Find relevant citations from peer-reviewed journals where specific research results were generated using Thermo Scientific Tandem Mass Tag (TMT) reagents. These citations are listed by disease area or topic. Learn more about TMT reagents and kits.

  1. Chaves DFS, Carvalho PC, Lima DB et al. (2013) Comparative Proteomic Analysis of the Aging Soleus and Extensor Digitorum Longus Rat Muscles Using TMT Labeling and Mass Spectrometry. J Proteome Res 12:4532–4546.
  2. Miwa S, Jow H, Baty K et al. (2014) Low abundance of the matrix arm of complex I in mitochondria predicts longevity in mice. Nat Commun May 12 ePub:5:3837.
  3. Wang P, Sun X, Xie Y et al. (2014) Melatonin regulates proteomic changes during leaf senescence in Malus hupehensis. J Pineal Res 57:291–307.
  1. Anders L, Ke N, Hydbring P et al. (2011) A Systematic Screen for CDK4/6 Substrates Links FOXM1 Phosphorylation to Senescence Suppression in Cancer Cells. Cancer Cell 20:620–634.
  2. Banh RS, Iorio C, Marcotte R et al. (2016) PTP1B controls non-mitochondrial oxygen consumption by regulating RNF213 to promote tumour survival during hypoxia. Nat Cell Biol 18:803–813.
  3. Bantscheff M, Hopf C, Savitski MM et al. (2011) Chemoproteomics profiling of HDACinhibitors reveals selective targeting of HDAC complexes. Nat Biotechnol 29(3):255–265.
  4. Betancourt A, Mobley JA, Wang J et al. (2014) Alterations in the Rat Serum Proteome Induced by Prepubertal Exposure to Bisphenol A and Genistein. J Proteome Res 13:1502–1514.
  5. Biancur DE, Paulo JA, Małachowska B et al. (2017) Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism. Nat Commun Jul 3 ePub:8:15965.
  6. Churchman ML, Low J, Qu C et al. (2015) Efficacy of Retinoids in IKZF1-Mutated BCR-ABL1 Acute Lymphoblastic Leukemia. Cancer Cell 28:343–356.
  7. Dillon R, Nilsson CL, Shi SDH et al. (2011) Discovery of a Novel B-Raf Fusion Protein Related to c-Met Drug Resistance. J Proteome Res 10:5084–5094.
  8. Gao W, Xu J, Wang F et al. (2015) Plasma membrane proteomic analysis of human Gastric Cancer tissues: revealing flotillin 1 as a marker for Gastric Cancer. BMC Cancer May 7 ePub:15:367.
  9. Grzmil M, Seebacher J, Hess D et al. (2016) Inhibition of MNK pathways enhances cancer cell response to chemotherapy with temozolomide and targeted radionuclide therapy. Cell Signal 28:1412–1421.
  10. Huan J, NI Hornick NI, NA Goloviznina NA et al. (2015) Coordinate regulation of residual bone marrow function by paracrine trafficking of AML exosomes. Leukemia 29(12):2285–2295.
  11. Hughes CS, McConechy MK, Cochrane DR et al. (2016) Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research. Sci Rep Oct 7 ePub:6:34949.
  12. Jordan NV, Bardia A, Wittner BS et al. (2016) HER2 expression identifies dynamic functional states within circulating breast cancer cells. Nature 537:102–106.
  13. Jung S, Bohm G, Schmid P et al. (2014) Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets. PLoS One Mar 26 ePub:9(3):e90948.
  14. Lee HJ, Cha HJ, Lim JS et al. (2014) Abundance-Ratio-Based Semiquantitative Analysis of Site-Specific N-Linked Glycopeptides Present in the Plasma of Hepatocellular Carcinoma Patients. J Proteome Res 13:2328–2338.
  15. Misuno K, Liu X, Feng S et al. (2013) Quantitative proteomic analysis of sphere-forming stem-like oral cancer cells. Stem Cell Res Ther Dec 25 ePub:4:156.
  16. Muellner MK, Mair B, Ibrahim Y et al. (2015) Targeting a cell state common to triple-negative breast cancers. Mol Syst Biol Feb 19 ePub:11:789.
  17. Patel AR, Mahavir B. Chougule MB et al. (2013) Efficacy of Aerosolized Celecoxib Encapsulated Nanostructured Lipid Carrier in Non-small Cell Lung Cancer in Combination with Docetaxel. Pharm Res 30:1435–1446.
  18. Perera RM, Stoykova S, Nicolay BN et al. (2015) Transcriptional control of autophagy–lysosome function drives pancreatic cancer metabolism. Nature 524:361–365.
  19. Radziwon-Balicka A, Medina C, O’Driscoll L et al. (2012) Platelets increase survival of adenocarcinoma cells challenged with anticancer drugs: mechanisms and implications for chemoresistance. Br J Pharmacol 167:787–804.
  20. Raso C, Cosentino C, Gaspari M et al. (2012) Characterization of Breast Cancer Interstitial Fluids by TmT Labeling, LTQ-Orbitrap Velos Mass Spectrometry, and Pathway Analysis. J Proteome Res 11:3199–3210.
  21. Salhia B, Van Cott C, Tegeler T et al. (2012) Differential Effects of AKT1(p.E17K) Expression on Human Mammary Luminal Epithelial and Myoepithelial Cells. Hum Mutat 33(8):1216–1227.
  22. Salony XS, Alves CP, Dey-Guha I et al. (2016) AKT Inhibition Promotes Nonautonomous Cancer Cell Survival. Mol Cancer Ther 15:142–153.
  23. Sandin M, Antberg L, Levander F et al. (2015) A Breast Cell Atlas: Organelle analysis of the MDA-MB-231 cell line by density-gradient fractionation using isotopic marking and label-free analysis. EuPA Open Proteom 8:68–77.
  24. Sherwood V, Chaurasiya SK, Ekström EJ et al. (2014) WNT5A-mediated β-catenin-independent signaling is a novel regulator of cancer cell metabolism. Carcinogenesis 35:784–794.
  25. Sinclair J, Metodieva G, Dafou D et al. (2011) Profiling signatures of ovarian cancer tumour suppression using 2D-DIGE and 2D-LC-MS/MS with tandem mass tagging. J Proteomics 74:451–465.
  26. Sinclair J, Timms JF (2011) Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC-MS/MS. Methods 54:361–369.
  27. Svinkina T, Gu H, Silva JC et al. (2015) Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow. Mol Cell Proteomics 14:2429–2440.
  28. Tien JF, Mazloomian A, Cheng SWG et al. (2017) CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion. Nucleic Acids Res 45(11):6698–6671.
