2024-04-09 A framework for quality control in quantitative proteomicsHomo sapiens, Mus musculus, Saccharomyces cerevisiae, Bos taurusOrbitrap Eclipse,Orbitrap Fusion Lumos,Orbitrap FusionKristine A Tsantilas, Gennifer E Merrihew, Juli...No9PXD051318
2024-03-10 Effect of burn wound treatment with fish skin on mouse skin proteomeMus musculusimpact IIGarrity C, Garcia-Rovetta C, Rivas I, Delatorre...No1PXD050514
2024-02-18 AD-BXD Mouse PreFrontal Cortex ProteomicsMus musculusOrbitrap Fusion,Orbitrap Fusion LumosNo50PXD045403
2024-01-26 Analysis of N-Glycosylation for SARS-CoV-2 expressed receptor-binding domain VOCs and membrane protein with LC-MS.Severe acute respiratory syndrome coronavirus 2SYNAPT G2-SiSchwarze M, Volke D, Rojas Echeverri JC, Schick...No1PXD048930
2024-01-26 Fecal Microbiota Transplant_Bile AcidHomo sapiens6560 Q-TOF LC/MSMetagenomic, metabolomic, and lipidomic shifts ...No2 
2024-01-15 Proteomics and machine learning identify a distinct blood biomarker panel to detect Parkinson’s disease up to 7 years before motor diseaseHomo sapiensXevo TQ MS,ACQUITY UPLCProteomics and machine learning identify a dist...No3PXD041419
2023-12-22 Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of GlycosylationHomo sapiensQTRAP 5500,nanoACQUITY UPLC,TSQ VantageSakson R, Beedgen L, Bernhard P, Alp KM, Lübbeh...Yes6PXD048072
2023-12-20 Development of a Mass Spectrometry-Based Method for Quantification of Total Cashew Protein in Roasting OilAnacardium occidentaleQ Exactive,Q Exactive PlusChen S, Downs ML. Development of a Mass Spectro...Yes9PXD047985
2023-12-15 Modeling the simultaneous dynamics of proteins in blood plasma and the cerebrospinal fluid in human in vivoHomo sapienstimsTOF Pro 2Publication pendingNo8PXD047851
2023-12-02 Evaluation of Solid Phase Adsorption Toxin Tracking (SPATTs) for passive monitoring of Per- and Polyfluoroalkyl Substances (PFAS) using Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) 6560 Q-TOF LC/MSExpected in the near future.No3 
2023-11-30 Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomicsHomo sapiensOrbitrap EclipsePublication pendingYes1PXD047419
2023-11-16 PRM quantification of interferon-induced proteins upon Type I IFN-beta, Type II IFN-gamma, and LPS stimulation of differentiated THP-1 cellsHomo sapiensQ Exactive HFNo1 
2023-11-01 Assessment of Kinome-wide Rewiring Upon Picornavirus InfectionHomo sapiensTSQ AltisVeth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wieren...Yes2PXD046598
2023-10-30 Metabolic, Neurotoxic and Immunotoxic Effects of PFAAs and their
Mixtures on the Proteome of Plasma and Head Kidney from Rainbow
Trout		Oncorhynchus mykiss6545 Q-TOF LC/MSPollard S, De Silva AO, Simmons DBD. Metabolic,...No2PXD046517
2023-10-30 METLIN-CCS: an ion mobility spectrometry
collision cross-section database		  Baker ES, Hoang C, Uritboonthai W, Heyman HM, P...No1 
2023-10-19 Acoustic Ejection Mass Spectrometry Empowers Ultra-Fast Peptide Biomarker Quantification... A Paradigm shiftHomo sapiens, SARS-CoV-2Triple Quad 6500+Publication pendingNo29PXD046249
2023-10-02 In-Gel Digest to identify Aspergillus fumigatus protein antigens in severe equine asthma (SEA)Aspergillus fumigatusSYNAPT G2-SiJentsch M-C, Lübke S, Schrödl W, Volke D, Kriz...No3PXD045869
2023-09-21 In-Gel digest and filter-aided sample preparation to identify Dermatophagoides - and yeast protein antigens in severe equine asthma.Saccharomyces cerevisiae, Dermatophagoides pteronyssinusSYNAPT G2-SiSchnabel CL, Jentsch MC, Lübke S, Kaiser-Thom S...No3PXD045568
2023-09-21 Cognitive Functions, Neurotransmitter Alterations, and Hippocampal Microstructural Changes in Mice Caused by Feeding on Western DietMus musculusQ ExactiveCustodio RJ, Hobloss Z, Myllys M, Hassan R, Gon...No3 
2023-09-17 AD-BXD Mouse Hippocampus ProteomicsMus musculusOrbitrap Fusion LumosNo49PXD045425
2023-09-09 Skeletal Muscle TFEB Signaling Promotes Central Nervous System Function and Reduces Neuroinflammation during Aging and Neurodegenerative DiseaseMus musculusOrbitrap Fusion LumosMatthews I, Birnbaum A, Gromova A, Huang AW, Li...No1PXD045241
2023-09-01 Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses 6560 Q-TOF LC/MSYes1 
2023-08-25 The phosphorylation landscape of infection-related development by the rice blast fungusMagnaporthe oryzaeOrbitrap FusionCruz-Mireles N, Osés-Ruiz M, Derbyshire P, Jégo...No1PXD044865
2023-08-08 Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis.Arabidopsis thalianaQ Exactive HF-X,Orbitrap Fusion LumosNo6PXD044142
2023-08-08 Validation of a proteomic signature of lung cancer risk from bronchial specimens of risk-stratified individualsHomo sapiensTSQ Altis,TSQ VantageCancers 2023, 15(18), 4504; https://doi.org/10....Yes5 
