of cellular redox networks. , 2011, Current opinion in chemical biology.

[136]  M. Mann,et al.  Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.

[137]  Joseph A Loo,et al.  Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. , 2006, Journal of proteome research.

[138]  K. Schey,et al.  Ion trap tandem mass spectrometry of intact GTP-binding protein γ-subunits , 2001 .

[139]  Matthias Mann,et al.  A Mass Spectrometry-based Proteomic Approach for Identification of Serine/Threonine-phosphorylated Proteins by Enrichment with Phospho-specific Antibodies , 2002, Molecular & Cellular Proteomics.

[140]  F. Regnier,et al.  GAPDH is conformationally and functionally altered in association with oxidative stress in mouse models of amyotrophic lateral sclerosis. , 2008, Journal of molecular biology.

[141]  André M Deelder,et al.  Glycoproteomics based on tandem mass spectrometry of glycopeptides. , 2007, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[142]  A. Pitt,et al.  Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples. , 2013, Journal of proteomics.

[143]  S. Gaskell Electrospray: Principles and Practice , 1997 .

[144]  P. Dorrestein,et al.  The spectral networks paradigm in high throughput mass spectrometry. , 2012, Molecular bioSystems.

[145]  K. Tang,et al.  Revisit of MALDI for small proteins. , 1995, Rapid communications in mass spectrometry : RCM.

[146]  T. Rabilloud,et al.  Two-dimensional gel electrophoresis in proteomics: Past, present and future. , 2010, Journal of proteomics.

[147]  E. Shacter QUANTIFICATION AND SIGNIFICANCE OF PROTEIN OXIDATION IN BIOLOGICAL SAMPLES* , 2000, Drug metabolism reviews.

[148]  Jason C Rouse,et al.  "Top Down" characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures. , 2003, Journal of proteome research.

[149]  P. Domingues,et al.  Characterization of in vitro protein oxidation using mass spectrometry: a time course study of oxidized alpha-amylase. , 2013, Archives of biochemistry and biophysics.

[150]  R. Recker,et al.  Quantitative proteomics: measuring protein synthesis using 15N amino acid labeling in pancreatic cancer cells. , 2009, Analytical chemistry.

[151]  F W McLafferty,et al.  Localization of labile posttranslational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. , 1999, Analytical chemistry.

[152]  F. Regnier,et al.  Determining the effects of antioxidants on oxidative stress induced carbonylation of proteins. , 2011, Analytical chemistry.

[153]  S. Rhee,et al.  Reversible Inactivation of Protein-tyrosine Phosphatase 1B in A431 Cells Stimulated with Epidermal Growth Factor* , 1998, The Journal of Biological Chemistry.

[154]  M. Mann,et al.  On the Proper Use of Mass Accuracy in Proteomics* , 2007, Molecular & Cellular Proteomics.

[155]  F. McLafferty,et al.  Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process , 1998 .

[156]  D. Reichmann,et al.  Using Quantitative Redox Proteomics to Dissect the Yeast Redoxome* , 2011, The Journal of Biological Chemistry.

[157]  D. Petersen,et al.  Cysteine modification by lipid peroxidation products inhibits protein disulfide isomerase. , 2005, Chemical research in toxicology.

[158]  A. Pitt,et al.  Use of narrow mass-window, high-resolution extracted product ion chromatograms for the sensitive and selective identification of protein modifications. , 2013, Analytical chemistry.

[159]  Knut Reinert,et al.  Tools for Label-free Peptide Quantification , 2012, Molecular & Cellular Proteomics.

[160]  J. Banoub,et al.  Mass Spectrometry, Review of the Basics: Electrospray, MALDI, and Commonly Used Mass Analyzers , 2009 .

[161]  H. Wenschuh,et al.  The dominance of arginine-containing peptides in MALDI-derived tryptic mass fingerprints of proteins. , 1999, Analytical chemistry.