  29. Tilghman SL, Townley I, Zhong Q et al. (2013) Proteomic Signatures of Acquired Letrozole Resistance in Breast Cancer: Suppressed Estrogen Signaling and Increased Cell Motility and Invasiveness. Mol Cell Proteomics 12:2440–2455.
  30. Van Rechem C, Black JC, Boukhali M et al. (2015) Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis. Cancer Discov 5(3):255–263.
  31. Vartanian S, Ma TP, Lee J et al. (2016) Application of Mass Spectrometry Profiling to Establish Brusatol as an Inhibitor of Global Protein Synthesis. Mol Cell Proteomics 15(4):1220–1231.
  32. Venkatesh HS, Johung TB, Caretti V et al. (2015) Neuronal Activity Promotes Glioma Growth through Neuroligin-3 Secretion. Cell 161:803–816.
  33. Wang Z, Liang S, Lian X et al. (2015) Identification of proteins responsible for adriamycin resistance in breast cancer cells using proteomics analysis. Sci Rep 5 March 30 ePub:9301.
  34. Ward CL, Boggio KJ, Johnson BN et al. (2014) A loss of FUS/TLS function leads to impaired cellular proliferation. Cell Death Dis Dec 11 ePub:5:e1572.
  35. Weeraratne SD, Amani V, Teider N et al. (2012) Pleiotropic effects of miR-183~96~182 converge to regulate cell survival, proliferation and migration in medulloblastoma. Acta Neuropathol 123:539–552.
  36. Xiong L, Darwanto A, Sharma S et al. (2011) Mass Spectrometric Studies on Epigenetic Interaction Networks in Cell Differentiation. J Biol Chem 286:13657–13668.
  37. Zahari MS, Wu X, Pinto SN et al. (2015) Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Sci Rep Sept 2 ePub:5:13660.
  38. Zheng Y, Miyamoto DT, Wittner BS et al. (2017) Expression of β-globin by cancer cells promotes cell survival during blood-borne dissemination. Nat Commun Feb 9 ePub:8:14344.
  39. Zhou C, Zhong Q, Rhodes LV et al. (2012) Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration. Breast Cancer Res Mar 14 ePub:14:R45.
  1. Andaya A, Jia W, Sokabe M et al. (2011) Phosphorylation of Human Eukaryotic Initiation Factor 2γ: Novel Site Identification and Targeted PKC Involvement. J Proteome Res 10:4613–4623.
  2. Arabi A, Ullah K, Branca RMM et al. (2012) Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway. Nat Commun Jul 31 ePub:3:976
  3. Bukhari SIA, Truesdell SS, Lee S et al. (2016) A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence. Mol Cell 61(5):760–673.
  4. Bulatov E, Martin EM, Chatterjee S et al. (2015) Biophysical Studies on Interactions and Assembly of Full-size E3 Ubiquitin Ligase Suppressor of Cytoline Signaling 2 (SOCS2)-Elongin BC-Cullin 5-Ring Box Protein 2 (RBX2). J Biol Chem 290:4178–4191.
  5. Byun K, Kim JY, Bayarsaikhan E et al. (2012) Quantitative proteomic analysis reveals that lipopolysaccharide induces mitogen-activated protein kinasedependent activation in human microglial cells. Electrophoresis 33:3756–3763.
  6. Chen M, Zhu A, Storey KB (2015) Comparative phosphoproteomic analysis of intestinal phosphorylated proteins in active versus aestivating sea cucumbers. J Proteomics 135:141–150.
  7. Heo JM, Ordureau A, Paulo JA et al. (2015) The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drivesa Programof OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy. Mol Cell 60:7–20.
  8. Jedrychowski MP, Liu L, Laflamme CJ et al. (2015) Adiporedoxin, an upstream regulator of ER oxidative folding and protein secretion in adipocytes. Mol Metab 4:758–770.
  9. Jia W, Andaya A, Leary JA (2012) Novel Mass Spectrometric Method for Phosphorylation Quantification Using Cerium Oxide Nanoparticles and Tandem Mass Tags. Anal Chem 84:2466−2473.
  10. McAllister FE, Niepel M, Haas W et al. (2013) Mass Spectrometry Based Method to Increase Throughput for Kinome Analyses Using ATP Probes. Anal Chem 85:4666−4674.
  11. Murphy JP, Stepanova E, Everley RA et al. (2015) Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae. Mol Cell Proteomics 14:2454–2465.
  12. Nirujogi RS, Wright Jr JD, Manda SS et al. (2015) Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats. Proteomics 15:487–499.
  13. Ogawa T, Hirokawa N (2015) Microtubule Destabilizer KIF2A Undergoes Distinct Site-Specific Phosphorylation Cascades that Differentially Affect Neuronal Morphogenesis. Cell Rep 12:1774–1788.
  14. Rainbolt TK, Atanassova N, Genereux JC et al. (2013) Stress-Regulated Translational Attenuation Adapts Mitochondrial Protein Import through Tim17A Degradation. Cell Metab 18:908–919.
  15. Rusin SF, Schlosser KA, Adamo ME et al. (2015) Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells. Sci Signal Oct 13 ePub:8:rs12.
  16. Singh SA, Winter D, Kirchner M et al. (2014) Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J 33:385–339.
  17. Sopko R, Foos M, Vinayagam A et al. (2014) Combining Genetic Perturbations and Proteomics to Examine Kinase-Phosphatase Networks in Drosophila Embryos. Dev Cell 31:114–127.
  18. Tagliabracci VS, Wiley SE, Guo X et al. (2015) A Single Kinase Generates the Majority of the Secreted Phosphoproteome. Cell 161:1619–1632.
  1. Alam MM, Solyakov L, Bottrill AR et al. (2015) Phosphoproteomics reveals malaria parasite Protein Kinase G as a signalling hub regulating egress and invasion. Nat Commun Jul 7 ePub:6:7285.
  2. Alexander S., Banks AS, McAllister FE et al. (2015) An ERK/Cdk5 axis controls the diabetogenic actions of PPARc. Nature 517(7534):391–395.
  3. Amaral A, Paiva C, Parrinello CA et al. (2014) Identification of Proteins Involved in Human Sperm Motility Using High-Throughput Differential Proteomics. J Proteome Res 13:5670−5684.
  4. Ashtona NJ, Kiddlea SJ, Graf J et al. (2015) Blood protein predictors of brain amyloid for enrichment in clinical trials? Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring 1:48–60.
  5. Azpiazu R, Amaral A, Castillo J et al. (2014) High-throughput sperm differential proteomics suggests that epigenetic alterations contribute to failed assisted reproduction. Hum Reprod 29:1225 –1237.