2023-07-23 Quantitative Measurement of Secretory Protein Mistargeting by Proximity Labeling and Parallel Reaction MonitoringHomo sapiensLTQ Orbitrap Velos Pro,LTQ Orbitrap VelosNo2PXD044008
2023-07-20 Breeding from 1891 to 2010 did not increase the content of amylase/trypsin-inhibitors in wheat (Triticum aestivum L.)Triticum aestivumTSQ VantageGeisslitz S, Pronin D, Neerukonda M, Curella V,...Yes25PXD043968
2023-07-20 Label-free Parallel Reaction Monitoring (PRM) analysis of selected novel potential targets of IFNg stimulation in Hela cells.Homo sapiensQ Exactive HFBorteçen T, Müller T, Krijgsveld J. An integrat...No1PXD043967
2023-07-14 A novel overlapping gene azyx-1 affects the translation of zyxin in C. elegansCaenorhabditis elegansQ Exactive HF-XPublication pendingYes2PXD034878
2023-07-06 Gut Microbiome IMS-MS ExperimentsHomo sapiens, Mus musculus6560 Q-TOF LC/MSNo2 
2023-07-02 Comparing peptide identifications by FAIMS versus quadrupole gas phase fractionationHomo sapiensOrbitrap EclipsePublication pendingNo4PXD043458
2023-06-22 Targeted Proteomics Quantitation of NRF2 and Predictive Biomarkers in HNSCCHomo sapiensOrbitrap EclipseNo4 
2023-06-21 Sensitive detection of HIV-1 and Mycobacterium tuberculosis peptides in blood for rapid diagnosis of co-infected individuals by immuno-affinity liquid chromatography tandem mass spectrometryHomo sapiensTSQ AltisLi L, Lyon CJ, LaCourse SM, Zheng W, Stern J, E...Yes24PXD043191
2023-06-16 Deep quantitative proteomics of North American Pacific coast star tunicateBotryllus schlosseriimpact IIKültz D, Gardell AM, DeTomaso A, Stoney G, Rink...No1PXD043046
2023-06-13 Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteomeHomo sapiensOrbitrap EclipsePublication pendingNo5PXD042947
2023-06-07 In-vitro differential redox-labeling of NTRCChlamydomonas reinhardtiiQ Exactive PlusNo1PXD042813
2023-06-04 Environmental Conditions Elicit a Slow but Enduring Response of Histone Post-Translational Modifications in Mozambique TilapiaOreochromis mossambicusimpact IINo2PXD042718
2023-06-02 Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent AcquisitionHomo sapiensOrbitrap Fusion Lumos,Orbitrap AstralHeil LR, Damoc E, Arrey TN, Pashkova A, Denisov...No15PXD042704
2023-05-23 Assessing the role of trypsin in quantitative plasma- and single-cell
proteomics towards clinical application		Homo sapiensTSQ Altis,Orbitrap Eclipse,Q Exactive HFWoessmann J, Petrosius V, Üresin N, Kotol D, Ar...Yes2PXD042450
2023-05-17 S-Adenosylmethionine Negatively Regulates the Mitochondrial Respiratory Chain Repressor MCJ in the LiverMus musculusOrbitrap Fusion LumosNo1PXD042309
2023-04-01 Tapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral FactorHomo sapiens, Human herpesvirus 8 strain GK18Q Exactive HFPublication pendingNo1PXD041269
2023-03-30 PRM data for "Functional analysis of a common BAG3 allele associated with protection from heart failure"Homo sapiensQ Exactive PlusFunctional analysis of a common BAG3 allele ass...No1PXD041228
2023-03-12 Global response of Octopus berrima to ocean warmingOctopus berrimaimpact IIPublication pendingNo1PXD040795
2023-03-09 Proteogenomic analysis of chemo-refractory high grade serous ovarian cancerHomo sapiensQTRAP 6500Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, H...Yes4PXD040742
2023-03-07 Targeted Proteomics of Lung Squamous Cell CarcinomasHomo sapiensTSQ AltisPutty Reddy S, Alontaga AY, Welsh EA, Haura EB,...Yes1PXD040680
2023-03-05 PRM quantification of MCS proteins and viral proteins in HCMV virus microenvironmentHomo sapiens, HHV-5Q Exactive HFSong B, Sheng X, Justice JL, Lum KK, Metzger PJ...No2PXD038466
2023-03-02 Development and validation of a matrix independent calibration strategy for targeted mass spectrometry-based quantification of milk protein allergens from complex food matricesBos taurusQ Exactive PlusRamachandran, B. and M.L. Downs, Development an...No15PXD040564
2023-03-02 Salinity-responsive histone PTMs identified in Mozambique tilapia tissuesOreochromis mossambicusimpact IIPublication pendingNo18PXD040557
2023-03-01 A strategy to characterize the global histone PTM landscape within tissues of non-model organismsOreochromis mossambicusimpact IIMojica EA, Kültz D. A Strategy to Characterize ...No9PXD040536
2023-02-27 Metrologically traceable quantification of three apolipoprotein E isoforms in cerebrospinal fluidHomo sapiensXevo TQ-SHuynh HH, Kuch K, Orquillas A, Forrest K, Barah...No27PXD038803
2023-02-17 Correlative study using immuno-MRM in the Cancer Immunotherapy Trials Network (CITN-10) phase 2 clinical trial of pembrolizumab for the treatment of refractory or relapsed Mycosis fungoides (MF) and Sezary syndrome (SS)Homo sapiensQTRAP 5500Whiteaker JR, Zhao L, Schoenherr RM, Huang D, L...No2 
