Current strategies and findings in clinically relevant post-translational modification-specific proteomics

References

• UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res 2015;43(D1):D204-12
   PubMed Web of Science ®Google Scholar
• Okada M. Post-translational isoprenylation of tryptophan. Biosci Biotechnol Biochem 2011;75(8):1413-17
   PubMed Web of Science ®Google Scholar
• Nolan EM, Walsh CT. Investigations of the MceIJ-catalyzed posttranslational modification of the microcin E492 C-terminus: linkage of ribosomal and nonribosomal peptides to form “trojan horse” antibiotics. Biochemistry 2008;47(35):9289-99
   PubMed Web of Science ®Google Scholar
• Hornbeck PV, Kornhauser JM, Tkachev S, et al. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 2012;40(Database issue):D261-70
   PubMedGoogle Scholar
• Thaysen-Andersen M, Packer NH. Advances in LC-MS/MS-based glycoproteomics: getting closer to system-wide site-specific mapping of the N- and O-glycoproteome. Biochim Biophys Acta 2014;1844(9):1437-52
   PubMed Web of Science ®Google Scholar
• Tutturen AE, Fleckenstein B, de Souza GA. Assessing the citrullinome in rheumatoid arthritis synovial fluid with and without enrichment of citrullinated peptides. J Proteome Res 2014;13(6):2867-73
   PubMed Web of Science ®Google Scholar
• Doll S, Burlingame AL. Mass spectrometry-based detection and assignment of protein posttranslational modifications. ACS Chem Biol 2015;10(1):63-71
   PubMed Web of Science ®Google Scholar
• Hornbeck PV, Zhang B, Murray B, et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 2015;43(Database issue):D512-20
   PubMed Web of Science ®Google Scholar
• Matic I, Ahel I, Hay RT. Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat Methods 2012;9(8):771-2
   PubMed Web of Science ®Google Scholar
• Martens L, Hermjakob H, Jones P, et al. PRIDE: the proteomics identifications database. Proteomics 2005;5(13):3537-45
   PubMed Web of Science ®Google Scholar
• Vizcaino JA, Deutsch EW, Wang R, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2014;32(3):223-6
   PubMed Web of Science ®Google Scholar
• Vaudel M, Burkhart JM, Zahedi RP, et al. PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 2015;33(1):22-4
   PubMed Web of Science ®Google Scholar
• Hunter T. The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol Cell 2007;28(5):730-8
   PubMed Web of Science ®Google Scholar
• Lothrop AP, Torres MP, Fuchs SM. Deciphering post-translational modification codes. FEBS Lett 2013;587(8):1247-57
   PubMed Web of Science ®Google Scholar
• Peng M, Scholten A, Heck AJ, van Breukelen B. Identification of enriched PTM crosstalk motifs from large-scale experimental data sets. J Proteome Res 2014;13(1):249-59
   PubMed Web of Science ®Google Scholar
• Venne AS, Kollipara L, Zahedi RP. The next level of complexity: crosstalk of posttranslational modifications. Proteomics 2014;14(4-5):513-24
   PubMed Web of Science ®Google Scholar
• Pasing Y, Sickmann A, Lewandrowski U. N-glycoproteomics: mass spectrometry-based glycosylation site annotation. Biol Chem 2012;393(4):249-58
   PubMed Web of Science ®Google Scholar
• Di Palma S, Zoumaro-Djayoon A, Peng M, et al. Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography. J Proteomics 2013;91:331-7
   PubMed Web of Science ®Google Scholar
• Beck F, Geiger J, Gambaryan S, et al. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood 2014;123(5):e1-e10
   PubMed Web of Science ®Google Scholar
• Loroch S, Zahedi RP, Sickmann A. Highly sensitive phosphoproteomics by tailoring solid-phase extraction to electrostatic repulsion-hydrophilic interaction chromatography. Anal Chem 2015;87(3):1596-604
   PubMed Web of Science ®Google Scholar
• Burkhart JM, Schumbrutzki C, Wortelkamp S, et al. Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J Proteomics 2012;75(4):1454-62
   PubMed Web of Science ®Google Scholar
• Meyer JG, Kim S, Maltby DA, et al. Expanding proteome coverage with orthogonal-specificity alpha-lytic proteases. Mol Cell Proteomics 2014;13(3):823-35
   PubMed Web of Science ®Google Scholar
• Loroch S, Dickhut C, Zahedi RP, Sickmann A. Phosphoproteomics–more than meets the eye. Electrophoresis 2013;34(11):1483-92
   PubMedGoogle Scholar
• Rogers LD, Overall CM. Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics 2013;12(12):3532-42
   PubMed Web of Science ®Google Scholar
• Pinkse MW, Uitto PM, Hilhorst MJ, et al. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 2004;76(14):3935-43
   PubMed Web of Science ®Google Scholar
• Mithoe SC, Boersema PJ, Berke L, et al. Targeted quantitative phosphoproteomics approach for the detection of phospho-tyrosine signaling in plants. J Proteome Res 2012;11(1):438-48
   PubMed Web of Science ®Google Scholar
• Batth TS, Francavilla C, Olsen JV. Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics. J Proteome Res 2014;13(12):6176-86
   PubMed Web of Science ®Google Scholar
• Parker BL, Thaysen-Andersen M, Solis N, et al. Site-specific glycan-peptide analysis for determination of N-glycoproteome heterogeneity. J Proteome Res 2013;12(12):5791-800
   PubMed Web of Science ®Google Scholar
• Peng J, Elias JE, Thoreen CC, et al. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2003;2(1):43-50
   PubMed Web of Science ®Google Scholar
• Lohrig K, Sickmann A, Lewandrowski U. Strong cation exchange chromatography for analysis of sialylated glycopeptides. Methods Mol Biol 2011;753:299-308
   PubMedGoogle Scholar
• Venne AS, Vogtle FN, Meisinger C, et al. Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase Icp55. J Proteome Res 2013;12(9):3823-30