  6. Banerjee S, Liao L, Russo R et al. (2012) Isobaric tagging-based quantification by mass spectrometry of differentially regulated proteins in synaptosomes of HIV/gp120 transgenic mice: Implications for HIV-associated neurodegeneration. Exp Neurol 236:298–306.
  7. Belin S, Nawabi H, Wang C et al. (2015) Injury-Induced Decline of Intrinsic Regenerative Ability Revealed by Quantitative Proteomics. Neuron 86:1000–1014.
  8. Butovsky O, Jedrychowski MP, Cialic R et al. (2015) Targeting miR-155 Restores Abnormal Microglia and Attenuates Disease in SOD1 Mice. Ann Neurol 77:75–99.
  9. Butovsky O, Jedrychowski MP, Moore CS et al. (2014) Identification of a unique TGF-b–dependent molecular and functional signature in microglia. Nat Neurosci 17:131–143.
  10. Carvalho AS, Ribeiro H, Voabil P et al. (2014) Global Mass Spectrometry and Transcriptomics Array Based Drug Profiling Provides Novel Insight into Glucosamine Induced Endoplasmic Reticulum Stress. Mol Cell Proteomics 13:3294–3307.
  11. Chen C, Xiao D, Zhou W et al. (2014) Global Protein Differential Expression Profiling of Cerebrospinal Fluid Samples Pooled from Chinese Sporadic CJD and non-CJD Patients. Mol Neurobiol 49:290–302.
  12. Chen Y, Yang F, Sun Z et al. (2015) Proteomic Analysis of Drug-Resistant Mycobacteria: Co-Evolution of Copper and INH Resistance. PLoS One Jun 2 ePub:10(6):e0127788.
  13. Cheng Y, Chen Y, Sun X et al. (2014) Identification of Potential Serum Biomarkers for Rheumatoid Arthritis by High-Resolution Quantitative Proteomic Analysis. Inflammation 37:1459–1467.
  14. Dayon L, Turck N, García-Berrocoso T et al. (2011) Brain Extracellular Fluid Protein Changes in Acute Stroke Patients. J Proteome Res 10:1043–1051.
  15. Dombkowski AA, Batista CE, Cukovic D et al. (2014) Cortical Tubers: Windows into Dysregulation of Epilepsy Risk and Synaptic Signaling Genes by MicroRNAs. Cereb Cortex 26:1059–1071.
  16. Dong G, Guo Y, Cao H et al. (2014) Long-term effects of repeated superovulation on ovarian structure and function in rhesus monkeys. Fertil Steril 102(5):1452–1457.
  17. Fields S, Song B, Rasoul B et al. (2014) New Candidate Biomarkers in the Female Genital Tract to Evaluate Microbicide Toxicity. PLoS One Oct 21 ePub9(10):e110980.
  18. Gu L, Evans AR, Robinson RAS (2015) Sample Multiplexing with Cysteine-Selective Approaches: cysDML and cPILOT. J Am Soc Mass Spectrom 26:615–630.
  19. Hong I, Kang T, Yun KN et al. (2013) Quantitative proteomics of auditory fear conditioning. Biochem Biophys Res Commun 434:87–94.
  20. Jastrab JB, Wang T, Murphy JP et al. (2015) An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci USA 112(14):E1763–1772.
  21. Keshishian H, Burgess MW, Gillette MA et al. (2015) Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury. Mol Cell Proteomics 14:2375–2393.
  22. Khor VK, Ahrends R, Lin Y et al. (2014) The Proteome of Cholesteryl-Ester-Enriched Versus Triacylglycerol-Enriched Lipid Droplets. PLoS One Aug 11 ePub:9(8):e105047.
  23. Kohr MJ, Aponte A, Sun J et al. (2012) Measurement of S-Nitrosylation Occupancy in the Myocardium With Cysteine-Reactive Tandem Mass Tags. Circ Res 111(10):1308–1312.
  24. Kronke J, Fink EC, Hollenbach PW et al. (2015) Lenalidomide induces ubiquitination and degradation of CK1a in del(5q) MDS. Nature 523:183–188.
  25. Licker V, Turck N, Kovari E et al. (2014) Proteomic analysis of human substantia nigra identifies novel candidates involved in Parkinson’s disease pathogenesis. Proteomics 14:784–794.
  26. Lv J, Ma S, Zhang X et al. (2014) Quantitative proteomics reveals that PEA15 regulates astroglial Aβ phagocytosis in an Alzheimer's disease mouse model. J Proteomics 110:45–58.
  27. Maes E, Valkenborg D, Baggerman G et al. (2015) Determination of Variation Parameters as a Crucial Step in Designing TMT-Based Clinical Proteomics Experiments. PLoS One Mar 16 ePub:10(3):e0120115.
  28. Mahesula S, Raphael I, Raghunathan R et al. (2012) Immunoenrichment microwave and magnetic proteomics for quantifying CD47 in the experimental autoimmune encephalomyelitis model of multiple sclerosis. Electrophoresis 33:3820–3829.
  29. Marancik DP, Fast MD, Camus AC (2013) Proteomic characterization of the acute-phase response of yellow stingrays Urobatis jamaicensis after injection with a Vibrio anguillarum-ordalii bacterin. Fish Shellfish Immunol 34:1383–1389.
  30. Matheson NJ, Sumner J, Wals K et al. (2015) Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. Cell Host Microbe 18:1–15.
  31. Matsumura CY, Menezes de Oliveira B, Durbeej M et al. (2013) Isobaric Tagging-Based Quantification for Proteomic Analysis: A Comparative Study of Spared and Affected Muscles from mdx Mice at the Early Phase of Dystrophy. PLoS One Jun 18 ePub:8(6):e65831.
  32. Mbongue JC, Nicholas DA, Zhang K et al. (2015) Induction of Indoleamine 2, 3-Dioxygenase in Human Dendritic Cells by a Cholera Toxin B Subunit—Proinsulin Vaccine. PLoS One Feb 25 ePub:10(2):e0118562.
  33. Mehrabian M, Brethour D, MacIsaac S et al. (2014) CRISPR-Cas9-Based Knockout of the Prion Protein and Its Effect on the Proteome. PLoS One Dec 9 ePub:9(12):e114594.
  34. Mehrabian M, Brethour D, Wang H et al. (2015) The Prion Protein Controls Polysialylation of Neural Cell Adhesion Molecule 1 during Cellular Morphogenesis. PLoS One Aug 19 ePub:10(8):e0133741.