2023-02-06 PeakDecoder enables machine learning-1 based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurementsPseudomonas putida KT2440TSQ AltisNature CommunicationsYes1 
2023-01-18 Degradation kinetics of lignocellulolytic enzymes in a biogas reactor by quanti-tative mass spectrometryLentinula edodestimsTOF ProKüchler, J.; Willenbücher, K.; Reiß, E.; Nuß, L...No3 
2022-12-20 Elucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modelingHomo sapiensTSQ AltisVeth TS, Francavilla C, Heck AJR, Altelaar M. E...Yes6PXD039005
2022-12-12 Synergistic targeting of DNA-PK and KIT signaling pathways in KIT mutant acute myeloid leukemiaMus musculusOrbitrap Exploris 480Murray HC, Miller K, Brzozowski JS, Kahl RGS, S...No6PXD030214
2022-12-07 Relative complement deficiency predicts development of islet autoimmunity and type 1 diabetesHomo sapiensTSQ AltisWebb-Robertson BM, Nakayasu ES, Dong F, Waugh K...Yes12 
2022-12-04 HIC1 interacts with FOXP3 multi protein complex: a novel mechanism to regulate human regulatory T cell differentiation and functionHomo sapiensTSQ VantageAndrabi SBA, Batkulwar K, Bhosale SD, Moulder R...Yes1PXD038532
2022-12-01 Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective AlignmentHomo sapiensOrbitrap Fusion LumosHeil LR, Remes PM, Canterbury JD, Yip P, Barsho...No2PXD038508
2022-11-30 Monitoring extended stable isotope-labeled synthetic peptides as a quality control for protease digestion in targeted, multiplexed mass spectrometry-based assaysHomo sapiensQTRAP 6500,QTRAP 5500Yes5PXD038465
2022-11-25 Dynamic monitoring of myeloma minimal residual disease with targeted mass spectrometryHomo sapiensOrbitrap Exploris 120Noori S, Wijnands C, Langerhorst P, Bonifay V, ...No47PXD038370
2022-11-17 Effects of alpha-crystallin gene knockout on zebrafish lens developmentDanio rerioQ Exactive HFNo1PXD030918
2022-11-10 Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkersHomo sapiensQ Exactive HFJohansson C, Hunt H, Signorelli M, Edfors F, Ho...Yes2PXD038089
2022-11-02 Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define putative diagnostic biosignatures for Parkinson’s diseaseHomo sapiensQ Exactive HF-XHadisurya, M., Li, L., Kuwaranancharoen, K. et ...No1PXD032175
2022-10-28 Sirtuin 5 Reduces Malonylation in Non-mitochondrial Metabolic Pathways in Diabetic Kidney DiseaseMus musculusQ ExactiveBaek J, Sas K, He C, Nair V, Giblin W, Inoki A,...Yes1PXD037819
2022-10-27 Characterizing the origin of blood plasma proteins from organ tissues in rainbow trout (Oncorhynchus mykiss) using a comparative non-targeted proteomics approachOncorhynchus mykiss6545 Q-TOF LC/MS,1200 series LC/MSD SLTannouri N, Simmons DBD. Characterizing the ori...No24PXD037782
2022-10-06 Analysis of the effect of ClpC1 directed antibiotics on ClpC1, ClpC2 and ClpC3 protein levels.Mycolicibacterium smegmatisQ Exactive HF-X,Orbitrap Exploris 480Hoi DM, Junker S, Junk L, Schwechel K, Fischel ...Yes3PXD037198
2022-09-27 Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetesHomo sapiensTSQ VantageHirvonen MK, Lietzén N, Moulder R, Bhosale SD, ...Yes6PXD033946
2022-09-24 Differential isotope labelling by amino acids (DILAC) reveals metabolic cross-feeding and phenotypic heterogeneity in a clonal cell populationSaccharomyces cerevisiaeTripleTOF 6600Stephan Kamrad, Clara Correia-Melo, Lukasz Szyr...No7PXD036959
2022-09-15 The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effectorArabidopsis thalianaOrbitrap Fusionaccepted for publication in EMBONo1PXD036761
2022-09-05 Activity-dependent regulation of SLK phosphorylationMus musculusQ ExactivePublication pendingNo2PXD036547
2022-09-05 Reduction of MRM protein target list using correlation analysisBos taurus6495A Triple Quadrupole LC/MSEbhardt HA, Ponchon P, Theodosiadis K, Fuerer C...No1PXD036543
2022-08-25 Multisite proteome provides insights into the biology and prognostic markers for head and neck cancerHomo sapiensOrbitrap Exploris 240Busso-Lopes AF, Neves LX, Câmara GA, Granato DC...No1PXD036311
2022-08-23 Absolute and relative quantitation of ATI in modified wheatTriticum aestivum subsp. aestivum, Triticum turgidum subsp. durumTSQ Vantage,Q Exactive PlusGeisslitz S, Islam S, Buck L, Grunwald-Gruber C...Yes3 
2022-08-16 Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfeiSyntrophomonas wolfeiOrbitrap Exploris 480No1PXD036088
2022-08-10 Validation of known and novel AKT, S6K and RSK targets by targeted MSMus musculusQ Exactive PlusFricke AL, Mühlhäuser WWD, Reimann L, Zimmerman...Yes1PXD035962
2022-07-29 Sampling the proteome by emerging single-molecule and mass-spectrometry based methodsHomo sapiensOrbitrap EclipseMacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu...No1PXD035637
2022-07-08 Kinase activity profiling in breast cancer samplesHomo sapiensTSQ AltisYes1PXD035186