[162]  J. Mieyal,et al.  Glutaredoxin: role in reversible protein s-glutathionylation and regulation of redox signal transduction and protein translocation. , 2005, Antioxidants & redox signaling.

[163]  Michael Karas,et al.  100% protein sequence coverage: a modern form of surrealism in proteomics , 2011, Amino Acids.

[164]  Michael J. MacCoss,et al.  Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline , 2012, Molecular & Cellular Proteomics.

[165]  Christodoulos A. Floudas,et al.  Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database , 2011, Scientific reports.

[166]  A. Sickmann,et al.  Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications , 2008, Proteomics.

[167]  G. Scheele,et al.  Two-dimensional gel analysis of soluble proteins. Charaterization of guinea pig exocrine pancreatic proteins. , 1975, The Journal of biological chemistry.

[168]  Andrew H. Thompson,et al.  Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. , 2003, Analytical chemistry.

[169]  Mark B Cannell,et al.  Redox proteomics of thiol proteins in mouse heart during ischemia/reperfusion using ICAT reagents and mass spectrometry. , 2013, Free radical biology & medicine.

[170]  Yinsheng Wang,et al.  Fragmentation of protonated ions of peptides containing cysteine, cysteine sulfinic acid, and cysteine sulfonic acid , 2004, Journal of the American Society for Mass Spectrometry.

[171]  António S. Barros,et al.  Finding new posttranslational modifications in salivary proline‐rich proteins , 2010, Proteomics.

[172]  Solomon H. Snyder,et al.  The Biotin Switch Method for the Detection of S-Nitrosylated Proteins , 2001, Science's STKE.

[173]  Claire O'Donovan,et al.  A guide to UniProt for protein scientists. , 2011, Methods in molecular biology.

[174]  J. R. Perkins,et al.  Application of electrospray mass spectrometry and matrix-assisted laser desorption ionization time-of-flight mass spectrometry for molecular weight assignment of peptides in complex mixtures , 1993, Journal of the American Society for Mass Spectrometry.

[175]  A. Pitt,et al.  Development of novel mass spectrometric methods for identifying HOCl‐induced modifications to proteins , 2009, Proteomics.

[176]  C. Winterbourn,et al.  Thiol chemistry and specificity in redox signaling. , 2008, Free radical biology & medicine.

[177]  Ruedi Aebersold,et al.  Reproducible isolation of distinct, overlapping segments of the phosphoproteome , 2007, Nature Methods.

[178]  S. Barnes,et al.  Modification of Cytochrome c by 4-hydroxy- 2-nonenal: Evidence for histidine, lysine, and arginine-aldehyde adducts , 2004, Journal of the American Society for Mass Spectrometry.

[179]  Christodoulos A Floudas,et al.  High Throughput Characterization of Combinatorial Histone Codes* , 2009, Molecular & Cellular Proteomics.

[180]  Wei Yu,et al.  Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. , 2013, Molecular cell.

[181]  P. Domingues,et al.  Identification of isomeric spin adducts of Leu-Tyr and Tyr-Leu free radicals using liquid chromatography-tandem mass spectrometry. , 2012, Biomedical chromatography : BMC.

[182]  Pedro R Cutillas,et al.  Approaches and applications of quantitative LC-MS for proteomics and activitomics. , 2010, Methods in molecular biology.

[183]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[184]  D. Hochstrasser,et al.  From Proteins to Proteomes: Large Scale Protein Identification by Two-Dimensional Electrophoresis and Arnino Acid Analysis , 1996, Bio/Technology.

[185]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[186]  S. Mohammed,et al.  Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. , 2011, Journal of proteome research.

[187]  K. Davies,et al.  Tyrosine oxidation products: analysis and biological relevance , 2003, Amino Acids.

[188]  M. A. Moseley,et al.  Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage , 2003, Journal of the American Society for Mass Spectrometry.

[189]  Douglas H. Phanstiel,et al.  Higher-energy Collision-activated Dissociation Without a Dedicated Collision Cell* , 2011, Molecular & Cellular Proteomics.