  35. Menezes de Oliveira B, Matsumura CY, Fontes-Oliveira CC et al. (2014) Quantitative Proteomic Analysis Reveals Metabolic Alterations, Calcium Dysregulation, and Increased Expression of Extracellular Matrix Proteins in Laminin α2 Chain–deficient Muscle. Mol Cell Proteomics 13:3001–3013.
  36. Misuno K, Tran SD, Khalili S et al. (2014) Quantitative Analysis of Protein and Gene Expression in Salivary Glands of Sjogren’s-Like Disease NOD Mice Treated by Bone Marrow Soup. PLoS One Jan 29 ePub:9(1):e87158.
  37. Ni X, Li X, Guo Y et al. (2014) Quantitative Proteomics Analysis of Altered Protein Expression in the Placental Villous Tissue of Early Pregnancy Loss Using Isobaric Tandem Mass Tags. Biomed Res Int Mar 13 ePub:647143.
  38. Ordureau A, Sarraf SA, Duda DM et al. (2014) Quantitative Proteomics Reveal a Feed forward Mechanism for Mitochondrial PARKIN Translocation and Ubiquitin Chain Synthesis. Mol Cell 56:360–375.
  39. Parker BL, Shepherd NE, Trefely S et al. (2014) Structural Basis for Phosphorylation and Lysine Acetylation Cross-talk in a Kinase Motif Associated with Myocardial Ischemia and Cardioprotection. J Biol Chem 289:25890–25906.
  40. Phillips RJ, Heesom K, Trinder J et al. (2014) Human maternalplasmaproteomicchangeswith parturition. EuPA Proteomics 5:10–20.
  41. Ræder H, Vesterhus M, El Ouaamari A et al. (2013) Absence of Diabetes and Pancreatic Exocrine Dysfunction in a Transgenic Model of Carboxyl-Ester Lipase-MODY (Maturity-Onset Diabetes of the Young). PLoS One Apr 2 ePub:8(4):e60229.
  42. Raphael I, Mahesula S, Kalsaria K et al. (2012) Microwave and magnetic (M2) proteomics of the experimental autoimmune encephalomyelitis animal model of multiple sclerosis. Electrophoresis 33:3810–3819.
  43. Raphael I, Mahesula S, Purkar A et al. (2014) Microwave & Magnetic (M2) Proteomics Reveals CNS-Specific Protein Expression Waves that Precede Clinical Symptoms of Experimental Autoimmune Encephalomyelitis. Sci Rep Sep 3 ePub:4:6210.
  44. Rauniyar N, Subramanian K, Lavallee-Adam M et al. (2015) Quantitative Proteomics of Human Fibroblasts with I1061T Mutation in Niemann–Pick C1 (NPC1) Protein Provides Insights into the Disease Pathogenesis. Mol Cell Proteomics 14:1734–1749.
  45. Salvisberg C, Tajouri N, Hainard A et al. (2014) Exploring the human tear fluid: Discovery of new biomarkers in multiple sclerosis. Proteomics Clin Appl 8:185–194.
  46. Schondorf DC, Aureli M, McAllister FE et al. (2014) iPSC-derived neurons from GBA1-associated Parkinson’s disease patients show autophagic defects and impaired calcium homeostasis. Nature Commun Jun 6 ePub:5:4028.
  47. Stella R, Cifani P, Peggion C et al. (2012) Relative Quantification of Membrane Proteins in Wild-Type and Prion Protein (PrP)-Knockout Cerebellar Granule Neurons. J Proteome Res 11:523–536.
  48. Syddall CM, Reynard LN, Young DA et al. (2013) The Identification of Trans-acting Factors That Regulate the Expression of GDF5 via the Osteoarthritis Susceptibility SNP rs143383. PLoS Genet Jun 27 ePub:9(6):e1003557.
  49. Tiberti N, Sanchez JC (2015) Comparative analysis of cerebrospinal fluid from the meningo-encephalitic stage of T.b. gambiense and rhodesiense sleeping sickness patients using TMT quantitative proteomics. Data Brief 4:400–405.
  50. Titz B, Sewer A, Schneider T et al. (2015) Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects. J Proteomics 128:306–320.
  51. Tsuchida S, Satoh M, Kawashima Y et al. (2013) Application of quantitative proteomic analysis using tandem mass tags for discovery and identification of novel biomarkers in periodontal disease. Proteomics 13:2339–2350.
  52. Wang H, Gottfries J, Barrenas F et al. (2011) Identification of Novel Biomarkers in Seasonal Allergic Rhinitis by Combining Proteomic, Multivariate and Pathway Analysis. PLoS One Aug 24 ePub:6(8):e23563.
  53. Zen Y, Britton D, Mitra V et al. (2015) A global proteomic study identifies distinct pathological features of IgG4-related and primary sclerosing cholangitis. Histopathology 68:796–809.
  54. Zhang K, Schrag M, Crofton A et al. (2012) Targeted proteomics for quantification of histone acetylation in Alzheimer’s disease. Proteomics 12:1261–1268.
  55. Zhao C, Wang F, Wang P et al. (2015) Early second-trimester plasma protein profiling using multiplexed isobaric tandem mass tag (TMT) labeling predicts gestational diabetes mellitus. Acta Diabetol 52:1103–
  56. Zhuang G, Yu K, Jiang Z et al. (2013) Phosphoproteomic Analysis Implicates the mTORC2-FoxO1 Axis in VEGF Signaling and Feedback Activation of Receptor Tyrosine Kinases. Sci Signal Apr 16 ePub:6(271):ra25.
  1. Gruber AR, Martin G, Muller P et al. (2014) Global 30 UTR shortening has a limited effect on protein abundance in proliferating T cells. Nat Commun Nov 21 ePub:5:5465.
  2. Minajigi A, Froberg JE, Wei C et al. (2015) A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 349:6245.
  3. Prabakaran S, Hemberg M, Chauhan R et al. (2014) Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun Nov 18 ePub:5:5429.
  4. Slavov N, Budnik BA, Schwab D et al. (2014) Constant Growth Rate Can Be Supported by Decreasing Energy Flux and Increasing Aerobic Glycolysis. Cell Rep 7:705–714.
  5. Vinken M, Maes M, Cavill R et al. (2013) Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures. Arch Toxicol 87:883–894.
  6. Wu L, Candille SI, Choi Y et al. (2013) Variation and genetic control of protein abundance in humans. Nature 499:79–82.
  1. Bonneil E, Pfammatter S, Thibault P (2015) Enhancement of mass spectrometry performance for proteomic analyses using high field asymmetric waveform ion mobility spectrometry (FAIMS). J Mass Spectrom 50:1181–1195.
