TMT Publications

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2017Post-translational modificationsAn 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.
2017OtherBergemalm 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.
2017Cancer researchBiancur 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.
2017NeurobiologyBrethour D, Mehrabian M, Williams D et al. (2017) A ZIP6-ZIP10 heteromer controls NCAM1 phosphorylation and integration into focal adhesion complexes during epithelial-to-mesenchymal transition.Sci Rep Jan 18 ePub:7:40313.
2017Stem cellsChoi 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.
2017Stem cellsChoi J, Huebner AJ, Clement K et al. (2017) Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells.Nature 548:219–223.
2017Post-translational modificationsChursa 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.
2017Method developmentErickson 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.
2017OtherFielding 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.
2017Microorganisms and model organismsGanter 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.
2017Method developmentHuang 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.
2017OtherJih 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.
2017Structural biology/protein interactionsMardakheh FK, Sailem HZ, Kümper S et al. (2017) Proteomics profiling of interactome dynamics by colocalisation analysis (COLA).Mol BioSyst 13:92–105.
2017Subcellular biologyMulvey CM, Breckels LM, Geladaki A et al. (2017) Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.Nat Protoc 12:1110–1135.
2017Method developmentNiu 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.
2017OtherPaek J, Kalocsay M, Staus DP et al. (2017) Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling.Cell 169(2):338–349.
2017OtherPlubell 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.
2017Post-translational modificationsPossemato AP, Paulo JA, Mulhern D et al.(2017) Multiplexed phosphoproteomic profiling using titanium dioxide and immuno-affinity enrichments reveals complementary phosphorylation events.J. Proteome Res 16(4):1506–1514.
2017NeurobiologyRussell CL, Heslegrave A, Mitra V et al. (2017) Combined tissue and fluid proteomics with Tandem Mass Tags to identify low-abundance protein biomarkers of disease in peripheral body fluid: An Alzheimer's Disease case study.Rapid Commun Mass Spectrom 31(2):153–159.
2017Post-translational modificationsShishkova 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.
2017Cancer researchTien 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.
2017OtherTrakarnsanga 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.
2017Stem cellsVethe 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.
2017Stem cellsYeung 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.
2017Post-translational modificationsYua 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.
2017Cancer researchZheng 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.
2016Proteome studyWhite Paper: High Throughput Quantitative Proteomics Using Isobaric Tags
2016Plant proteomicsAzeem 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.
2016Cancer researchBanh 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.
2016Cell signalingBukhari 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.
2016OtherCarvalho 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.
2016OtherCehofski 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.
2016OtherChick JM, Munger SC, Simecek P et al. (2016) Defining the consequences of genetic variation on a proteome-wide scale.Nature 534:500–505.
2016Post-translational modificationsChoi 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.
2016Subcellular biologyChouchani ET, Kazak L, Jedrychowski MP et al. (2016) Mitochondrial ROS regulate thermogenic energy expenditure and sulfenylation of UCP1.Nature 532:112–116.
2016Stem cellsChristoforou 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.
2016OtherFisher 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.
2016OtherFunnell 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.
2016Post-translational modificationsGreenwood 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.
2016Cancer researchGrzmil 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.
2016OtherHe H, Ye A, Kim H et al. (2016) PEG3 Interacts with KAP1 through KRAB-A.PLoS One Nov 29 ePub:11(11):e0167541.
2016Cancer researchHughes 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.
2016Cancer researchJordan NV, Bardia A, Wittner BS et al. (2016) HER2 expression identifies dynamic functional states within circulating breast cancer cells.Nature 537:102–106.
2016Microorganisms and model organismsKugadas 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.
2016Method developmentLiu 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.
2016Subcellular biologyLong JZ, Svensson KJ, Bateman LA et al. (2016) The Secreted Enzyme PM20D1 Regulates Lipidated Amino Acid Uncouplers of Mitochondria.Cell 166:424–435.
2016Microorganisms and model organismsMcEwan 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.
2016NeurobiologyMehrabian M, Brethour D, Williams D et al. (2016) Prion Protein Deficiency Causes Diverse Proteome Shifts in Cell Models That Escape Detection in Brain Tissue.PLoS One Jun 21 ePub:11(6):e0156779.
2016Structural biology/protein interactionsMünch C, Harper JW (2016) Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation.Nature 534:710–713.
2016OtherPaulo 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).
2016Microorganisms and model organismsPaulo 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.
2016Method developmentPaulo 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.