2022-07-07 MRM based validation of target antigen expression in Pituitary Adenoma patientsHomo sapiensTSQ AltisEvaluation of autoantibody signatures in Pituit...No1PXD035165
2022-06-27 NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotencyHomo sapiensTripleTOF 5600+,TripleTOF 5600No1PXD021497
2022-06-26 Longitudinal evaluation of biomarkers in wound fluids of venous leg ulcers treated with a protease-modulating wound dressingHomo sapiensOrbitrap Exploris 480Mikosiński J, Kalogeropoulos K, Bundgaard L, La...Yes4PXD025748
2022-06-25 Tandem Mass Tag-Based Quantitative Proteomic Profiling Identifies Novel Serum Biomarkers of Drug-Induced Liver Injury in HumansHomo sapiensOrbitrap Exploris 480Ravindra KC, Vaidya VS, Wang Z, Federspiel JD, ...No3PXD034882
2022-06-20 Mass spectrometry-driven discovery of neuropeptides mediating nictation behavior of nematodesCaenorhabditis elegansQ Exactive HF-XCockx B, Van Bael S, Boelen R, Vandewyer E, Yan...No2 
2022-06-15 A Peptide-Centric Quantitative Proteomics Dataset for the Phenotypic Assessment of Alzheimer’s DiseaseHomo sapiensOrbitrap Fusion LumosMerrihew GE, Park J, Plubell D, Searle BC, Keen...No27PXD034525
2022-06-13 Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipidsHomo sapiensQ Exactive HFSortase A-cleavable CD1d identifies sphingomyel...Yes1PXD034495
2022-06-08 Retrospective longitudinal monitoring of multiple myeloma patients by mass spectrometry using archived serum protein electrophoresis gels and de novo sequence analysisHomo sapiensQ Exactive HFNoori S, Zajec M, Russcher H, Tintu AN, Broijl ...No10PXD034406
2022-06-02 Multiple phosphorylation combinatorially regulates IFI16 antiviral immune signalingHomo sapiensQ Exactive HFNo2 
2022-05-25 Rapid assessment of lipidomics sample purity and quantity using attenuated total reflectance Fourier-transform infrared spectroscopyHomo sapiens6470A Triple Quadrupole LC/MSRobinson, H.; Molendijk, J.; Shah, A.K.; Rahman...No1 
2022-05-09 SARS-CoV-2 PRM-MS Assay with Clinical Patient SamplesHomo sapiensQ Exactive HFGajbhiye A, Nalbant A, Heunis T, Sidgwick F, Po...No1PXD033790
2022-05-03 Addressing the Protease Bias in Quantitative ProteomicsHomo sapiensTSQ AltisWoessmann J, Kotol D, Hober A, Uhlén M, Edfors ...Yes12PXD033574
2022-04-28 A proteomics investigation of cigarette smoke exposed Wistar rats revealed improved anti-inflammatory effects of the cysteamine nanoemulsions delivered via inhalationRattus norvegicusTSQ AltisSharma G, Pund S, Govindan R, Nissa MU, Biswas ...No1PXD033559
2022-04-28 Iron-Regulated Assembly of the Cytosolic Iron-Sulfur Cluster Biogenesis MachineryHomo sapiensOrbitrap Fusion LumosFan X, Barshop WD, Vashisht AA, Pandey V, Leal ...No3PXD033557
2022-04-21 Targeted proteomics (parallel reaction monitoring) to quantify starch-biosynthetic proteins in yeastSaccharomyces cerevisiae, Arabidopsis thalianaQ ExactivePublication pendingYes2PXD033364
2022-04-14 An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemiaHomo sapiensTripleTOF 6600,TripleTOF 5600No1PXD031500
2022-04-07 Elevation of fatty acid desaturase 2 in esophageal adenocarcinoma increases polyunsaturated lipids and may exacerbate bile acid-induced genotoxicityHomo sapiens6470A Triple Quadrupole LC/MSMolendijk J, Kolka CM, Cairns H, Brosda S, Moha...No2 
2022-03-29 Mouse apolipoproteome study - hyperlipidemic mouse modelsMus musculusTSQ AltisSteffensen LB, Larsen JH, Hansen DR, Tha TML, L...Yes8PXD032868
2022-03-24 The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor BiopsiesHomo sapiensOrbitrap Fusion LumosSweet S, Chain D, Yu W, Martin P, Rebelatto M, ...Yes5PXD027134
2022-03-09 Prediction and experimental validation of a new salinity-responsive cis-regulatory element (CRE) in tilapiaOreochromis mossambicusimpact IIKim C, Wang X, Kültz D. Prediction and Experime...No1PXD032181
2022-02-23 HDL Proteomics in Coronary Artery Calcification in Type 1 Diabetes (CACTI) StudyHomo sapiensOrbitrap Fusion LumosShao B, Snell-Bergeon JK, Pyle LL, Thomas KE, d...No6PXD031854
2022-02-23 IFI16-mediated suppression of HSV-1 protein expressionHomo sapiens, Human herpesvirus 1Q Exactive HFPublication pendingNo1PXD031850
2022-02-16 Absolute Protein Quantitation of the Mouse Macrophage Toll-Like Receptor and Chemotaxis PathwaysMus musculusQ Exactive HFManes NP, Calzola JM, Kaplan PR, Fraser IDC, Ge...Yes1PXD031697
2022-02-14 Skin cancer-associated S. aureus downregulates DNA repair mechanisms, and promotes oxidative stress and DNA damage in human keratinocytesStaphylococcus capitis, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus6470A Triple Quadrupole LC/MSKrueger A, Mohamed A, Kolka CM, Stoll T, Zaugg ...No1PXD031676
2022-02-03 PrP concentration in the central nervous system: regional variability, genotypic effects, and pharmacodynamic impactHomo sapiens, Rattus norvegicusTSQ QuantivaMortberg MA, Zhao HT, Reidenbach AG, Gentile JE...Yes2PXD031432