   PubMed Web of Science ®Google Scholar
• Engholm-Keller K, Birck P, Storling J, et al. TiSH–a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC. J Proteomics 2012;75(18):5749-61
   PubMed Web of Science ®Google Scholar
• Zhou H, Di Palma S, Preisinger C, et al. Toward a comprehensive characterization of a human cancer cell phosphoproteome. J Proteome Res 2013;12(1):260-71
   PubMed Web of Science ®Google Scholar
• Cheng K, Chen R, Seebun D, et al. Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. J Proteomics 2014;110:145-54
   PubMed Web of Science ®Google Scholar
• Valastyan S, Weinberg RA. Tumor metastasis: molecular insights and evolving paradigms. Cell 2011;147(2):275-92
   PubMed Web of Science ®Google Scholar
• Kabashima-Niibe A, Higuchi H, Takaishi H, et al. Mesenchymal stem cells regulate epithelial-mesenchymal transition and tumor progression of pancreatic cancer cells. Cancer Sci 2013;104(2):157-64
   PubMed Web of Science ®Google Scholar
• Ficarro SB, Zhang Y, Carrasco-Alfonso MJ, et al. Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis. Mol Cell Proteomics 2011;10(11):O111 011064
   Web of Science ®Google Scholar
• Megger DA, Bracht T, Meyer HE, Sitek B. Label-free quantification in clinical proteomics. Biochim Biophys Acta 2013;1834(8):1581-90
   PubMed Web of Science ®Google Scholar
• Hu B, Niu X, Cheng L, et al. Discovering cancer biomarkers from clinical samples by protein microarrays. Proteomics Clin Appl 2015;9(1-2):98-110
   PubMed Web of Science ®Google Scholar
• Parker CE, Borchers CH. Mass spectrometry based biomarker discovery, verification, and validation – Quality assurance and control of protein biomarker assays. Mol Oncol 2014;8(4):840-58
   PubMed Web of Science ®Google Scholar
• Manza LL, Stamer SL, Ham AJ, et al. Sample preparation and digestion for proteomic analyses using spin filters. Proteomics 2005;5(7):1742-5
   PubMed Web of Science ®Google Scholar
• Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Meth 2009;6(5):359-62
   PubMed Web of Science ®Google Scholar
• Hughes CS, Foehr S, Garfield DA, et al. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 2014;10:757
   PubMed Web of Science ®Google Scholar
• Masuda T, Sugiyama N, Tomita M, Ishihama Y. Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. Anal Chem 2011;83(20):7698-703
   PubMed Web of Science ®Google Scholar
• Lam MP, Lau E, Siu SO, et al. Online combination of reversed-phase/reversed-phase and porous graphitic carbon liquid chromatography for multicomponent separation of proteomics and glycoproteomics samples. Electrophoresis 2011;32(21):2930-40
   PubMed Web of Science ®Google Scholar
• Olsen JV, Mann M. Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics 2013;12(12):3444-52
   PubMed Web of Science ®Google Scholar
• Zybailov B, Mosley AL, Sardiu ME, et al. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 2006;5(9):2339-47
   PubMed Web of Science ®Google Scholar
• Wang W, Zhou H, Lin H, et al. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 2003;75(18):4818-26
   PubMed Web of Science ®Google Scholar
• Vaudel M, Burkhart JM, Breiter D, et al. A complex standard for protein identification, designed by evolution. J Proteome Res 2012;11(10):5065-71
   PubMed Web of Science ®Google Scholar
• Cox J, Hein MY, Luber CA, et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Molecular Cell Proteomics 2014;13(9):2513-26
   PubMed Web of Science ®Google Scholar
• Luber CA, Cox J, Lauterbach H, et al. Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010;32(2):279-89
   PubMed Web of Science ®Google Scholar
• Geiger T, Cox J, Ostasiewicz P, et al. Super-SILAC mix for quantitative proteomics of human tumor tissue. Nat Methods 2010;7(5):383-5
   PubMed Web of Science ®Google Scholar
• Schweppe DK, Rigas JR, Gerber SA. Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors. J Proteomics 2013;91:286-96
   PubMed Web of Science ®Google Scholar
• Boersema PJ, Geiger T, Wisniewski JR, Mann M. Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Mol Cell Proteomics 2013;12(1):158-71
   PubMed Web of Science ®Google Scholar
• Melo-Braga MN, Schulz M, Liu Q, et al. Comprehensive quantitative comparison of the membrane proteome, phosphoproteome, and sialiome of human embryonic and neural stem cells. Mol Cell Proteomics 2014;13(1):311-28
   PubMed Web of Science ®Google Scholar
• Jentoft N, Dearborn DG. Labeling of proteins by reductive methylation using sodium cyanoborohydride. J Biol Chem 1979;254(11):4359-65
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3(12):1154-69
   PubMed Web of Science ®Google Scholar
• Treitz C, Cassidy L, Hockendorf A, et al. Quantitative proteome analysis of Caenorhabditis elegans upon exposure to nematicidal Bacillus thuringiensis. J Proteomics 2015;113:337-50
   PubMed Web of Science ®Google Scholar
• Thompson A, Schafer J, Kuhn K, et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003;75(8):1895-904
   PubMed Web of Science ®Google Scholar
• Erickson BK, Jedrychowski MP, McAlister GC, et al. Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/Orbitrap mass spectrometer. Anal Chem 2015;87(2):1241-9
   PubMed Web of Science ®Google Scholar
• Venne AS, Solari FA, Faden F, et al. An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana, Proteomics 2015; In press
   Google Scholar
• Thingholm TE, Palmisano G, Kjeldsen F, Larsen MR. Undesirable charge-enhancement of isobaric tagged phosphopeptides leads to reduced identification efficiency. J Proteome Res 2010;9(8):4045-52