2016OtherPaulo 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.
2016OtherRon-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.
2016Post-translational modificationsRose CM, Isasa M, Ordureau A et al. (2016) Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes.Cell Syst 3(4):395–403.e4.
2016Cancer researchSalony XS, Alves CP, Dey-Guha I et al. (2016) AKT Inhibition Promotes Nonautonomous Cancer Cell Survival.Mol Cancer Ther 15:142–153.
2016Post-translational modificationsScott DC, Rhee DY, David M. (2016) Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation.Cell 166:1198–1214.
2016DevelopmentTaylor KM, Muraina IA, Brethour D et al. (2016) Zinc transporter ZIP10 forms a heteromer with ZIP6 which regulates embryonic development and cell migration.Biochem J 473:2531–2544.
2016NeurobiologyVannini E, Olimpico F, Middei S et al. (2016) Electrophysiology of glioma: a Rho GTPase-activating protein reduces tumor growth and spares neuron structure and function.Neuro Oncol 18(12):1634–1643.
2016Cancer researchVartanian 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.
2016Structural biology/protein interactionsYu 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.
2015Plant proteomicsAburaya 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.
2015Subcellular biologyAhrné 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.
2015Disease study-biomarker researchAlam 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.
2015Disease study-biomarker researchAlexander S., Banks AS, McAllister FE et al. (2015) An ERK/Cdk5 axis controls the diabetogenic actions of PPARc.Nature 517(7534):391–395.
2015Disease study-biomarker researchAshtona 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.
2015Plant proteomicsBalmant 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.
2015Disease study-biomarker researchBelin S, Nawabi H, Wang C et al. (2015) Injury-Induced Decline of Intrinsic Regenerative Ability Revealed by Quantitative Proteomics.Neuron 86:1000–1014.
2015Personalized medicineBershtein S, Choi JM, Bhattacharyya S et al. (2015) Systems-Level Response to Point Mutations in a Core Metabolic Enzyme Modulates Genotype-Phenotype Relationship.Cell Rep 11:645–656.
2015Method developmentBonneil 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.
2015Tissue analysis- biomarker researchBoylston 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.
2015Cell signalingBulatov 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.
2015Disease study-biomarker researchButovsky 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.
2015Method developmentCao Z, Evans AR, Robinson RAS (2015) MS3-based quantitative proteomics using pulsed-Q dissociation.Rapid Commun Mass Spectrom 29:1025–1030.
2015Structural biology/protein interactionsChang 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.
2015Cell signalingChen M, Zhu A, Storey KB (2015) Comparative phosphoproteomic analysis of intestinal phosphorylated proteins in active versus aestivating sea cucumbers.J Proteomics 135:141–150.
2015Disease study-biomarker researchChen 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.
2015Method developmentChung 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.
2015Cancer researchChurchman ML, Low J, Qu C et al. (2015) Efficacy of Retinoids in IKZF1-Mutated BCR-ABL1 Acute Lymphoblastic Leukemia.Cancer Cell 28:343–356.
2015Method developmentCurran 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.
2015Subcellular biologyDittenhafer-Reed KE, Richards AL, Fan J et al. (2015) SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching.Cell Metab 21:637–646.
2015Microorganisms and model organismsEsaka 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.
2015Drug mechanismFranken H, Mathieson T, Childs D et al. (2015) Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.Nat Protoc 10:1567–1593.
2015Cancer researchGao 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.
2015Tissue analysis- biomarker researchGardner 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.
2015BioPharmaGautier V, Boumeester AJ, Lo P et al. (2015) Lysine conjugation properties in human IgGs studied by integrating high-resolution native mass spectrometry and bottom-up proteomics.Proteomics 15:2756–2765.
2015Tissue analysis- biomarker researchGeorge PM, Mlynash M, Adams CM et al. (2015) Novel TIA biomarkers identified by mass spectrometry-based proteomics.Int J Stroke 10(8):1204-1211.
2015Disease study-biomarker researchGu L, Evans AR, Robinson RAS (2015) Sample Multiplexing with Cysteine-Selective Approaches: cysDML and cPILOT. J Am Soc Mass Spectrom 26:615–630.
2015Structural biology/protein interactionsGunawardana 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.
2015Drug mechanismHagner PR, Man HW, Fontanillo C et al. (2015) CC-122, a pleiotropic pathway modifier, mimics an interferon response and has antitumor activity in DLBCL.Blood 126(6):779–789.