2022-02-03 A scalable, targeted mass spectrometry-based assay for monitoring the progression of herpesvirus infectionsHuman betaherpesvirus 5, Herpes simplex virus 1, Kaposi's sarcoma-associated herpesvirus, Homo sapiensQ Exactive HFKennedy MA, Tyl MD, Betsinger CN, Federspiel JD...No17PXD025879
2022-02-03 Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum.Plasmodium falciparumXevo TQ-XS,Xevo G2-XS TofHollin T, Abel S, Falla A, Pasaje CFA, Bhatia A...No6 
2022-02-02 Cov²MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid proteinSARS-CoV-2Xevo TQ-XS,TripleTOF 6600No36PXD031401
2022-02-01 Profiling the diversity of agonist-selective effects on the proximal proteome environment of G protein-coupled receptorsHomo sapiensTSQ QuantivaPolacco BJ, Lobingier BT, Blythe EE, Abreu N, K...No1PXD031393
2022-01-31 Imetelstat Is a Potent Inducer of Ferroptosis That Effectively Diminishes Acute Myeloid Leukemia Burden and Delays Relapse Following Pro-Oxidant TherapyHomo sapiens6470A Triple Quadrupole LC/MSBruedigam C, Porter AH, Song A, Vroeg In de Wei...No2 
2022-01-18 The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5Homo sapiensTSQ QuantivaMaven et al., The multi-lineage transcription f...Yes1PXD031059
2022-01-10 One-Pot Isotope Dilution PRM for Quantitative Protein Heterogeneity in Red Blood CellsHomo sapiensOrbitrap Fusion ETD,Orbitrap Exploris 480,6495B Triple Quadrupole LC/MSEshghi A, Xie X, Hardie D, Chen MX, Izaguirre F...Yes14PXD030875
2022-01-05 FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standardsHomo sapiensQ Exactive HFpublication pendingYes1PXD030762
2021-12-22 OE240 PFAS Method Validation Orbitrap Exploris 240TBDNo1 
2021-12-15 Improving peptide fragment ion detection using travelling wave ion mobility spectrometry with signal enhancement MSE (seMSE)Escherichia coli, Bos taurus, Saccharomyces cerevisiae, Oryctolagus cuniculusSYNAPT G2-SiRojas Echeverri JC, Volke D, Milkovska-Stamenov...No3PXD030431
2021-12-15 Proteomic Blueprint of the Pituitary anterior and posterior lobes for better understanding of the physiology of pituitary gland.Homo sapiensOrbitrap FusionBanerjee A, Biswas D, Barpanda A, Halder A, Sib...No1PXD029991
2021-12-13 Proteomic Analysis of Oil-Roasted Cashew Using a Customized Allergen-Focused Protein DatabaseAnacardium occidentaleQ Exactive PlusChen S, Downs ML. Proteomic Analysis of Oil-Roa...No1PXD030375
2021-12-09 Preserving the phosphoproteome of clinical biopsies using a quick freeze collection deviceMus musculusQTRAP 5500Publication pendingYes3PXD030367
2021-12-09 Check of selected NTR peptide spectra by comparison with synthetic peptidesHomo sapiensOrbitrap Fusion LumosBogaert A, Fijalkowska D, Staes A, Van de Steen...No1PXD030285
2021-12-08 Relative quantification of acetylated histone peptides in HAP1 cells after treatment with MS-275Homo sapiensQ Exactive HF-XPublication pendingNo1PXD030272
2021-11-30 MRM quantification of circulating CFP-10 in TB patientsMycobacterium tuberculosisTSQ AltisShu Q, Liu S, Alonzi T, LaCourse SM, Singh DK, ...Yes10PXD021150
2021-11-25 Evaluation of volumetric absorptive microsampling and mass spectrometry data-independent acquisition in hemoglobin related clinical markersHomo sapiensQ Exactive HF-XLima DA, Schuch RA, Salgueiro JS, Pintão MCT, C...No1PXD029918
2021-11-22 Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning 6560 Q-TOF LC/MSFoster M, Rainey M, Watson C, Dodds JN, Kirkwoo...No1 
2021-11-17 Absolute quantification of influenza virus proteinsInfluenza A virus (A/Puerto Rico/8/1934(H1N1))timsTOF ProKüchler J, Püttker S, Lahmann P, Genzel Y, Kupk...Yes8PXD029784
2021-11-16 A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomicsHomo sapiens, Escherichia coli, Saccharomyces cerevisiaeTripleTOF 5600,TripleTOF 6600,timsTOF Pro,Q Exactive HF-X,SYNAPT G2-Si,Synapt MSVan Puyvelde B, Daled S, Willems S, Gabriels R,...No6 
2021-11-10 Skyline Batch: An Intuitive User Interface for Batch Processing with SkylineSaccharomyces cerevisiaeTripleTOF 5600Marsh AN, Sharma V, Mani SK, Vitek O, MacCoss M...No4PXD029665
2021-11-10 Skyline Batch: An Intuitive User Interface for Batch Processing with SkylineHomo sapiensQ ExactiveMarsh AN, Sharma V, Mani SK, Vitek O, MacCoss M...Yes2PXD029663
2021-11-01 Targeted proteomic validation of dysregulated proteins in liver tissue of Labeo rohita after Aeromonas hydrophila infectionLabeo rohitaTSQ AltisNissa MU, Pinto N, Ghosh B, Singh U, Goswami M,...Yes1PXD029483
2021-10-20 Gill proteome networks explain salinity tolerance of Oreochromis mossambicusOreochromis mossambicusimpact IIRoot L, Kültz D. Effects of pejus and pessimum ...No4PXD029254