   PubMed Web of Science ®Google Scholar
• Pichler P, Köcher T, Holzmann J, et al. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-Plex Compared to TMT 6-Plex and iTRAQ 8-Plex on LTQ Orbitrap. Anal Chem 2010;82(15):6549-58
   PubMed Web of Science ®Google Scholar
• Vaudel M, Burkhart JM, Radau S, et al. Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI). J Proteome Res 2012;11(10):5072-80
   PubMed Web of Science ®Google Scholar
• Karp NA, Huber W, Sadowski PG, et al. Addressing accuracy and precision issues in iTRAQ quantitation. Mol Cell Proteomics 2010;9(9):1885-97
   PubMed Web of Science ®Google Scholar
• Ting L, Rad R, Gygi SP, Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Meth 2011;8(11):937-40
   PubMed Web of Science ®Google Scholar
• Zhao Y, Szeto SS, Kong RP, et al. Online two-dimensional porous graphitic carbon/reversed phase liquid chromatography platform applied to shotgun proteomics and glycoproteomics. Anal Chem 2014;86(24):12172-9
   PubMed Web of Science ®Google Scholar
• Fahlman RP, Chen W, Overall CM. Absolute proteomic quantification of the activity state of proteases and proteolytic cleavages using proteolytic signature peptides and isobaric tags. J Proteomics 2014;100:79-91
   PubMed Web of Science ®Google Scholar
• Glibert P, Meert P, Van Steendam K, et al. Phospho-iTRAQ: assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry. J Proteome Res 2015;14(2):839-49
   PubMed Web of Science ®Google Scholar
• Ahn JM, Sung HJ, Yoon YH, et al. Integrated glycoproteomics demonstrates fucosylated serum paraoxonase 1 alterations in small cell lung cancer. Mol Cell Proteomics 2014;13(1):30-48
   PubMed Web of Science ®Google Scholar
• Ren Y, Hao P, Law SK, Sze SK. Hypoxia-induced changes to integrin alpha 3 glycosylation facilitate invasion in epidermoid carcinoma cell line A431. Mol Cell Proteomics 2014;13(11):3126-37
   PubMed Web of Science ®Google Scholar
• Hebert AS, Merrill AE, Bailey DJ, et al. Neutron-encoded mass signatures for multiplexed proteome quantification. Nat Methods 2013;10(4):332-4
   PubMed Web of Science ®Google Scholar
• Hebert AS, Merrill AE, Stefely JA, et al. Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation. Mol Cell Proteomics 2013;12(11):3360-9
   PubMed Web of Science ®Google Scholar
• Frost DC, Greer T, Li L. High-Resolution Enabled 12-Plex DiLeu Isobaric Tags for Quantitative Proteomics. Anal Chem 2015;87(3):1646-54
   PubMed Web of Science ®Google Scholar
• Mohammed Y, Domanski D, Jackson AM, et al. PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J Proteomics 2014;106:151-61
   PubMed Web of Science ®Google Scholar
• Domon B, Gallien S. Recent advances in targeted proteomics for clinical applications. Proteomics Clin Appl 2014. [Epub ahead of print]
   Web of Science ®Google Scholar
• Carr SA, Abbatiello SE, Ackermann BL, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014;13(3):907-17
   PubMed Web of Science ®Google Scholar
• Abbatiello SE, Mani DR, Schilling B, et al. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics 2013;12(9):2623-39
   PubMed Web of Science ®Google Scholar
• Percy AJ, Chambers AG, Yang J, et al. Method and platform standardization in MRM-based quantitative plasma proteomics. J Proteomics 2013;95:66-76
   PubMed Web of Science ®Google Scholar
• Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clini Appl 2015;9(1-2):17-32
   PubMed Web of Science ®Google Scholar
• Narumi R, Murakami T, Kuga T, et al. A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples. J Proteome Res 2012;11(11):5311-22
   PubMed Web of Science ®Google Scholar
• Yoneyama T, Ohtsuki S, Ono M, et al. Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated alpha-fibrinogen in plasma for pancreatic cancer diagnosis. J Proteome Res 2013;12(2):753-62
   PubMed Web of Science ®Google Scholar
• Hernandez B, Parnell A, Pennington SR. Why have so few proteomic biomarkers "survived" validation? (Sample size and independent validation considerations). Proteomics 2014;14(13-14):1587-92
   PubMed Web of Science ®Google Scholar
• Christin C, Hoefsloot HC, Smilde AK, et al. A critical assessment of feature selection methods for biomarker discovery in clinical proteomics. Mol Cell Proteomics 2013;12(1):263-76
   PubMed Web of Science ®Google Scholar
• Skates SJ, Gillette MA, LaBaer J, et al. Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies. J Proteome Res 2013;12(12):5383-94
   PubMed Web of Science ®Google Scholar
• Kammers K, Cole RN, Tiengwe C, Ruczinski I. Detecting Significant Changes in Protein Abundance. EuPA Open Proteomics 2015;7:11-19
   PubMedGoogle Scholar
• Dunkler D, Sanchez-Cabo F, Heinze G. Statistical analysis principles for Omics data. Methods Mol Biol 2011;719:113-31
   PubMedGoogle Scholar
• Wheelock AM, Wheelock CE. Trials and tribulations of ’omics data analysis: assessing quality of SIMCA-based multivariate models using examples from pulmonary medicine. Mol Biosyst 2013;9(11):2589-96
   PubMedGoogle Scholar
• Ting L, Cowley MJ, Hoon SL, et al. Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling. Mol Cell Proteomics 2009;8(10):2227-42
   PubMed Web of Science ®Google Scholar
• Margolin AA, Ong SE, Schenone M, et al. Empirical Bayes analysis of quantitative proteomics experiments. PLoS ONE 2009;4(10):e7454
   Web of Science ®Google Scholar
• Datta S, Satten GA, Benos DJ, et al. An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments. Bioinformatics 2004;20(2):235-42
   PubMed Web of Science ®Google Scholar