2015Cel signalingHeo 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.
2015Tissue analysis- biomarker researchHoffman 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.
2015Cancer researchHuan 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.
2015Drug mechanismHuber KVM, Olek KM, Müller AC et al. (2015) Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling.Nat Methods 12(11):1055–1057.
2015Structural biology/protein interactionsHuttlin EL, Ting L, Bruckner RJ et al. (2015) The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 162:425–440.
2015NeurobiologyIchinose S, Ogawa T, Hirokawa N (2015) Mechanism of Activity-Dependent Cargo Loading via the Phosphorylation of KIF3A by PKA and CaMKIIa.Neuron 87:1022–1035.
2015Disease study-biomarker researchJastrab 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.
2015Cel signalingJedrychowski 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.
2015Disease study-biomarker researchKeshishian 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.
2015Disease study-biomarker researchKronke J, Fink EC, Hollenbach PW et al. (2015) Lenalidomide induces ubiquitination and degradation of CK1a in del(5q) MDS.Nature 523:183–188.
2015Microorganisms and model organismsKwan 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.
2015BioPharmaLiu Z, Dai S, Bones J et al. (2015)A Quantitative Proteomic Analysis of Cellular Responses to High Glucose Media in Chinese Hamster Ovary Cells.Biotechnol Prog 31(4):1026–1038.
2015Disease study-biomarker researchMaes 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.
2015Disease study-biomarker researchMatheson 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.
2015Disease study-biomarker researchMbongue 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.
2015Disease study-biomarker researchMehrabian 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.
2015Gene expressionMinajigi A, Froberg JE, Wei C et al. (2015) A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation.Science 349:6245.
2015Microorganisms and model organismsMosier 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.
2015Cancer researchMuellner 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.
2015Stem cellsMulvey 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.
2015Cel signalingMurphy 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.
2015Plant proteomicsNambu M, Tatsukami Y, Morisaka H et al. (2015) Quantitative time-course proteome analysis of Mesorhizobiumloti during nodule maturation.J Proteomics 125:112–120.
2015Cel signalingNirujogi 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.
2015Cel signalingOgawa T, Hirokawa N (2015) Microtubule Destabilizer KIF2A Undergoes Distinct Site-Specific Phosphorylation Cascades that Differentially Affect Neuronal Morphogenesis.Cell Rep 12:1774–1788.
2015Structural biology/protein interactionsOrelle C, Carlson ED, Szal T et al. (2015) Protein synthesis by ribosomes with tethered subunits.Nature 524(7563):119–124.
2015Method developmentParker J, Balmant K, Zhu F et al. (2015) cysTMTRAQ—An Integrative Method for Unbiased Thiol-based Redox Proteomics.Mol Cell Proteomics 14:237–242.
2015Tissue analysis- biomarker researchPaulo 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.
2015Drug mechanismPaulo JA, Gygi SP (2015) A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin.Proteomics 15:474–486.
2015Drug mechanismPaulo JA, McAllister FE, Everley RA et al. (2015) Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics.Proteomics 15:462–473.
2015Stem cellsPeláez-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.
2015Cancer researchPerera RM, Stoykova S, Nicolay BN et al. (2015) Transcriptional control of autophagy–lysosome function drives pancreatic cancer metabolism.Nature 524:361–365.
2015Personalized medicineRao RR, Long JZ, White JP et al. (2014) Meteorin-like Is a Hormone that Regulates Immune-Adipose Interactions to Increase Beige Fat Thermogenesis.Cell 157:1279–1291.
2015Plant proteomicsRaorane 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.
2015Disease study-biomarker researchRauniyar 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.
2015Method developmentRicchiuto 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.
2015Cel signalingRusin 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.
2015Microorganisms and model organismsRußmayer H, Buchetics M, Gruber C et al. (2015) Systems-level organization of yeast methylotrophic lifestyle.BMC Biol Sep 25 ePub:13:80.
2015Cancer researchSandin 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.
2015Tissue analysis- biomarker researchShao 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.
2015Proteome studySopko 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.
2015Food proteomicsStella R, Biancotto G, Arrigoni G et al. (2015) Proteomics for the detection of indirect markers of steroids treatment in bovine muscle.Proteomics 15:2332–2341.
2015Cancer researchSvinkina 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.
2015Cel signalingTagliabracci VS, Wiley SE, Guo X et al. (2015) A Single Kinase Generates the Majority of the Secreted Phosphoproteome.Cell 161:1619–1632.