2021-10-14 Quantification of Soy-Derived Ingredients in Model Bread and Frankfurter Matrices with an Optimized LC-MS/MS External Standard Calibration WorkflowGlycine maxQ Exactive PlusKrager J, Baumert JL, Downs M. Quantification o...Yes2PXD029137
2021-10-13 RGI-GOLVEN signalling promotes FLS2 abundance to regulate plant immunityArabidopsis thalianaQ Exactive HF-XNo2PXD023855
2021-10-08 Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury SeverityHomo sapiens6560 Q-TOF LC/MSKirkwood KI, Christopher MW, Burgess JL, Littau...No6 
2021-10-07 Selected reaction monitoring based analysis of proteins in liver tissue of Labeo rohitaLabeo rohitaTSQ AltisNissa MU, Pinto N, Varshnay A, Goswami M, Sriva...Yes2PXD028997
2021-10-07 Monitoring of histidine methylated Rpl3pSaccharomyces cerevisiaeOrbitrap Fusion LumosNo1 
2021-10-05 Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment AnalysisHomo sapiens, SARS-CoV-2Xevo TQ-XSHober A, Tran-Minh KH, Foley D, McDonald T, Vis...Yes1PXD026366
2021-10-05 MS quantification of circulating CFP-10, p24 and VP40Human immunodeficiency virus 1, EBOV, SUDV, Mycobacterium tuberculosisTSQ Altis,Orbitrap Fusion LumosShu Q, Kenny T, Fan J, Lyon CJ, Cazares LH, Hu ...Yes12PXD021149
2021-10-01 Quantification of organelle membrane contact site protein abundances during infection with human virusesHomo sapiens, HHV-5, HSV-1, HCoV-OC43, Influenza A virus (A/Puerto Rico/8/1934(H1N1))Q Exactive HFPublication pendingNo4PXD023761
2021-10-01 Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approachHomo sapiensXevo TQ-SMarques TM, van Rumund A, Kersten I, Bruinsma I...Yes1PXD028888
2021-09-27 Diagnosing pleural effusions using mass spectrometry-based multiplexed targeted proteomics quantitating mid- to high-abundance markers of cancer, infection/inflammation and tuberculosisHomo sapiensXevo TQ MSRobak, A., Kistowski, M., Wojtas, G. et al. Dia...No1 
2021-09-21 Highly multiplexed quantitative phosphosite assay for biology and preclinical studiesHomo sapiensTSQ QuantivaKeshishian H, McDonald ER 3rd, Mundt F, Melanso...Yes9PXD026939
2021-09-18 Next-generation Serology by Mass Spectrometry:Readout of the SARS-CoV-2 Antibody RepertoireHomo sapiensQ Exactive HFMelani RD, Des Soye BJ, Kafader JO, Forte E, Ho...No1PXD028627
2021-09-13 SARS-CoV2 Immunocomplex by LC-MS/MS on vaccinated cohortHomo sapiensXevo TQ-SPublication pendingNo3PXD028450
2021-09-06 HDL proteomics on CPROBE samplesHomo sapiensOrbitrap FusionShao B, Mathew AV, Thornock C, Pennathur S; Mic...No2PXD028216
2021-09-03 Organ wise targeted mass spectrometric analysis of proteins in Labeo rohita using SRM/MRM approachLabeo rohitaTSQ AltisNissa MU, Pinto N, Mukherjee A, Reddy PJ, Ghosh...Yes1PXD028017
2021-09-03 Ocular proteomic and transcriptomic changes with aging in response to lensectomy in a rabbit model of lensectomy with intraocular lens insertionNew Zealand rabbitOrbitrap Fusion LumosNo1PXD028205
2021-09-02 Triage of >1300 candidate biomarkers in plasma using internal standard-triggered parallel reaction monitoring mass spectrometryHomo sapiensOrbitrap EclipsePublication pendingYes16 
2021-08-31 Mitochondrial inorganic polyphosphate (polyP) is a contributor towards maintaining cellular bioenergetics in SH-SY5Y cells: a proteomics and metabolomics approachHomo sapiensOrbitrap Fusion LumosGuitart-Mampel M, Urquiza P, Carnevale Neto F, ...No2PXD028185
2021-08-30 2020_Human BAK125 kit _Room TemperatureHomo sapiens6495B Triple Quadrupole LC/MS,Xevo TQ-XSGaither C, Popp R, Borchers SP, Skarphedinsson ...Yes13PXD028179
2021-08-24 Plasma Protein Biomarker Model for Screening Alzheimer Disease Using Multiple Reaction Monitoring-Mass SpectrometryHomo sapiens6490 Triple Quadrupole LC/MSKim Y, Kim J, Son M, Lee J, Yeo I, Choi KY, Kim...Yes1 
2021-08-20 A hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzaeMagnaporthe oryzaeOrbitrap Eclipse,Orbitrap FusionOsés-Ruiz M, Cruz-Mireles N, Martin-Urdiroz M, ...No1PXD028052
2021-08-17 Simultaneous quantitative profiling of clinically relevant immune markers in neonatal stool swabs to reveal inflammationHomo sapiens6495B Triple Quadrupole LC/MSVidova V, Benesova E, Klanova J, Thon V, Spacil...Yes13PXD027988
2021-08-17 A comparative study of synthetic winged peptides for absolute protein quantificationHomo sapiens6495B Triple Quadrupole LC/MSBenesova E, Vidova V, Spacil Z. A comparative s...Yes9PXD027985
2021-08-17 Multisite proteome provides insights into the biology and prognostic markers for head and neck cancerHomo sapiensXevo TQ-XS,ACQUITY UPLCBusso-Lopes AF, Neves LX, Câmara GA, Granato DC...Yes2PXD027984
2021-08-16 Targeted MS based multi-omic analysis of blood plasma from COVID-19 patients to predict survivalHomo sapiens6495B Triple Quadrupole LC/MSRichard VR, Gaither C, Popp R, Chaplygina D, Br...Yes1PXD027959