• Wettenhall JM, Smyth GK. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 2004;20(18):3705-6
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015. [Epub ahead of print]
   Web of Science ®Google Scholar
• Van Hoof D, Munoz J, Braam SR, et al. Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell 2009;5(2):214-26
   PubMed Web of Science ®Google Scholar
• Kaibuchi K, Sano K, Hoshijima M, et al. Phosphatidylinositol turnover in platelet activation; calcium mobilization and protein phosphorylation. Cell Calcium 1982;3(4-5):323-35
   PubMed Web of Science ®Google Scholar
• Dephoure N, Zhou C, Villen J, et al. A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci USA 2008;105(31):10762-7
   PubMed Web of Science ®Google Scholar
• Tepper K, Biernat J, Kumar S, et al. Oligomer formation of tau protein hyperphosphorylated in cells. J Biol Chem 2014;289(49):34389-407
   PubMed Web of Science ®Google Scholar
• Ohno M. Roles of eIF2alpha kinases in the pathogenesis of Alzheimer’s disease. Front Mol Neurosci 2014;7:22
   PubMed Web of Science ®Google Scholar
• Grundke-Iqbal I, Iqbal K, Tung YC, et al. Abnormal phosphorylation of the microtubule-associated protein tau (tau) in Alzheimer cytoskeletal pathology. Proc Natl Acad Sci USA 1986;83(13):4913-17
   PubMed Web of Science ®Google Scholar
• Scheuner D, Mierde DV, Song B, et al. Control of mRNA translation preserves endoplasmic reticulum function in beta cells and maintains glucose homeostasis. Nat Med 2005;11(7):757-64
   PubMed Web of Science ®Google Scholar
• Ortsäter H, Grankvist N, Honkanen RE, Sjöholm Å. Protein phosphatases in pancreatic islets. J Endocrinol 2014;221(3):R121-44
   PubMed Web of Science ®Google Scholar
• Meyerovitch J, Backer JM, Kahn CR. Hepatic phosphotyrosine phosphatase activity and its alterations in diabetic rats. J Clin Invest 1989;84(3):976-83
   PubMed Web of Science ®Google Scholar
• Blume-Jensen P, Hunter T. Oncogenic kinase signalling. Nature 2001;411(6835):355-65
   PubMed Web of Science ®Google Scholar
• Zanivan S, Meves A, Behrendt K, et al. In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis. Cell reports 2013;3(2):552-66
   PubMed Web of Science ®Google Scholar
• Huelsemann MF, Patz M, Beckmann L, et al. Hypoxia-induced p38 MAPK activation reduces Mcl-1 expression and facilitates sensitivity towards BH3 mimetics in chronic lymphocytic leukemia. Leukemia 2014;29(4):981-4
   PubMed Web of Science ®Google Scholar
• Decker RS, Decker ML, Kulikovskaya I, et al. Myosin-binding protein C phosphorylation, myofibril structure, and contractile function during low-flow ischemia. Circulation 2005;111(7):906-12
   PubMed Web of Science ®Google Scholar
• El-Armouche A, Pohlmann L, Schlossarek S, et al. Decreased phosphorylation levels of cardiac myosin-binding protein-C in human and experimental heart failure. J Mol Cell Cardiol 2007;43(2):223-9
   PubMed Web of Science ®Google Scholar
• Schoutsen B, Blom JJ, Verdouw PD, Lamers JM. Calcium transport and phospholamban in sarcoplasmic reticulum of ischemic myocardium. J Mol Cell Cardiol 1989;21(7):719-27
   PubMed Web of Science ®Google Scholar
• Tedford NC, Hall AB, Graham JR, et al. Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics. Proteomics 2009;9(6):1469-87
   PubMed Web of Science ®Google Scholar
• Kumar A, Baycin-Hizal D, Shiloach J, et al. Coupling enrichment and proteomics methods for understanding and treating disease. Proteomics Clin Appl 2015;9(1-2):33-47
   PubMed Web of Science ®Google Scholar
• Soderblom EJ, Thompson JW, Schwartz EA, et al. Proteomic analysis of ERK1/2-mediated human sickle red blood cell membrane protein phosphorylation. Clin Proteomics 2013;10(1):1
   PubMedGoogle Scholar
• Nyman E, Rajan MR, Fagerholm S, et al. A Single Mechanism Can Explain Network-wide Insulin Resistance in Adipocytes from Obese Patients with Type 2 Diabetes. J Biological Chem 2014;289(48):33215-30
   PubMed Web of Science ®Google Scholar
• Andersson L, Porath J. Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem 1986;154(1):250-4
   PubMed Web of Science ®Google Scholar
• Ruprecht B, Koch H, Medard G, et al. Comprehensive and reproducible phosphopeptide enrichment using Fe-IMAC columns. Mol Cell Proteomics 2015;14(1):205-15
   PubMed Web of Science ®Google Scholar
• Yu Z, Han G, Sun S, et al. Preparation of monodisperse immobilized Ti(4+) affinity chromatography microspheres for specific enrichment of phosphopeptides. Anal Chim Acta 2009;636(1):34-41
   PubMed Web of Science ®Google Scholar
• de Graaf EL, Giansanti P, Altelaar AF, Heck AJ. Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution. Mol Cell Proteomics 2014;13(9):2426-34
   PubMed Web of Science ®Google Scholar
• Paulo JA, McAllister FE, Everley RA, et al. Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics 2015;15(2-3):462-73
   PubMed Web of Science ®Google Scholar
• Kelstrup CD, Jersie-Christensen RR, Batth TS, et al. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer. J Proteome Res 2014;13(12):6187-95
   PubMed Web of Science ®Google Scholar
• Gruhler A, Olsen JV, Mohammed S, et al. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 2005;4(3):310-27
   PubMed Web of Science ®Google Scholar
• Olsen JV, Blagoev B, Gnad F, et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006;127(3):635-48
   PubMed Web of Science ®Google Scholar
• McNulty DE, Annan RS. Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol Cell Proteomics 2008;7(5):971-80
   PubMed Web of Science ®Google Scholar