2015Disease study-biomarker researchTiberti 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.
2015Disease study-biomarker researchTitz 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.
2015Plant proteomicsTurek 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.
2015Cancer researchVan 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.
2015Structural biology/protein interactionsVenable JD, Steckler C, Ou W et al. (2015) Isotope-Coded Labeling for Accelerated Protein Interaction Profiling Using MS.Anal Chem 87:7540−7544.
2015Cancer researchVenkatesh HS, Johung TB, Caretti V et al. (2015) Neuronal Activity Promotes Glioma Growth through Neuroligin-3 Secretion.Cell 161:803–816.
2015Tissue analysis- biomarker researchWang Y, Zhang P, Xu Z et al. (2015) S-nitrosylationofPDE5increasesitsubiquitin–proteasomal degradation.Free Radic Biol Med 86:343–351.
2015Cancer researchWang 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.
2015Microorganisms and model organismsWojdyla K, Williamson J, Roepstorff P et al. (2015) The SNO/SOH TMT strategy for combinatorial analysis of reversible cysteine oxidations.J Proteomics 113:415–434.
2015Subcellular biologyWuhr M, Guttler T, Peshkin L et al. (2015) The Nuclear Proteome of a Vertebrate.Curr Biol 25:1–9.
2015Plant proteomicsXiong 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.
2015Microorganisms and model organismsXu 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.
2015Drug mechanismYe H, Hill J, Gucinski AC et al. (2015) Direct Site-Specific Glycoform Identification and Quantitative Comparison of Glycoprotein Therapeutics: Imiglucerase and Velaglucerase Alfa.AAPS J 17(2):405–415.
2015Cancer researchZahari 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.
2015Disease study-biomarker researchZen 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.
2015Food proteomicsZeng J, He X, Quan S et al. (2015) Identification of the proteins associated with low potassium tolerance in cultivated and Tibetan wild barley.J Proteomics 126:1–11.
2015Plant proteomicsZhang H, Deery MJ, Gannon Let al. (2015) Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.Proteomics 15:2447–2457.
2015Disease study-biomarker researchZhao 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–
2014Disease study-biomarker researchAmaral 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.
2014Disease study-biomarker researchAzpiazu 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.
2014Stem cellsBenevento 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.
2014Cancer researchBetancourt 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.
2014Disease study-biomarker researchButovsky 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.
2014Disease study-biomarker researchCarvalho 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.
2014Microorganisms and model organismsChasman 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.
2014Disease study-biomarker researchChen 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.
2014Disease study-biomarker researchCheng 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.
2014Method developmentChiva 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.
2014DevelopmentChung JJ, Shim SH, Everley RA et al. (2014) Structurally Distinct Ca2+ Signaling Domains of Sperm Flagella Orchestrate Tyrosine Phosphorylation and Motility.Cell 157:808–822.
2014Disease study-biomarker researchDombkowski 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.
2014Disease study-biomarker researchDong 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.
2014Tissue analysis- biomarker researchEvans 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.
2014Disease study-biomarker researchFields 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.
2014Drug mechanismFloyd CN, Goodman T, Becker S et al. (2014) Increased platelet expression of glycoprotein IIIa following aspirin treatment in aspirin-resistant but not aspirin-sensitive subjects.Br J Clin Pharmacol 78(2):320–328.
2014Gene expressionGruber 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.
2014Microorganisms and model organismsGuerreiro 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.
2014Plant proteomicsGuo 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.
2014Tissue analysis- biomarker researchHellström 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.
2014Method developmentHelm 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.
2014Method developmentHughes CS, Foehr S, Garfield DA et al. (2014) Ultrasensitive proteome analysis using paramagnetic bead technology.Mol Syst Biol Oct 30 ePub:10:757.
2014Stem cellsHussein SMI, Puri MC, Tonge PD et al. (2014) Genome-wide characterization of the routes to pluripotency.Nature 516:198–206.
2014Cancer researchJung 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.
2014Disease study-biomarker researchKhor 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.
2014Tissue analysis- biomarker researchKonIarevic 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.
2014Cancer researchLee 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.
2014Disease study-biomarker researchLicker 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.
2014Tissue analysis- biomarker researchLittlejohns 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.
2014Tissue analysis- biomarker researchLittlejohns 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.
2014Plant proteomicsLiu 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.
2014Disease study-biomarker researchLv 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.