[190]  O. Jensen Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. , 2004, Current opinion in chemical biology.

[191]  Gajendra P. S. Raghava,et al.  GlycoPP: A Webserver for Prediction of N- and O-Glycosites in Prokaryotic Protein Sequences , 2012, PloS one.

[192]  D. Liebler,et al.  Provided for Non-commercial Research and Educational Use Only. Not for Reproduction, Distribution or Commercial Use. Use of Dimedone-based Chemical Probes for Sulfenic Acid Detection: Methods to Visualize and Identify Labeled Proteins Author's Personal Copy , 2022 .

[193]  T. Niwa Mass spectrometry for the study of protein glycation in disease. , 2006, Mass spectrometry reviews.

[194]  E. W. McDaniel,et al.  Electrospray Ion Source. Another Variation on the Free-Jet Theme , 1984 .

[195]  R. Hoffmann,et al.  Mass spectrometric characterization of peptides containing different oxidized tryptophan residues. , 2011, Journal of mass spectrometry : JMS.

[196]  R. Zubarev,et al.  Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer. , 1999, Analytical chemistry.

[197]  A. Robichon,et al.  Approach to systematic analysis of serine/threonine phosphoproteome using Beta elimination and subsequent side effects: Intramolecular linkage and/or racemisation , 2007, Journal of cellular biochemistry.

[198]  Christoph H Borchers,et al.  A comparison of MS/MS‐based, stable‐isotope‐labeled, quantitation performance on ESI‐quadrupole TOF and MALDI‐TOF/TOF mass spectrometers , 2009, Proteomics.

[199]  Jie Dai,et al.  Proteome, Phosphoproteome, and Hydroxyproteome of Liver Mitochondria in Diabetic Rats at Early Pathogenic Stages* , 2009, Molecular & Cellular Proteomics.

[200]  Albert J R Heck,et al.  Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. , 2012, Analytical chemistry.

[201]  Kate S Carroll,et al.  Mining the thiol proteome for sulfenic acid modifications reveals new targets for oxidation in cells. , 2009, ACS chemical biology.

[202]  M. Isobe,et al.  Extensive investigations on oxidized amino acid residues in H(2)O(2)-treated Cu,Zn-SOd protein with LC-ESI-Q-TOF-MS, MS/MS for the determination of the copper-binding site. , 2001, Journal of the American Chemical Society.

[203]  S. Fields Proteomics in Genomeland , 2001, Science.

[204]  Alan Bridge,et al.  New and continuing developments at PROSITE , 2012, Nucleic Acids Res..

[205]  M. Hernáez,et al.  Differential carbonylation of cytoskeletal proteins in blood group O erythrocytes: potential role in protection against severe malaria. , 2012, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[206]  Suresh Mathivanan,et al.  Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry , 2007, Proceedings of the National Academy of Sciences.

[207]  R. Bose,et al.  Identification of Targets of c-Src Tyrosine Kinase by Chemical Complementation and Phosphoproteomics* , 2012, Molecular & Cellular Proteomics.

[208]  C. Enke,et al.  Predicting electrospray response from chromatographic retention time. , 2001, Analytical chemistry.

[209]  J. Fíla,et al.  Enrichment techniques employed in phosphoproteomics , 2011, Amino Acids.

[210]  Qiang Gao,et al.  Oxidative stress induced carbonylation in human plasma. , 2011, Journal of proteomics.

[211]  M. Davies,et al.  Quantification of protein modification by oxidants. , 2009, Free radical biology & medicine.

[212]  D. Barofsky,et al.  Complementary use of MALDI and ESI for the HPLC-MS/MS analysis of DNA-binding proteins. , 2004, Analytical chemistry.

[213]  F. Oesch,et al.  Fractionation of membrane proteins on immobilized lectins by high-performance liquid affinity chromatography. , 1985, Analytical biochemistry.