• Herskowitz JH, Seyfried NT, Duong DM, et al. Phosphoproteomic analysis reveals site-specific changes in GFAP and NDRG2 phosphorylation in frontotemporal lobar degeneration. J Proteome Res 2010;9(12):6368-79
   PubMed Web of Science ®Google Scholar
• Gauci S, Helbig AO, Slijper M, et al. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem 2009;81(11):4493-501
   PubMed Web of Science ®Google Scholar
• Alpert AJ. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem 2008;80(1):62-76
   PubMed Web of Science ®Google Scholar
• Chien KY, Liu HC, Goshe MB. Development and application of a phosphoproteomic method using electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), IMAC, and LC-MS/MS analysis to study Marek’s Disease Virus infection. J Proteome Res 2011;10(9):4041-53
   PubMed Web of Science ®Google Scholar
• Hao P, Ren Y, Dutta B, Sze SK. Comparative evaluation of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and high-pH reversed phase (Hp-RP) chromatography in profiling of rat kidney proteome. J Proteomics 2013;82:254-62
   PubMed Web of Science ®Google Scholar
• Chen X, Wu D, Zhao Y, et al. Increasing phosphoproteome coverage and identification of phosphorylation motifs through combination of different HPLC fractionation methods. J Chromatogr B Analyt Technol Biomed Life Sci 2011;879(1):25-34
   PubMed Web of Science ®Google Scholar
• Gan CS, Guo T, Zhang H, et al. A comparative study of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) versus SCX-IMAC-based methods for phosphopeptide isolation/enrichment. J Proteome Res 2008;7(11):4869-77
   PubMed Web of Science ®Google Scholar
• Loroch S, Schommartz T, Brune W, et al. Multidimensional electrostatic repulsion–hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research. Biochi Biophys Acta 2015;1854(5(0):460-8
   PubMed Web of Science ®Google Scholar
• Dickhut C, Feldmann I, Lambert J, Zahedi RP. Impact of Digestion Conditions on Phosphoproteomics. J Proteome Res 2014;13(6):2761-70
   PubMed Web of Science ®Google Scholar
• Glatter T, Ludwig C, Ahrne E, et al. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J Proteome Res 2012;11(11):5145-56
   PubMed Web of Science ®Google Scholar
• Bian Y, Ye M, Song C, et al. Improve the coverage for the analysis of phosphoproteome of HeLa cells by a tandem digestion approach. J Proteome Res 2012;11(5):2828-37
   PubMed Web of Science ®Google Scholar
• Gonczarowska-Jorge H, Dell’Aica M, Dickhut C, RP Z. Variable digestion strategies for phosphoproteomics analysis. Methods Mol Biol Clifton, N.J 2015; In press
   Google Scholar
• Taus T, Kocher T, Pichler P, et al. Universal and confident phosphorylation site localization using phosphoRS. J Proteome Res 2011;10(12):5354-62
   PubMed Web of Science ®Google Scholar
• Vaudel M, Breiter D, Beck F, et al. D-score: a search engine independent MD-score. Proteomics 2013;13(6):1036-41
   PubMed Web of Science ®Google Scholar
• Fermin D, Walmsley SJ, Gingras AC, et al. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics 2013;12(11):3409-19
   PubMed Web of Science ®Google Scholar
• Savitski MM, Lemeer S, Boesche M, et al. Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 2011;10(2):M110 003830
   Web of Science ®Google Scholar
• Beausoleil SA, Villen J, Gerber SA, et al. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 2006;24(10):1285-92
   PubMed Web of Science ®Google Scholar
• Syka JE, Coon JJ, Schroeder MJ, et al. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 2004. 101(26):9528-33
   Google Scholar
• Frese CK, Altelaar AF, van den Toorn H, et al. Toward full peptide sequence coverage by dual fragmentation combining electron-transfer and higher-energy collision dissociation tandem mass spectrometry. Anal Chem 2012;84(22):9668-73
   PubMed Web of Science ®Google Scholar
• Schroeder MJ, Shabanowitz J, Schwartz JC, et al. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal Chem 2004;76(13):3590-8
   PubMed Web of Science ®Google Scholar
• Fleitz A, Nieves E, Madrid-Aliste C, et al. Enhanced detection of multiply phosphorylated peptides and identification of their sites of modification. Anal Chem 2013;85(18):8566-76
   PubMed Web of Science ®Google Scholar
• Halim A, Brinkmalm G, Ruetschi U, et al. Site-specific characterization of threonine, serine, and tyrosine glycosylations of amyloid precursor protein/amyloid beta-peptides in human cerebrospinal fluid. Proc Natl Acad Sci USA 2011;108(29):11848-53
   PubMed Web of Science ®Google Scholar
• Vakhrushev SY, Steentoft C, Vester-Christensen MB, et al. Enhanced mass spectrometric mapping of the human GalNAc-type O-glycoproteome with SimpleCells. Mol Cell Proteomics 2013;12(4):932-44
   PubMed Web of Science ®Google Scholar
• Solis D, Bovin NV, Davis AP, et al. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta 2015;1850(1):186-235
   PubMed Web of Science ®Google Scholar
• Mitra N, Sinha S, Ramya TN, Surolia A. N-linked oligosaccharides as outfitters for glycoprotein folding, form and function. Trends Biochem Sci 2006;31(3):156-63
   PubMed Web of Science ®Google Scholar
• Shental-Bechor D, Levy Y. Effect of glycosylation on protein folding: a close look at thermodynamic stabilization. Proc Natl Acad Sci USA 2008;105(24):8256-61
   PubMed Web of Science ®Google Scholar
• Parodi AJ. Reglucosylation of glycoproteins and quality control of glycoprotein folding in the endoplasmic reticulum of yeast cells. Biochim Biophys Acta 1999;1426(2):287-95
   PubMed Web of Science ®Google Scholar
• Yoshida Y, Adachi E, Fukiya K, et al. Glycoprotein-specific ubiquitin ligases recognize N-glycans in unfolded substrates. EMBO Rep 2005;6(3):239-44