2014Method developmentMcAlister 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.
2014Method developmentMegger 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.
2014Disease study-biomarker researchMehrabian 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.
2014Disease study-biomarker researchMenezes 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.
2014DevelopmentMiao Z, Chen M, Wu H et al. (2014) Comparative Proteomic Profile of the Human Placenta in Normal and Fetal Growth Restriction Subjects.Cell Physiol Biochem 34:1701–1710.
2014Disease study-biomarker researchMisuno 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.
2014AgingMiwa 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.
2014Method developmentMurphy 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.
2014Disease study-biomarker researchNi 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.
2014Disease study-biomarker researchOrdureau 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.
2014Disease study-biomarker researchParker 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.
2014Microorganisms and model organismsPeciulyte 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.
2014Stem cellsPfaffeneder 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.
2014Disease study-biomarker researchPhillips RJ, Heesom K, Trinder J et al. (2014) Human maternalplasmaproteomicchangeswith parturition.EuPA Proteomics 5:10–20.
2014Gene expressionPrabakaran S, Hemberg M, Chauhan R et al. (2014) Quantitative profiling of peptides from RNAs classified as noncoding.Nat Commun Nov 18 ePub:5:5429.
2014Proteome studyQu 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.
2014Microorganisms and model organismsRaju 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.
2014Disease study-biomarker researchRaphael 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.
2014Disease study-biomarker researchSalvisberg 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.
2014Method developmentSandberg 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.
2014Disease study-biomarker researchSchondorf 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.
2014Cancer researchSherwood 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.
2014Cell signalingSingh 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.
2014Gene expressionSlavov 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.
2014Cell signalingSopko 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.
2014Stem cellsTrakarnsanga 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.
2014Neurobiologyvon Tobel JS, Antinori P, Zurich MG et al. (2014) Repeated exposure to Ochratoxin A generates a neuroinflammatory response, characterized by neurodegenerative M1 microglial phenotype.NeuroToxicology 44:61–70.
2014AgingWang P, Sun X, Xie Y et al. (2014) Melatonin regulates proteomic changes during leaf senescence in Malus hupehensis.J Pineal Res 57:291–307.
2014Cancer researchWard 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.
2014Tissue analysis- biomarker researchWeekes MP, Tomasec P, Huttlin EL et al. (2014) Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction.Cell 157:1460–1472.
2014Subcellular biologyYang 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.
2014Microorganisms and model organismsYue 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.
2014DevelopmentZheng B, Zhou Q, Guo Y et al. (2014) Establishment of a proteomic profile associated with gonocyte and spermatogonial stem cell maturation and differentiation in neonatal mice.Proteomics 14:274–285.
2013Microorganisms and model organismsAoki 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.
2013AgingChaves 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.
2013Tissue analysis- biomarker researchDayon 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.
2013Method developmentDiedrich 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.
2013Method developmentEvans AR, Robinson RAS (2013) Global combined precursor isotopic labeling and isobaric tagging (cPILOT) approach with selective MS3 acquisition.Proteomics 13:3267–3272.
2013Microorganisms and model organismsGhiaci P, Norbeck J, Larsson C (2013) Physiological adaptations of Saccharomyces cerevisiae evolved for improved butanol tolerance.Biotechnol Biofuels July 15 ePub:6:101.
2013Tissue analysis- biomarker researchHebert 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.
2013Disease study-biomarker researchHong I, Kang T, Yun KN et al. (2013) Quantitative proteomics of auditory fear conditioning.Biochem Biophys Res Commun 434:87–94.
2013Disease study-biomarker researchMarancik 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.
2013Disease study-biomarker researchMatsumura 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.
2013Cel signalingMcAllister 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.
2013Cancer researchMisuno 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.
2013Plant proteomicsNeilson 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.
2013Cancer researchPatel 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.
2013Tissue analysis- biomarker researchPaulo 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.
2013Disease study-biomarker researchRæder 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.
2013Cel signalingRainbolt TK, Atanassova N, Genereux JC et al. (2013) Stress-Regulated Translational Attenuation Adapts Mitochondrial Protein Import through Tim17A Degradation.Cell Metab 18:908–919.
2013Tissue analysis- biomarker researchSajic 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.
2013Disease study-biomarker researchSyddall 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.
2013Cancer researchTilghman 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.
2013Disease study-biomarker researchTsuchida 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.
2013Gene expressionVinken M, Maes M, Cavill R et al. (2013) Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures.Arch Toxicol 87:883–894.