  2. Cao Z, Evans AR, Robinson RAS (2015) MS3-based quantitative proteomics using pulsed-Q dissociation. Rapid Commun Mass Spectrom 29:1025–1030.
  3. Chiva C, Sabidó E (2014) HCD-only fragmentation method balances peptide identification and quantitation of TMT-labeled samples in hybrid linear ion trap/orbitrap mass spectrometers. J Proteomics 96:263–270.
  4. Chung HS, Murray CI, Venkatraman V et al. (2015) Dual Labeling Biotin Switch Assay to Reduce Bias Derived from Different Cysteine Subpopulations: A Method to Maximize S-Nitrosylation Detection. Circ Res 117:846–857.
  5. Curran TG, Zhang Y, Ma DJ et al. (2015) MARQUIS: A multiplex method for absolute quantification of peptides and posttranslational Modifications. Nat Commun Jan 12 ePub:6:5924.
  6. Dayon L, Pasquarello C, Hoogland C et al. (2010) Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags. J Proteomics 73:769–777.
  7. Dayon L, Sonderegger B, Kussmann M (2012) Combination of Gas-Phase Fractionation and MS3 Acquisition Modes for Relative Protein Quantification with Isobaric Tagging. J Proteome Res 11:5081−5089.
  8. Diedrich JK, Pinto AFM, Yates III JR (2013) Energy Dependence of HCD on Peptide Fragmentation: Stepped Collisional Energy Finds the Sweet Spot. J Am Soc Mass Spectrom 24:1690-1699.
  9. Dephoure D, Gygi SP (2012) Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast. Sci Signal Mar 27 ePub:5(217):rs2.
  10. Engmann O, Campbell J, Ward M et al. (2010) Comparison of a Protein-Level and Peptide-Level Labeling Strategy for Quantitative Proteomics of Synaptosomes Using Isobaric Tags. J Proteome Res 9:2725–2733.
  11. Erickson BK, Rose CM, Braun CR et al. (2017) A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization. Mol Cell 65(2):361–370.
  12. Evans AR, Robinson RAS (2013) Global combined precursor isotopic labeling and isobaric tagging (cPILOT) approach with selective MS3 acquisition. Proteomics 13:3267–3272.
  13. Feng S, Tia E, Zhan L et al. (2012) Development of the Fc-III Tagged Protein Expression System for Protein Purification and Detection. PLoS One Aug 29 ePub:7(8):e44208.
  14. Giron P, Dayon L, Turck N et al. (2011) Quantitative Analysis of Human Cerebrospinal Fluid Proteins Using a Combination of Cysteine Tagging and Amine-Reactive Isobaric Labeling. J Proteome Res 10:249–258.
  15. Helm D, Vissers JPC, Hughes CJ et al. (2014) Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics. Mol Cell Proteomics 13:3709–3715.
  16. Huang FK, Zhang G, Lawlor K et al. (2017) Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling. J Proteome Res 16(3):1121–1132.
  17. Hughes CS, Foehr S, Garfield DA et al. (2014) Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol Oct 30 ePub:10:757.
  18. Hung CW, Tholey A (2012) Tandem Mass Tag Protein Labeling for Top-Down Identification and Quantification. Anal Chem 84:161–170.
  19. Ledvina AR, Lee MV, McAlister GC et al. (2012) Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics. Anal Chem 84:4513−4519.
  20. Liu JM, Sweredoski MJ, Hess S (2016) Improved 6‑Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap−High-Energy Collision Induced Dissociation MS3 Scan. Anal Chem 88(150):7471–7475.
  21. McAlister GC, Nusinow DP, Jedrychowski MP et al. (2014) MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes. Anal Chem 86:7150−7158.
  22. Megger DA, Pott LL, Ahrens MA et al. (2014) Comparison of label-free and label-based strategies for proteome analysis of hepatoma cell lines. Biochim Biophys Acta 1844:967–976.
  23. Murphy JP, Everley RA, Coloff JL et al. (2014) Combining Amine Metabolomics and Quantitative Proteomics of Cancer Cells Using Derivatization with Isobaric Tags. Anal Chem 86:3585−3593.
  24. Murray CI, Uhrigshardt H, O’Meally RN et al. (2012) Identification and Quantification of S-Nitrosylation by Cysteine Reactive Tandem Mass Tag Switch Assay. Mol Cell Proteomics 11:1–12.
  25. Nguyen-Lefebvre AT, Gonin-Giraud S, Scherl A et al. (2011) Identification of human, rat and chicken ribosomal proteins by a combination of two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. J Proteomics 74:167–185.
  26. Niu M, JH, Kodali K et al. (2017) Extensive Peptide Fractionation and y 1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry. Anal Chem 89(5):2956–2963.
  27. Pachl F, Fellenberg K, Wagner C et al. (2012) Ultra-high intra-spectrum mass accuracy enables unambiguous identification of fragment reporter ions in isobaric multiplexed quantitative proteomics. Proteomics 12:1328–1332.
  28. Parker J, Balmant K, Zhu F et al. (2015) cysTMTRAQ—An Integrative Method for Unbiased Thiol-based Redox Proteomics. Mol Cell Proteomics 14:237–242.
  29. Paulo JA, O’Connell JD, Gygi SP (2016) A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. J Am Soc Mass Spectrom 27(10):1620–1625.
  30. Pichler P, K€ocher T, Holzmann J et al. (2011) Improved Precision of iTRAQ and TMT Quantification by an Axial Extraction Field in an Orbitrap HCD Cell. Anal Chem 83:1469–1474.
  31. Ricchiuto P, Iwata H, Yabusaki K et al. (2015) mIMT-visHTS: A novel method for multiplexing isobaric mass tagged datasets with an accompanying visualization high throughput screening tool for protein profiling. J Proteomics 128:132–140.
  32. Sandberg A, Branca RMM, LehtiöJ et al. (2014) Quantitative accuracy in mass spectrometry based proteomics of complex samples: The impact of labeling and precursor interference. J Proteomics 96:133–144.
  33. Ting L, Rad R, Gygi SP et al. (2011) MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 8(11):937–940.
  34. Viner RI, Zhang T, Second T et al. (2009) Quantification of post-translationally modified peptides of bovine α-crystallin using tandem mass tags and electron transfer dissociation. J Proteomics 72:874–885.
  35. Wenger CD, Lee MV, Hebert AS et al. (2011) Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods 8:933–935.
  36. Werner T, Becher I, Sweetman G et al. (2012) High-Resolution Enabled TMT 8-plexing. Anal Chem 84:7188−7194.
  37. Wühr M, Haas W, McAlister G et al. (2012) Accurate Multiplexed Proteomics at the MS2 Level Using the Complement Reporter Ion Cluster. Anal Chem 84:9214−9221.