   PubMed Web of Science ®Google Scholar
• Helenius A, Aebi M. Intracellular functions of N-linked glycans. Science 2001;291(5512):2364-9
   PubMed Web of Science ®Google Scholar
• Tate MD, Job ER, Deng YM, et al. Playing hide and seek: how glycosylation of the influenza virus hemagglutinin can modulate the immune response to infection. Viruses 2014;6(3):1294-316
   PubMed Web of Science ®Google Scholar
• Christiansen MN, Chik J, Lee L, et al. Cell surface protein glycosylation in cancer. Proteomics 2014;14(4-5):525-46
   PubMed Web of Science ®Google Scholar
• Stuchlova Horynova M, Raska M, Clausen H, Novak J. Aberrant O-glycosylation and anti-glycan antibodies in an autoimmune disease IgA nephropathy and breast adenocarcinoma. Cell Mol Life Sci 2013;70(5):829-39
   PubMed Web of Science ®Google Scholar
• Schedin-Weiss S, Winblad B, Tjernberg LO. The role of protein glycosylation in Alzheimer disease. FEBS J 2014;281(1):46-62
   PubMed Web of Science ®Google Scholar
• Zhu Y, Shan X, Yuzwa SA, Vocadlo DJ. The Emerging Link between O-GlcNAc and Alzheimer Disease. J Biol Chem 2014;289(50):34472-81
   PubMed Web of Science ®Google Scholar
• Grigorian A, Mkhikian H, Li CF, et al. Pathogenesis of multiple sclerosis via environmental and genetic dysregulation of N-glycosylation. Semin Immunopathol 2012;34(3):415-24
   PubMed Web of Science ®Google Scholar
• Xu YX, Ashline D, Liu L, et al. The glycosylation-dependent interaction of perlecan core protein with LDL: implications for atherosclerosis. J Lipid Res 2015;56(2):266-76
   PubMed Web of Science ®Google Scholar
• Willig TB, Breton-Gorius J, Elbim C, et al. Macrothrombocytopenia with abnormal demarcation membranes in megakaryocytes and neutropenia with a complete lack of sialyl-Lewis-X antigen in leukocytes–a new syndrome? Blood 2001;97(3):826-8
   PubMed Web of Science ®Google Scholar
• Brooks AR, Sim D, Gritzan U, et al. Glycoengineered factor IX variants with improved pharmacokinetics and subcutaneous efficacy. J Thromb Haemost 2013;11(9):1699-706
   PubMed Web of Science ®Google Scholar
• Ma J, Hart GW. Protein O-GlcNAcylation in diabetes and diabetic complications. Expert Rev Proteomics 2013;10(4):365-80
   PubMed Web of Science ®Google Scholar
• Scott DW, Patel RP. Endothelial heterogeneity and adhesion molecules N-glycosylation: implications in leukocyte trafficking in inflammation. Glycobiology 2013;23(6):622-33
   PubMed Web of Science ®Google Scholar
• Zhang Y, Jiao J, Yang P, Lu H. Mass spectrometry-based N-glycoproteomics for cancer biomarker discovery. Clin Proteomics 2014;11(1):18
   PubMedGoogle Scholar
• Song E, Mayampurath A, Yu CY, et al. Glycoproteomics: Identifying the Glycosylation of Prostate Specific Antigen at Normal and High Isoelectric Points by LC-MS/MS. J Proteome Res 2014;13(12):5570-80
   PubMed Web of Science ®Google Scholar
• Yen TY, Macher BA, McDonald CA, et al. Glycoprotein profiles of human breast cells demonstrate a clear clustering of normal/benign versus malignant cell lines and basal versus luminal cell lines. J Proteome Res 2012;11(2):656-67
   PubMed Web of Science ®Google Scholar
• Malaguarnera G, Giordano M, Paladina I, et al. Serum markers of hepatocellular carcinoma. Dig Dis Sci 2010;55(10):2744-55
   PubMed Web of Science ®Google Scholar
• Cho HJ, Kim SS, Ahn SJ, et al. Serum transferrin as a liver fibrosis biomarker in patients with chronic hepatitis B. Clin Mol Hepatol 2014;20(4):347-54
   PubMedGoogle Scholar
• Bertino G, Ardiri A, Malaguarnera M, et al. Hepatocellualar carcinoma serum markers. Semin Oncol 2012;39(4):410-33
   PubMed Web of Science ®Google Scholar
• Lee JH, Cho CH, Kim SH, et al. Semi-quantitative Measurement of a Specific Glycoform Using a DNA-tagged Antibody and Lectin Affinity Chromatography for Glyco-biomarker Development. Mol Cell Proteomics 2015;14(3):782-95
   PubMed Web of Science ®Google Scholar
• Palmisano G, Parker BL, Engholm-Keller K, et al. A novel method for the simultaneous enrichment, identification, and quantification of phosphopeptides and sialylated glycopeptides applied to a temporal profile of mouse brain development. Mol Cell Proteomics 2012;11(11):1191-202
   PubMed Web of Science ®Google Scholar
• Lewandrowski U, Zahedi RP, Moebius J, et al. Enhanced N-glycosylation site analysis of sialoglycopeptides by strong cation exchange prefractionation applied to platelet plasma membranes. Mol Cell Proteomics 2007;6(11):1933-41
   PubMed Web of Science ®Google Scholar
• Zhu J, Sun Z, Cheng K, et al. Comprehensive mapping of protein N-glycosylation in human liver by combining hydrophilic interaction chromatography and hydrazide chemistry. J Proteome Res 2014;13(3):1713-21
   PubMed Web of Science ®Google Scholar
• Ma C, Zhao X, Han H, et al. N-linked glycoproteome profiling of human serum using tandem enrichment and multiple fraction concatenation. Electrophoresis 2013;34(16):2440-50
   PubMed Web of Science ®Google Scholar
• Yin X, Bern M, Xing Q, et al. Glycoproteomic analysis of the secretome of human endothelial cells. Mol Cell Proteomics 2013;12(4):956-78
   PubMed Web of Science ®Google Scholar
• Palmisano G, Lendal SE, Engholm-Keller K, et al. Selective enrichment of sialic acid-containing glycopeptides using titanium dioxide chromatography with analysis by HILIC and mass spectrometry. Nat Protoc 2010;5(12):1974-82
   PubMed Web of Science ®Google Scholar
• Beck F, Lewandrowski U, Wiltfang M, et al. The good, the bad, the ugly: Validating the mass spectrometric analysis of modified peptides. Proteomics 2011;11(6):1099-109