2021-08-16 Whole blood peptide assay stability by MRM-MSHomo sapiens6495B Triple Quadrupole LC/MSGaither C, Popp R, Zahedi RP, Borchers CH. Mult...Yes1PXD027957
2021-08-16 Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS) 6560 Q-TOF LC/MSYes2 
2021-08-13 Plasma proteomic analysis to identify potential biomarkers of histologic chorioamnionitis in women with preterm premature rupture of membranesHomo sapiens6495A Triple Quadrupole LC/MSLee JE, Dan K, Kim HJ, Kim YM, Park KH. Plasma ...Yes2 
2021-08-02 Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profilingHomo sapiensQ Exactive HF-X,Orbitrap Fusion LumosZecha J, Gabriel W, Spallek R, Chang YC, Mergne...No7PXD023234
2021-08-02 Targeted MRM assay Complement System AMD cohortHomo sapiensXevo TQ-SAcar IE, Willems E, Kersten E, Keizer-Garritsen...Yes1PXD027689
2021-07-31 Targeted mass spectrometry enables multiplexed quantification of immunomodulatory proteins in clinical biospecimensHomo sapiensQTRAP 5500Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM...No3PXD029167
2021-07-27 Profiling Tryptophan Catabolites of Human Gut Microbiota and Acute-Phase Protein Levels in Neonatal Dried Blood SpecimensHomo sapiens6495B Triple Quadrupole LC/MSAust AC, Benesova E, Vidova V, Coufalikova K, S...Yes5PXD027606
2021-07-23 Quantification of the ratio between the two PsbO protein isoforms in the thylakoids lumen of Arabidopsis thalianaArabidopsis thalianaTSQ VantageGollan PJ, Trotta A, Bajwa AA, Mancini I, Aro E...No1PXD027514
2021-07-20 Age-Related Disruption of the Proteome and Acetylome in Mouse Hearts Correlates with Differential Loss of Function that is Attenuated by SS-31 and NMNMus musculusQ Exactive HF-XWhitson JA, Johnson R, Wang L, Bammler TK, Imai...No3PXD027458
2021-07-19 The metabolome as a biomarker of aging in Drosophila melanogasterDrosophila melanogasterTSQ VantageZhao X, Golic FT, Harrison BR, Manoj M, Hoffman...No2 
2021-07-19 DDR2 pharmacodynamic profilingHomo sapiensQTRAP 5500Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Ke...Yes4 
2021-07-16 Loss of DNAJC3 impairs cholesterol metabolism and mitochondrial functionHomo sapiensOrbitrap Fusion LumosJennings MJ, Hathazi D, Nguyen CDL, Munro B, Mü...Yes1PXD027372
2021-07-10 Comparison of allergen quantification strategies for egg, milk, and peanut in food using targeted LC-MS/MS QTRAP 6500Xiong W, Parker CH, Boo CC, Fiedler KL. Compari...No6 
2021-07-09 Optimized liquid and gas phase fractionations increase HLA-peptidome coverage for primary cell and tissue samplesHomo sapiensTSQ QuantisKlaeger S, Apffel A, Clauser KR, Sarkizova S, O...Yes1PXD027165
2021-07-01 Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantificationEscherichia coliQTRAP 5500Johnson J, Harman VM, Franco C, Emmott E, Rockl...No1PXD027047
2021-06-28 Targeted Proteomics Using Stable Isotope Labeled Protein Fragments Enables Precise and Robust Determination of Total Apolipoprotein(a) in Human PlasmaHomo sapiensTSQ Altis,6490 Triple Quadrupole LC/MSHober A, Rekanovic M, Forsström B, Hansson S, K...Yes6PXD026976
2021-06-21 Targeted Detection of SARS-CoV-2 Protein Variants by Mass SpectrometryHomo sapiensOrbitrap Exploris 480Maus A, Renuse S, Kemp J, Madugundu AK, Vanderb...Yes2 
2021-06-21 Targeted validation of significantly altered semen proteins in COVID-19 patientsHomo sapiensTSQ AltisGhosh S, Parikh S, Nissa MU, Acharjee A, Singh ...Yes2PXD026849
2021-06-21 Validation of proteins showing significant dysregulation from shotgun proteomics experiments in longitudinal plasma samples of COVID-19 patientsHomo sapiensTSQ AltisSuvarna K, Salkar A, Palanivel V, Bankar R, Ban...Yes1PXD026848
2021-06-17 Multiple reaction monitoring (MRM) based data for targeted validation of proteins in Labeo rohitaLabeo rohitaTSQ AltisNissa MU, Reddy PJ, Pinto N, Sun Z, Ghosh B, Mo...No1PXD026757
2021-06-10 The global Proteome and Ubiquitinome of bacterial and viral co-infected Bronchial Epithelial CellsHomo sapiens, Streptococcus pyogenes, Influenza A virus (A/Germany-BY/74/2009(H1N1)), Staphylococcus aureusQ ExactiveSura T, Surabhi S, Maaß S, Hammerschmidt S, Sie...No1PXD026625
2021-06-10 Targeted validation of interaction between ErbB4 JM-a isoform and β1 integrinHomo sapiensOrbitrap Fusion LumosPublication pendingNo1PXD026617
2021-06-07 GFAP and MBP peptides in Traumatic Brain InjuryHomo sapiensTSQ AltisSarkis GA, Lees-Gayed N, Banoub J, Abbatielo SE...Yes1PXD026550
2021-05-25 Analytical Comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cellsMus musculusQ Exactive HFLi T, Hentschel A, Ahrends R. Analytical compar...Yes5PXD026204
2021-05-19 Cell cycle phosphorylation dynamics in vivo reveals switch-like control of intrinsic disorderXenopus laevisQ Exactive HFValverde JM, Dubra G, Phillips M, Haider A, Ele...Yes1PXD026088