  38. Ye H, Boyne MT, Buhse LF et al. (2013) Direct Approach for Qualitative and Quantitative Characterization of Glycoproteins Using Tandem Mass Tags and an LTQ Orbitrap XL Electron Transfer Dissociation Hybrid Mass Spectrometer. Anal Chem 85:1531−1539.
  1. Aoki W, Tatsukami Y, Kitahara N et al. (2013) Elucidation of potentially virulent factors of Candida albicans during serum adaptation by using quantitative time-course proteomics. J Proteomics 91:417–429.
  2. Chasman D, Ho YH, Berry DB et al. (2014) Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Mol Syst Biol Nov 19 ePub:10:759.
  3. Esaka K, Aburaya S, Morisaka H et al. (2015) Exoproteome analysis of Clostridium cellulovorans in natural soft-biomass degradation. AMB Express Jan 24 ePub:5:2.
  4. Ganter M, Goldberg JM, Dvorin JD et al. (2017) Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol Feb 17 ePub:2:17017.
  5. Ghiaci P, Norbeck J, Larsson C (2013) Physiological adaptations of Saccharomyces cerevisiae evolved for improved butanol tolerance. Biotechnol Biofuels July 15 ePub:6:101.
  6. Guerreiro ACL, Benevento M, Lehmann R et al. (2014) Daily Rhythms in the Cyanobacterium Synechococcus elongatus Probed by High-resolution Mass Spectrometry–based Proteomics Reveals a Small Defined Set of Cyclic Proteins. Mol Cell Proteomics 13:2042–2055.
  7. Kugadas A, Christiansen SH, Sankaranarayanan S et al. (2016) Impact of Microbiota on Resistance to Ocular Pseudomonas aeruginosa-Induced Keratitis. PLoS Pathog Sep 22 ePub:12(9):e1005855.
  8. Kwan BW, Osbourne DO, Hu Y et al. (2015) Phosphodiesterase DosP Increases Persistence by Reducing cAMP Which Reduces the Signal Indole. Biotechnol Bioengin 112:588–600.
  9. Lee MV, Topper SE, Hubler SL et al. (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol Jul 19 ePub:7:514.
  10. McEwan DL, Feinbaum RL, Stroustrup N et al. (2016) Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. BMC Biol Dec 7 ePub:14:105.
  11. Mosier AC, Li Z, Thomas BC et al. (2015) Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J 9:180–194.
  12. Paulo JA, O'Connell JD, Everley RA et al. (2016) Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. J Proteomics 148:85–93.
  13. Peciulyte A, Anasontzis GE, Karlström K et al. (2014) Morphology and enzyme production of Trichoderma reesei Rut C-30 are affected by the physical and structural characteristics of cellulosic substrates. Fungal Genet Biol 72:64–72.
  14. Raju RM, Jedrychowski MP, Wei JR et al. (2014) Post-Translational Regulation via Clp Protease Is Critical for Survival of Mycobacterium tuberculosis. PLoS Pathog Mar 6 ePub:10(3):e1003994.
  15. Rußmayer H, Buchetics M, Gruber C et al. (2015) Systems-level organization of yeast methylotrophic lifestyle. BMC Biol Sep 25 ePub:13:80.
  16. Westman JO, Taherzadeh MJ, Franzen CJ (2012) Proteomic Analysis of the Increased Stress Tolerance of Saccharomyces cerevisiae Encapsulated in Liquid Core Alginate-Chitosan Capsules. PLoS One Nov 9 ePub:7(11):e49335.
  17. Weston AJ, Dunlap WC, Shick JM et al. (2012) A Profile of an Endosymbiont-enriched Fraction of the Coral Stylophora pistillata Reveals Proteins Relevant to Microbial-Host Interactions. Mol Cell Proteomics 11:1–19.
  18. Wojdyla K, Williamson J, Roepstorff P et al. The SNO/SOH TMT strategy for combinatorial analysis of reversible cysteine oxidations. J Proteomics 113:415–434.
  19. Xu H, Bygdell J, Wingsle G et al. (2015) Yeast Elongator protein Elp1p does not undergo proteolytic processing in exponentially growing cells. Microbiologyopen 4:867–878.
  20. Yue H, Ling C, Yang T et al. (2014) A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates. Biotechnol Biofuels July 22 ePub:7:108.
  1. Bergemalm D, Kruse R, Sapnara M et al. (2017) Elevated fecal peptidase D at onset of colitis in Galphai2-/- mice, a mouse model of IBD. PLoS One Mar 21 ePub:12(3):e0174275.
  2. Carvalho PC, Lima DB, Leprevost FV et al. (2016) Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0. Nat Protocols 11:102–117.
  3. Cehofski LJ, Kruse A, Bøgsted M et al. (2016) Retinal proteome changes following experimental branch retinal vein occlusion and intervention with ranibizumab. Exp Eye Res 152:49–56.
  4. Chick JM, Munger SC, Simecek P et al. (2016) Defining the consequences of genetic variation on a proteome-wide scale. Nature 534:500–505.
  5. Fielding CA, Weekes MP, Nobre LV et al. (2017) Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation. eLife Feb 10 ePub:6:e22206.
  6. Fisher HS, Jacobs-Palmer E, Lassance JM et al. (2016) The genetic basis and fitness consequences of sperm midpiece size in deer mice. Nat Commun Dec 2 ePub:7:13652.
  7. Funnell T, Tasaki S, Oloumi A et al. (2017) CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. Nat Commun Feb 23 ePub:8:7.
  8. He H, Ye A, Kim H et al. (2016) PEG3 Interacts with KAP1 through KRAB-A. PLoS One Nov 29 ePub:11(11):e0167541.
  9. Jih G, Iglesias N, Currie MA et al. (2017) Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature 547:463–467.
  10. Paek J, Kalocsay M, Staus DP et al. (2017) Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell 169(2):338–349.
  11. Paulo JA, Gygi SP (2016) Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines. Proteomics Nov 12 ePub:17(1-2).
  12. Paulo JA, O’Connell JD, Gygi SP (2016) A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. J Am Soc Mass Spectrom 27:1620–1625.
  13. Plubell DL, Wilmarth PA, Zhao Y et al. (2017) Extended multiplexing of TMT labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue. Mol Cell Proteomics 16(5):873–890.
  14. Ron-Harel N, Santos D, Ghergurovich JM et al. (2016) Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation. Cell Metabol 24:104–117.
  15. Trakarnsanga K, Griffiths RE, Wilson MC et al. (2017) An immortalized adult human erythroid line facilitates sustainable and scalable generation of functional red cells. Nat Commun Mar 14 ePub:8:14750.