   PubMed Web of Science ®Google Scholar
• Levery SB, Steentoft C, Halim A, et al. Advances in mass spectrometry driven O-glycoproteomics. Biochim Biophys Acta 2015;1850(1):33-42
   PubMed Web of Science ®Google Scholar
• Froehlich JW, Dodds ED, Wilhelm M, et al. A classifier based on accurate mass measurements to aid large scale, unbiased glycoproteomics. Mol Cell Proteomics 2013;12(4):1017-25
   PubMed Web of Science ®Google Scholar
• Lewandrowski U, Lohrig K, Zahedi R, et al. Glycosylation Site Analysis of Human Platelets by Electrostatic Repulsion Hydrophilic Interaction Chromatography. Clin Proteom 2008;4(1-2):25-36
   Google Scholar
• Zhang H, Guo T, Li X, et al. Simultaneous characterization of glyco- and phosphoproteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography. Mol Cell Proteomics 2010;9(4):635-47
   PubMed Web of Science ®Google Scholar
• Cao L, Yu L, Guo Z, et al. Application of a strong anion exchange material in electrostatic repulsion-hydrophilic interaction chromatography for selective enrichment of glycopeptides. J Chromatogr A 2013;1299:18-24
   PubMed Web of Science ®Google Scholar
• Hao P, Guo T, Sze SK. Simultaneous analysis of proteome, phospho- and glycoproteome of rat kidney tissue with electrostatic repulsion hydrophilic interaction chromatography. PLoS One 2011;6(2):e16884
   Web of Science ®Google Scholar
• Blobel G, Dobberstein B. Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J Cell Biol 1975;67(3):835-51
   PubMed Web of Science ®Google Scholar
• Silver P, Goodson H. Nuclear protein transport. Crit Rev Biochem Mol Biol 1989;24(4):419-35
   PubMed Web of Science ®Google Scholar
• Pfanner N, Hartl FU, Neupert W. Import of proteins into mitochondria: a multi-step process. Eur J Biochem 1988;175(2):205-12
   PubMedGoogle Scholar
• Chung JJ, Shikano S, Hanyu Y, Li M. Functional diversity of protein C-termini: more than zipcoding? Trends Cell Biol 2002;12(3):146-50
   PubMed Web of Science ®Google Scholar
• Lopez-Otin C, Bond JS. Proteases: multifunctional enzymes in life and disease. J Biol Chem 2008;283(45):30433-7
   PubMed Web of Science ®Google Scholar
• Nerelius C, Alvelius G, Jornvall H. N-terminal segment of proinsulin C-peptide active in insulin interaction/desaggregation. Biochem Biophys Res Commun 2010;403(3-4):462-7
   PubMed Web of Science ®Google Scholar
• Hildebrand D, Merkel P, Eggers LF, Schluter H. Proteolytic processing of angiotensin-I in human blood plasma. PLoS One 2013;8(5):e64027
   Web of Science ®Google Scholar
• Kurokawa M, Kornbluth S. Caspases and Kinases in a Death Grip. Cell 2009;138(5):838-54
   PubMed Web of Science ®Google Scholar
• Gervais FG, Thornberry NA, Ruffolo SC, et al. Caspases cleave focal adhesion kinase during apoptosis to generate a FRNK-like polypeptide. J Biol Chem 1998;273(27):17102-8
   PubMed Web of Science ®Google Scholar
• Petrera A, Lai ZW, Schilling O. Carboxyterminal protein processing in health and disease: key actors and emerging technologies. J Proteome Res 2014;13(11):4497-504
   PubMed Web of Science ®Google Scholar
• Mossmann D, Vogtle FN, Taskin AA, et al. Amyloid-beta peptide induces mitochondrial dysfunction by inhibition of preprotein maturation. Cell Metab 2014;20(4):662-9
   PubMed Web of Science ®Google Scholar
• McCarty SM, Percival SL. Proteases and Delayed Wound Healing. Adv Wound Care 2013;2(8):438-47
   PubMedGoogle Scholar
• Csiszar A, Kutay B, Wirth S, et al. Interleukin-like epithelial-to-mesenchymal transition inducer activity is controlled by proteolytic processing and plasminogen-urokinase plasminogen activator receptor system-regulated secretion during breast cancer progression. Breast Cancer Res 2014;16(5):433
   PubMed Web of Science ®Google Scholar
• Smith H, Edman P, Owen JA. N-Terminal amino-acids of human haptoglobins. Nature 1962;193:286-7
   PubMed Web of Science ®Google Scholar
• Edman P. A method for the determination of amino acid sequence in peptides. Arch Biochem 1949;22(3):475
   PubMedGoogle Scholar
• Agard NJ, Wells JA. Methods for the proteomic identification of protease substrates. Curr Opin Chem Biol 2009;13(5-6):503-9
   PubMed Web of Science ®Google Scholar
• Tanco S, Gevaert K, Van Damme P. C-terminomics: Targeted analysis of natural and post-translationally modified protein and peptide C-termini. Proteomics 2015;15(5-6):903-14
   PubMed Web of Science ®Google Scholar
• Gevaert K, Goethals M, Martens L, et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 2003;21(5):566-9
   PubMed Web of Science ®Google Scholar
• Vogtle FN, Wortelkamp S, Zahedi RP, et al. Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 2009;139(2):428-39
   PubMed Web of Science ®Google Scholar
• Holmberg C, Ghesquiere B, Impens F, et al. Mapping proteolytic processing in the secretome of gastric cancer-associated myofibroblasts reveals activation of MMP-1, MMP-2, and MMP-3. J Proteome Res 2013;12(7):3413-22
   PubMed Web of Science ®Google Scholar
• Staes A, Van Damme P, Helsens K, et al. Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 2008;8(7):1362-70
   PubMed Web of Science ®Google Scholar
• Kleifeld O, Doucet A, auf dem Keller U, et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat Biotechnol 2010;28(3):281-8
   PubMed Web of Science ®Google Scholar
• auf dem Keller U, Prudova A, Eckhard U, et al. Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation. Sci Signal 2013;6(258):rs2
   PubMed Web of Science ®Google Scholar