[214]  K. Tomer,et al.  Discrimination effects and sensitivity variations in matrix‐assisted laser desorption/ionization , 1997 .

[215]  L. Huc,et al.  Chemistry and biochemistry of lipid peroxidation products. Free Radic Res , 2010 .

[216]  S. Carr,et al.  Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry. , 2001, Analytical chemistry.

[217]  Daniel S Spellman,et al.  Characterization by tandem mass spectrometry of stable cysteine sulfenic acid in a cysteine switch peptide of matrix metalloproteinases , 2007, Journal of the American Society for Mass Spectrometry.

[218]  Hamid Mirzaei,et al.  Enrichment of carbonylated peptides using Girard P reagent and strong cation exchange chromatography. , 2006, Analytical chemistry.

[219]  B Alex Merrick,et al.  Proteomic Profiling of S-acylated Macrophage Proteins Identifies a Role for Palmitoylation in Mitochondrial Targeting of Phospholipid Scramblase 3* , 2011, Molecular & Cellular Proteomics.

[220]  D. Petersen,et al.  Reactions of 4-hydroxynonenal with proteins and cellular targets. , 2004, Free radical biology & medicine.

[221]  S. Mohammed,et al.  Phosphopeptide Fragmentation and Analysis by Mass Spectrometry , 2010 .

[222]  P. Domingues,et al.  Cross-oxidation of angiotensin II by glycerophosphatidylcholine oxidation products. , 2011, Rapid communications in mass spectrometry : RCM.

[223]  S. Patterson Data analysis—the Achilles heel of proteomics , 2003, Nature Biotechnology.

[224]  Hui Li,et al.  In silico prediction of post-translational modifications. , 2011, Methods in molecular biology.

[225]  N G Anderson,et al.  High resolution two-dimensional electrophoresis of human plasma proteins. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[226]  Yin-kun Liu,et al.  Lectin‐based glycoproteomics to explore and analyze hepatocellular carcinoma‐related glycoprotein markers , 2009, Electrophoresis.

[227]  H. Masumoto,et al.  Comprehensive profiling of histone modifications using a label-free approach and its applications in determining structure-function relationships. , 2008, Analytical chemistry.

[228]  J. Workman,et al.  Introducing the acetylome , 2009, Nature Biotechnology.

[229]  P. Cutillas,et al.  Advances in phosphopeptide enrichment techniques for phosphoproteomics , 2012, Amino Acids.

[230]  Samie R Jaffrey,et al.  Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling , 2010, Nature Biotechnology.

[231]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[232]  Dirkje S Postma,et al.  Protein tyrosine nitration: selectivity, physicochemical and biological consequences, denitration, and proteomics methods for the identification of tyrosine-nitrated proteins. , 2009, Journal of proteome research.

[233]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[234]  C. Spickett The lipid peroxidation product 4-hydroxy-2-nonenal: Advances in chemistry and analysis☆ , 2013, Redox biology.

[235]  Albert Sickmann,et al.  State‐of‐the‐art in phosphoproteomics , 2005, Proteomics.

[236]  M. Larsen,et al.  Technologies and challenges in large‐scale phosphoproteomics , 2013, Proteomics.

[237]  J. W. Finch,et al.  Mass spectrometric identification of modifications to human serum albumin treated with hydrogen peroxide. , 1993, Archives of biochemistry and biophysics.

[238]  Yu Xue,et al.  A summary of computational resources for protein phosphorylation. , 2010, Current protein & peptide science.

[239]  R. Aebersold,et al.  Mass Spectrometry and Protein Analysis , 2006, Science.

[240]  K. Dreisewerd The Desorption Process in MALDI , 2003 .

[241]  K. Resing,et al.  Mapping protein post-translational modifications with mass spectrometry , 2007, Nature Methods.

[242]  J. Ellenberg,et al.  The quantitative proteome of a human cell line , 2011, Molecular systems biology.

[243]  P. Argos,et al.  Automated protein sequence pattern handling and PROSITE searching , 1991, Comput. Appl. Biosci..