  1. Aburaya S, Esaka K, Morisaka H et al. (2015) Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis.AMB Expr May 23 ePub:5:29.
  2. Azeem S, Li Z, Zheng H et al. (2016) Quantitative proteomics study on Lsi1 in regulation of rice (Oryza sativa L.) cold resistance. Plant Growth Regul 78(3):307–323.
  3. Balmant KM, Parker J, Yoo MJ et al. (2015) Redox proteomics of tomato in response to Pseudomonas syringae infection. Hortic Res Sep 16 ePub:2:15043.
  4. Guo J, Nguyen AY, Dai Z et al. (2014) Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-specific Redox Proteomics. Mol Cell Proteomics 13:3270–3285.
  5. Liu T, Shen C, Wang Y et al. (2014) New Insights into Regulation of Proteome and Polysaccharide in Cell Wall of Elsholtzia splendens in Response to Copper Stress. PLoS One Oct 23 ePub:9(10):e109573.
  6. Nambu M, Tatsukami Y, Morisaka H et al. (2015) Quantitative time-course proteome analysis of Mesorhizobiumloti during nodule maturation. J Proteomics 125:112–120.
  7. Neilson KA, Scafaro AP, Chick JM et al. (2013) The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings. Proteomics 13:1922–1933.
  8. Raorane ML, Pabuayon IM, Varadarajan AR et al. (2015) Proteomic insights into the role of the large-effect QTL qDTY12.1 for rice yield under drought. Mol Breed Jun 2 ePub:35:139.
  9. Rose CM, Venkateshwaran M, Volkening JD et al. (2012) Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis. Mol Cell Proteomics 11:724–744.
  10. Turek I, Wheeler JI, Gehring C et al. (2015) Quantitative proteome changes in Arabidopsis thaliana suspension-cultured cells in responseto plant natriuretic peptides. Data Brief 4:336–343.
  11. Xiong Q, Feng J, Li S et al. (2015) Integrated Transcriptomic and Proteomic Analysis of the Global Response of Synechococcus to High Light Stress. Mol Cell Proteomics 14:1038–1053.
  12. Zhang H, Deery MJ, Gannon L et al. (2015) Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots. Proteomics 15:2447–2457.
  1. An J, Ponthier CM, Sack R et al. (2017) pSILAC mass spectrometry reveals ZFP91 as IMiD-dependent substrate of the CRL4CRBN ubiquitin ligase. Nat Commun May 22 ePub:8:15398.
  2. Choi WH, de Poot SAH, Lee JH et al. (2016) Open-gate mutants of the mammalian proteasome show enhanced ubiquitin-conjugate degradation. Nat Commun Mar 9 ePub:7:10963.
  3. Chursa U, Nuñez-Durán E, Cansby E et al.(2017) Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle. Diabetologia 60(3):553–567.
  4. Greenwood EJD, Nich Matheson NJ, Wals K et al. (2016) Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants. eLife Sep 30 ePub:5:e18296.
  5. Possemato AP, Paulo JA, Mulhern D et al. Multiplexed phosphoproteomic profiling using titanium dioxide and immuno-affinity enrichments reveals complementary phosphorylation events. J. Proteome Res 16(4):1506–1514.
  6. Rose CM, Isasa M, Ordureau A et al. (2016) Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. Cell Syst 3(4):395–403.e4.
  7. Scott DC, Rhee DY, David M. Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation. Cell 166:1198–1214.
  8. Shishkova E, Zeng H, Liu F et al. (2017) Global mapping of CARM1 substrates defines enzyme specificity and substrate recognition. Nat Commun May 24 ePub:8:15571.
  9. Yua Q, Shib X, Fenga Y et al. (2017) Improving Data Quality and Preserving HCD-Generated Reporter Ions with EThcD for Isobaric Tag-based Quantitative Proteomics and Proteome-wide PTM Studies. Anal Chim Acta 968:40–49.
  1. Sopko R, Lin YB, Makhijani K et al. (2015) A Systems-Level Interrogation Identifies Regulators of Drosophila Blood Cell Number and Survival. PLoS Genet Mar 6 ePub:11(3):e1005056.
  2. Qu M, Ma L, Chen P et al. (2014) Proteomic Analysis of Insect Molting Fluid with a Focus on Enzymes Involved in Chitin Degradation. J Proteome Res 13:2931−2940.
  1. Benevento M, Tonge PD, Puri MC et al. (2014) Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks. Nat Commun Dec 10 ePub:5:5613.
  2. Choi J, Clement K, Huebner AJ et al. (2017) DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell 20(5):706–719.e7.
  3. Choi J, Huebner AJ, Clement K et al. (2017) Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature 548:219–223.
  4. Christoforou A, Mulvey CM, Breckels LM et al. (2016) A draft map of the mouse pluripotent stem cell spatial proteome. Nat Commun Jan 12 ePub:7:9992.
  5. Hussein SMI, Puri MC, Tonge PD et al. (2014) Genome-wide characterization of the routes to pluripotency. Nature 516:198–206.
  6. Mulvey CM, Schroter C, Gatto L et al. (2015) Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Stem Cells 33:2712–2725.
  7. Peláez-García A, Barderas R, Mendes M et al. (2015) Data from proteomic characterization of the role of Snail1 in murine mesenchymal stem cells and 3T3-L1 fibroblasts differentiation. Data Brief 4:606–613.
  8. Pfaffeneder T, Spada F, Wagner M et al. (2014) Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol 10:574–581.
  9. Trakarnsanga K, Wilson MC, Griffiths RE et al. (2014) Qualitative and Quantitative Comparison of the Proteome of Erythroid Cells Differentiated from Human iPSCs and Adult Erythroid Cells by Multiplex TMT Labelling and NanoLC-MS/MS. PLoS One Jul 14 ePub:9(7):e100874.
  10. Vethe H, Bjørlykke Y, Ghila LM et al. (2017) Probing the missing mature β-cell proteomic landscape in differentiating patient iPSC-derived cells. Sci Rep Jul 6 ePub:7:4780.
  11. Yeung ATY, Hale C, Lee AH et al. (2017) Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis. Nat Commun Apr 25 ePub:8:15013.
  1. Bloem E, Meems H, van den Biggelaar M et al. (2012) Mass Spectrometry-assisted Study Reveals That Lysine Residues 1967 and 1968 Have Opposite Contribution to Stability of Activated Factor VIII. J Biol Chem 287(8):5775–5783.
  2. Chang JW, Zhang W, Yeh HS et al. (2015) mRNA 30-UTR shortening is a molecular signature of mTORC1 activation. Nat Commun Jun 15 ePub:7218.