• Wilson CH, Indarto D, Doucet A, et al. Identifying natural substrates for dipeptidyl peptidases 8 and 9 using terminal amine isotopic labeling of substrates (TAILS) reveals in vivo roles in cellular homeostasis and energy metabolism. J Biol Chem 2013;288(20):13936-49
   PubMed Web of Science ®Google Scholar
• Sabino F, Hermes O, Egli FE, et al. In Vivo Assessment of Protease Dynamics in Cutaneous Wound Healing by Degradomics Analysis of Porcine Wound Exudates. Mol Cell Proteomics 2015;14(2):354-70
   PubMed Web of Science ®Google Scholar
• Prudova A, Serrano K, Eckhard U, et al. TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage. Blood 2014;124(26):e49-60
   PubMed Web of Science ®Google Scholar
• Venne AS, Zahedi RP. The potential of fractional diagonal chromatography strategies for the enrichment of post-translational modifications. EuPA Open Proteomics 2014;4(0):165-70
   Google Scholar
• Breuker K, Jin M, Han X, et al. Top-Down Identification and Characterization of Biomolecules by Mass Spectrometry. J Am Soc Mass Spectrom 2008;19(8):1045-53
   PubMed Web of Science ®Google Scholar
• Catherman AD, Skinner OS, Kelleher NL. Top Down proteomics: facts and perspectives. Biochem Biophys Res Commun 2014;445(4):683-93
   PubMed Web of Science ®Google Scholar
• Barnidge DR, Dasari S, Botz CM, et al. Using mass spectrometry to monitor monoclonal immunoglobulins in patients with a monoclonal gammopathy. J Proteome Res 2014;13(3):1419-27
   PubMed Web of Science ®Google Scholar
• Mao P, Wang D. Top-down proteomics of a drop of blood for diabetes monitoring. J Proteome Res 2014;13(3):1560-9
   PubMed Web of Science ®Google Scholar
• Seeley EH, Caprioli RM. MALDI imaging mass spectrometry of human tissue: method challenges and clinical perspectives. Trends Biotechnol 2011;29(3):136-43
   PubMed Web of Science ®Google Scholar
• Rauser S, Marquardt C, Balluff B, et al. Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. J Proteome Res 2010;9(4):1854-63
   PubMed Web of Science ®Google Scholar
• Smith LM, Kelleher NL. Proteoform: a single term describing protein complexity. Nat Methods 2013;10(3):186-7
   PubMed Web of Science ®Google Scholar
• Tran JC, Zamdborg L, Ahlf DR, et al. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 2011;480(7376):254-8
   PubMed Web of Science ®Google Scholar
• Kellie JF, Catherman AD, Durbin KR, et al. Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry. Anal Chem 2012;84(1):209-15
   PubMed Web of Science ®Google Scholar
• Catherman AD, Durbin KR, Ahlf DR, et al. Large-scale top-down proteomics of the human proteome: membrane proteins, mitochondria, and senescence. Mol Cell Proteomics 2013;12(12):3465-73
   PubMed Web of Science ®Google Scholar
• Ntai I, Kim K, Fellers RT, et al. Applying label-free quantitation to top down proteomics. Anal Chem 2014;86(10):4961-8
   PubMed Web of Science ®Google Scholar
• Rhoads TW, Rose CM, Bailey DJ, et al. Neutron-encoded mass signatures for quantitative top-down proteomics. Anal Chem 2014;86(5):2314-19
   PubMed Web of Science ®Google Scholar
• Nagaraj N, Wisniewski JR, Geiger T, et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 2011;7:548
   PubMed Web of Science ®Google Scholar
• Hebert AS, Richards AL, Bailey DJ, et al. The one hour yeast proteome. Mol Cell Proteomics 2014;13(1):339-47
   PubMed Web of Science ®Google Scholar
• Nguyen LK, Kolch W, Kholodenko BN. When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Commun Signal 2013;11:52
   PubMed Web of Science ®Google Scholar
• Hietakangas V, Anckar J, Blomster HA, et al. PDSM, a motif for phosphorylation-dependent SUMO modification. Proc Natl Acad Sci USA 2006;103(1):45-50
   PubMed Web of Science ®Google Scholar
• Yang WH, Kim JE, Nam HW, et al. Modification of p53 with O-linked N-acetylglucosamine regulates p53 activity and stability. Nat Cell Biol 2006;8(10):1074-83
   PubMed Web of Science ®Google Scholar
• Cheung P, Tanner KG, Cheung WL, et al. Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Mol Cell 2000;5(6):905-15
   PubMed Web of Science ®Google Scholar
• Kowenz-Leutz E, Pless O, Dittmar G, et al. Crosstalk between C/EBPβ phosphorylation, arginine methylation, and SWI/SNF/Mediator implies an indexing transcription factor code. EMBO J 2010;29(6):1105-15
   PubMed Web of Science ®Google Scholar
• Smith LE, White MY. The role of post-translational modifications in acute and chronic cardiovascular disease. Proteomics Clin Appl 2014;8(7-8):506-21
   PubMed Web of Science ®Google Scholar
• Sajic T, Liu Y, Aebersold R. Using data-independent, high resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications. Proteomics. Clin Appl 2014. [Epub ahead of print]
   Web of Science ®Google Scholar
• Liu Y, Chen J, Sethi A, 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. Mol Cell Proteomics 2014;13(7):1753-68
   PubMed Web of Science ®Google Scholar
• Guo T, Kouvonen P, Koh CC, et al. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med 2015;21(4):407-13
   PubMed Web of Science ®Google Scholar
• Nagel T, Meyer B. Simultaneous characterization of sequence polymorphisms, glycosylation and phosphorylation of fibrinogen in a direct analysis by LC-MS. Biochim Biophys Acta 2014;1844(12):2284-9
   PubMed Web of Science ®Google Scholar
• Sidoli S, Schwammle V, Ruminowicz C, et al. Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Proteomics 2014;14(19):2200-11
   PubMed Web of Science ®Google Scholar
• Diehl HC, Beine B, Elm J, et al. The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments. Anal Bioanal Chem 2015;407(8):2223-43
   PubMed Web of Science ®Google Scholar