[244]  P. Domingues,et al.  Oxidation of bovine serum albumin: identification of oxidation products and structural modifications. , 2009, Rapid communications in mass spectrometry : RCM.

[245]  Kuo-Chen Chou,et al.  Predicting protein oxidation sites with feature selection and analysis approach , 2012, Journal of biomolecular structure & dynamics.

[246]  M. J. Wood,et al.  A genetically encoded probe for cysteine sulfenic acid protein modification in vivo. , 2007, Biochemistry.

[247]  K. Tomer,et al.  Effects of anion proximity in peptide primary sequence on the rate and mechanism of leucine oxidation. , 2006, Analytical chemistry.

[248]  P. Cutillas,et al.  Global profiling of protein kinase activities in cancer cells by mass spectrometry. , 2012, Journal of proteomics.

[249]  E. Stadtman,et al.  Free radical-mediated oxidation of free amino acids and amino acid residues in proteins , 2003, Amino Acids.

[250]  F. Dubois,et al.  The Matrix Suppression Effect and Ionization Mechanisms in Matrix‐assisted Laser Desorption/Ionization , 1996 .

[251]  J. Tabet,et al.  Study of protein modification by 4-hydroxy-2-nonenal and other short chain aldehydes analyzed by electrospray ionization tandem mass spectrometry , 2003, Journal of the American Society for Mass Spectrometry.

[252]  Søren Brunak,et al.  Prediction of Glycosylation Across the Human Proteome and the Correlation to Protein Function , 2001, Pacific Symposium on Biocomputing.

[253]  Sean L Seymour,et al.  The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra*S , 2007, Molecular & Cellular Proteomics.

[254]  Koichi Tanaka,et al.  Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry , 1988 .

[255]  K. Davies,et al.  Protein turnover by the proteasome in aging and disease. , 2002, Free radical biology & medicine.

[256]  Michael G. Ikonomou,et al.  Investigations of the electrospray interface for liquid chromatography/mass spectrometry , 1990 .

[257]  D. Figeys,et al.  Advancements in top-down proteomics. , 2012, Analytical chemistry.

[258]  Jonathan C Trinidad,et al.  O-Linked N-Acetylglucosamine Proteomics of Postsynaptic Density Preparations Using Lectin Weak Affinity Chromatography and Mass Spectrometry*S , 2006, Molecular & Cellular Proteomics.

[259]  R. Hoffmann,et al.  Identification of carbonylated peptides by tandem mass spectrometry using a precursor ion-like scan in negative ion mode. , 2011, Journal of proteomics.

[260]  J. Tabet,et al.  Immunoaffinity purification and characterization of 4-hydroxy-2-nonenal- and malondialdehyde-modified peptides by electrospray ionization tandem mass spectrometry. , 2002, Analytical chemistry.

[261]  Andrea Urbani,et al.  Unraveling the different proteomic platforms. , 2013, Journal of separation science.

[262]  A. Guttman,et al.  Boronic acid lectin affinity chromatography (BLAC). 2. Affinity micropartitioning-mediated comparative glycosylation profiling , 2008, Analytical and bioanalytical chemistry.

[263]  D. Petersen,et al.  Inhibition of Hsp72-mediated protein refolding by 4-hydroxy-2-nonenal. , 2004, Chemical research in toxicology.

[264]  Karl Mechtler,et al.  Improved Precision of iTRAQ and TMT Quantification by an Axial Extraction Field in an Orbitrap HCD Cell , 2011, Analytical chemistry.

[265]  Ruedi Aebersold,et al.  Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry , 2003, Nature Biotechnology.

[266]  Akira Sano,et al.  Titania as a Chemo-affinity Support for the Column-switching HPLC Analysis of Phosphopeptides: Application to the Characterization of Phosphorylation Sites in Proteins by Combination with Protease Digestion and Electrospray Ionization Mass Spectrometry , 2004, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.