  3. Gunawardana CG, Mehrabian M, Wang X et al. (2015) The human tau interactome: binding to the ribonucleoproteome, and impaired binding of the P301L mutant to chaperones and the proteasome. Mol Cell Proteomics 14:3000–3014.
  4. Huttlin EL, Ting L, Bruckner RJ et al. (2015) The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 162:425–440.
  5. Mardakheh FK, Sailem HZ, Kümper S et al. (2017) Proteomics profiling of interactome dynamics by colocalisation analysis (COLA). Mol BioSyst 13:92–105.
  6. Münch C, Harper JW (2016) Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation. Nature 534:710–713.
  7. Orelle C, Carlson ED, Szal T et al. (2015) Protein synthesis by ribosomes with tethered subunits. Nature 524(7563):119–124.
  8. Venable JD, Steckler C, Ou W et al. (2015) Isotope-Coded Labeling for Accelerated Protein Interaction Profiling Using MS. Anal Chem 87:7540−7544.
  9. Yu C, Huszagh AS, Viner R et al. (2016) Developing a Multiplexed Quantitative Cross-linking Mass Spectrometry Platform for Comparative Structural Analysis of Protein Complexes. Anal Chem 88(20):10301–10308.
  10. Zhou Y, Vachet RW (2013) Covalent Labeling with Isotopically Encoded Reagents for Faster Structural Analysis of Proteins by Mass Spectrometry. Anal Chem 85:9664−9670.
  1. Ahrné E, Martinez-Segur A, Syed AP et al. (2015) Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry. Methods 85:100–107.
  2. Chouchani ET, Kazak L, Jedrychowski MP et al. (2016) Mitochondrial ROS regulate thermogenic energy expenditure and sulfenylation of UCP1. Nature 532:112–116.
  3. Dittenhafer-Reed KE, Richards AL, Fan J et al. (2015) SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching. Cell Metab 21:637–646.
  4. Long JZ, Svensson KJ, Bateman LA et al. (2016) The Secreted Enzyme PM20D1 Regulates Lipidated Amino Acid Uncouplers of Mitochondria. Cell 166:424–435.
  5. Mulvey CM, Breckels LM, Geladaki A et al. (2017) Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. Nat Protoc 12:1110–1135.
  6. van Breevoort D, van Agtmaal EL, Dragt BS et al. (2012) Proteomic Screen Identifies IGFBP7 as a Novel Component of Endothelial Cell-Specific Weibel-Palade Bodies. J Proteome Res 11:2925−2936.
  7. Wuhr M, Guttler T, Peshkin L et al. (2015) The Nuclear Proteome of a Vertebrate. Curr Biol 25:1–9.
  8. Yang Z, Guo Q, Goto S et al. (2014) Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence. Protein Cell 5(5):394–407.
  1. Acosta-Martin AE, Panchaud A, Chwastyniak M et al. (2011) Quantitative Mass Spectrometry Analysis Using PAcIFIC for the Identification of Plasma Diagnostic Biomarkers for Abdominal Aortic Aneurysm. PLoS One Dec 7 ePub:6(12):e28698.
  2. Boylston JA, Sun J, Chen Y et al. (2015) Characterization of the cardiac succinylome and its role in ischemia–reperfusion injury. J Mol Cell Cardiol 88:73–81.
  3. Dayon L, Kussmann M (2013) Proteomics of human plasma: A critical comparison ofanalytical workflows in terms of effort, throughput and outcome. EuPA Open Proteom 1:8–16.
  4. Evans TM, Van Remmen H, Purkar A et al. (2014) Microwave and magnetic (M 2) proteomics of a mouse model of mild traumatic brain injury. Transl Proteom 3:10–21.
  5. Gardner S, Gross SM, David LL et al. (2015) Separating myoblast differentiation from muscle cell fusion using IGF-I and the p38 MAP kinase inhibitor SB202190. Am J Physiol Cell Physiol 309:C491–C500.
  6. George PM, Mlynash M, Adams CM et al. (2015) Novel TIA biomarkers identified by mass spectrometry-based proteomics. Int J Stroke 10(8):1204-1211.
  7. Hebert AS, Dittenhafer-Reed KE, Yu W et al. (2013) Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Mol Cell 49:186–199.
  8. Hellström M, El-Akouri RR, Sihlbom C et al. (2014) Towards the development of a bioengineered uterus: Comparison of different protocols for rat uterus decellularization. Acta Biomater 10:5034–5042.
  9. Hoffman NJ, Parker BL, Chaudhuri R et al. (2015) Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates. Cell Metabol 22:1–14.
  10. KonIarevic S, Lößner C, Kuhn K et al. (2014) In-Depth Profiling of the Peripheral Blood Mononuclear Cells Proteome for Clinical Blood Proteomics. Int J Proteomics Mar 3 ePub:2014:129259.
  11. Littlejohns B, Heesom K, Angelini GD et al. (2014) The effect of disease on human cardiac protein expression profiles in paired samples from right and left ventricles. Clin Proteomics Sep 1 ePub:11:34.
  12. Littlejohns B, Pasdois P, Duggan S et al. (2014) Hearts from Mice Fed a Non-Obesogenic High-Fat Diet Exhibit Changes in Their Oxidative State, Calcium and Mitochondria in Parallel with Increased Susceptibility to Reperfusion Injury. PLoS One Jun 20 ePub:9(6):e100579.
  13. Paulo JA, Gaun A, Gygi SP (2015) Global Analysis of Protein Expression and Phosphorylation Levels in Nicotine-Treated Pancreatic Stellate Cells. J Proteome Res 14:4246−4256.
  14. Paulo JA, Kadiyala V, Banks PA et al. (2013) Mass Spectrometry-based Quantitative Proteomic Profiling of Human Pancreatic and Hepatic Stellate Cell Lines. Genomics Proteomics Bioinformatics 11:105–113.
  15. Sajic T, Hainard A, Scherl A et al. (2013) STAT6 promotes bi-directional modulation of PKM2 in liver and adipose inflammatory cells in Rosiglitazone-treated mice. Sci Rep Aug 6 ePub:3:2350.
  16. Shao B, Guo Y, Wang L et al. (2015) Unraveling the proteomic profile of mice testis during the initiation of meiosis. J Proteomics 120:35–43.
  17. Wang Y, Zhang P, Xu Z et al. (2015) S-nitrosylationofPDE5increasesitsubiquitin–proteasomal degradation. Free Radic Biol Med 86:343–351.
  18. Weekes MP, Tomasec P, Huttlin EL et al. (2014) Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction. Cell 157:1460–1472.