2013Gene expressionWu L, Candille SI, Choi Y et al. (2013) Variation and genetic control of protein abundance in humans.Nature 499:79–82.
2013Method developmentYe 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.
2013Structural biology/protein interactionsZhou Y, Vachet RW (2013) Covalent Labeling with Isotopically Encoded Reagents for Faster Structural Analysis of Proteins by Mass Spectrometry.Anal Chem 85:9664−9670.
2013Disease study-biomarker researchZhuang 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.
2012Cel signalingArabi 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
2012Disease study-biomarker researchBanerjee 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.
2012Structural biology/protein interactionsBloem 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.
2012Cel signalingByun 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.
2012Personalized medicineChen R, Mias GI, Li-Pook-Than J et al. (2012) Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes.Cell 148:1293–1307.
2012Method developmentDayon 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.
2012Method developmentDephoure 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.
2012Method developmentFeng 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.
2012Method developmentHung CW, Tholey A (2012) Tandem Mass Tag Protein Labeling for Top-Down Identification and Quantification.Anal Chem 84:161–170.
2012Cel signalingJia 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.
2012Disease study-biomarker researchKohr 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.
2012Method developmentLedvina AR, Lee MV, McAlister GC et al. (2012) Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics.Anal Chem 84:4513−4519.
2012Disease study-biomarker researchMahesula 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.
2012Drug mechanismMalki K, Campbell J, Davies M et al. (2012) Pharmacoproteomic investigation into antidepressant response in two mouse inbred strains.Proteomics 12:2355–2365.
2012Method developmentMurray 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.
2012Method developmentPachl 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.
2012Cancer researchRadziwon-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.
2012Disease study-biomarker researchRaphael 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.
2012Cancer researchRaso 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.
2012Plant proteomicsRose CM, Venkateshwaran M, Volkening JD et al. (2012) Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis.Mol Cell Proteomics 11:724–744.
2012Cancer researchSalhia 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.
2012Disease study-biomarker researchStella 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.
2012Subcellular biologyvan 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.
2012Cancer researchWeeraratne 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.
2012Method developmentWerner T, Becher I, Sweetman G et al. (2012) High-Resolution Enabled TMT 8-plexing.Anal Chem 84:7188−7194.
2012Microorganisms and model organismsWestman 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.
2012Microorganisms and model organismsWeston 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.
2012Method developmentWühr 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.
2012Disease study-biomarker researchZhang K, Schrag M, Crofton A et al. (2012) Targeted proteomics for quantification of histone acetylation in Alzheimer’s disease.Proteomics 12:1261–1268.
2012Cancer researchZhou 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.
2011Tissue analysis- biomarker researchAcosta-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.
2011Cel signalingAndaya 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.
2011Cancer researchAnders 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.
2011Cancer researchBantscheff M, Hopf C, Savitski MM et al. (2011) Chemoproteomics profiling of HDACinhibitors reveals selective targeting of HDAC complexes.Nat Biotechnol 29(3):255–265.
2011Disease study-biomarker researchDayon L, Turck N, García-Berrocoso T et al. (2011) Brain Extracellular Fluid Protein Changes in Acute Stroke Patients.J Proteome Res 10:1043–1051.
2011Cancer researchDillon 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.
2011Method developmentGiron 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.
2011Microorganisms and model organismsLee 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.
2011Method developmentNguyen-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.
2011Method developmentPichler 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.
2011Cancer researchSinclair 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.
2011Cancer researchSinclair J, Timms JF (2011) Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC-MS/MS.Methods 54:361–369.
2011Method developmentTing L, Rad R, Gygi SP et al. (2011) MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics.Nat Methods 8(11):937–940.
2011Disease study-biomarker researchWang 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.
2011Method developmentWenger CD, Lee MV, Hebert AS et al. (2011) Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging.Nat Methods 8:933–935.
2011Cancer researchXiong L, Darwanto A, Sharma S et al. (2011) Mass Spectrometric Studies on Epigenetic Interaction Networks in Cell Differentiation.J Biol Chem 286:13657–13668.
2010Method developmentDayon 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.
2010Method developmentEngmann 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.
2010Drug mechanismWest GM, Tucker CL, Xu T et al. (2010) Quantitative proteomics approach for identifying proteindrug interactions in complex mixtures using protein stability measurements.Proc Natl Acad Sci USA107(20):9078–9082.
 Method developmentViner 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.

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