2021-05-06 Mapping interactome networks of FOSL1 and FOSL2 in human Th17 cellsHomo sapiensQ Exactive HFShetty A, Bhosale SD, Tripathi SK, Buchacher T,...Yes2PXD025840
2021-05-03 C.auto_3gas_absquant: Spike-in SIL-protein stock absolute quantificationClostridium autoethanogenumQ Exactive HF-XPublication pendingNo1PXD025760
2021-05-03 C.auto_3gas_absquant: Label-free proteome-wide absolute quantificationClostridium autoethanogenumQ Exactive HF-XNo1 
2021-05-03 C.auto_3gas_absquant: Anchor protein absolute quantificationClostridium autoethanogenumQ Exactive HF-XYes1 
2021-04-28 Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoringHomo sapiensOrbitrap Eclipse,Orbitrap Fusion LumosHeil LR, Remes PM, MacCoss MJ. Comparison of Un...No6PXD023334
2021-04-27 Proteomic analysis of spermatozoa reveals caseins play a pivotal role in preventing short-term periods of subfertility in stallionsEquus caballusOrbitrap Exploris 480Griffin RA, Swegen A, Baker MA, Ogle RA, Smith ...No1 
2021-04-27 Alzheimer's Disease IsomerizationHomo sapiensOrbitrap Fusion LumosHubbard EE, Heil LR, Merrihew GE, Chhatwal JP, ...No33PXD025668
2021-04-13 Quantitation of frataxin-related proteins in I151F miceMus musculus6420 Triple Quadrupole LC/MSMedina-Carbonero M, Sanz-Alcázar A, Britti E, D...Yes3 
2021-04-02 A Workflow Towards The Reproducible Identification and Quantitation of Protein Carbonylation Sites in Human PlasmaHomo sapiensSYNAPT G2-SiRojas Echeverri JC, Milkovska-Stamenova S, Hoff...No3 
2021-03-31 Biomarker Discovery in FFPE tissues by SRMHomo sapiensTSQ VantageSteiner C, Lescuyer P, Cutler P, Tille JC, Ducr...Yes6PXD025135
2021-03-29 Towards zero variance in proteomics - positive pressure FASP in 96-well format (PF96) enables highly reproducible and time-efficient analysis of sample cohortsMus musculusQ Exactive HFLoroch S, Kopczynski D, Schneider AC, Schumbrut...Yes1PXD025089
2021-03-29 Targeted Phosphoinositides Analysis Using High Performance Ion Chromatography-Coupled Selected Reaction Monitoring Mass SpectrometryHomo sapiens, Rattus norvegicus, Mus musculusQ Exactive HF,QTRAP 6500Cheung HYF, Coman C, Westhoff P, Manke M, Sickm...Yes11 
2021-03-24 A microbial supply chain for production of anti-cancer drug vinblastineSaccharomyces cerevisiae6460 Triple Quadrupole LC/MSZhang J, Hansen LG, Gudich O, Viehrig K, Lassen...No1PXD024976
2021-03-22 Quantification of Raloxifene Specific 471 Da Adducts in CYP3A4 and P450-ReductaseHomo sapiens, Rattus norvegicusQ Exactive HFRiffle M, Hoopmann MR, Jaschob D, Zhong G, Mori...No2PXD024932
2021-03-20 Standardized workflow for precise mid- and high-throughput proteomics of blood biofluidsHomo sapiensOrbitrap Exploris 480Mc Ardle A, Binek A, Moradian A, Chazarin Orgel...No3PXD024884
2021-03-19 Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological BackgroundsHomo sapiensQ Exactive HFDele-Oni DO, Christianson KE, Egri SB, Vaca Jac...Yes28PXD017458
2021-03-18 Quantitative Proteomics Reveals that the OGT Interactome is
Remodeled in Response to Oxidative Stress		Mus musculusOrbitrap Fusion LumosMartinez M, Renuse S, Kreimer S, O'Meally R, Na...No2PXD021091
2021-03-15 Quantitative proteomic approach for discriminating major depressive disorder and bipolar disorder by multiple reaction monitoring-mass spectrometryHomo sapiens6490 Triple Quadrupole LC/MSShin D, Rhee SJ, Lee J, Yeo I, Do M, Joo EJ, Ju...No1PXD024752
2021-03-11 MRM for validation of Brain tumor biomarkersHomo sapiensTSQ AltisGhantasala S, Pai MGJ, Biswas D, Gahoi N, Mukhe...No8PXD024238
2021-03-11 Acute temperature-induced liver proteome changes in two populations of threespine stickleback (Gasterosteus aculeatus) revealed by data-independent acquisition mass spectrometryGasterosteus aculeatusimpact IIin prep.No4PXD024677
2021-03-10 Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic GenotypingHomo sapiensQ Exactive Plus,Orbitrap Fusion Lumos,6495A Triple Quadrupole LC/MSGoecker ZC, Legg KM, Salemi MR, Herren AW, Phin...Yes4PXD024651
2021-03-10 Highly multiplexed kinase profiling in spleen with targeted mass spectrometry reveals kinome plasticity across speciesHomo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Macaca fascicularisTSQ Altis,Orbitrap Exploris 480Marholz LJ, Federspiel JD, Suh H, Fernandez Oca...Yes7PXD024650
2021-03-10 Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticusOreochromis niloticusimpact IIRoot L, Campo A, MacNiven L, Con P, Cnaani A, K...No1PXD024648
2021-03-09 Chronic temperature-induced liver proteome changes in two populations of threespine stickleback (Gasterosteus aculeatus) revealed by data-independent acquisition mass spectrometryGasterosteus aculeatusimpact IIin prep.No1PXD024617
2021-03-04 Targeted plasma proteome analysis using vacuum-dried protein standardsHomo sapiensQ Exactive HFKotol D, Hober A, Strandberg L, Svensson AS, Uh...Yes12PXD024536
2021-03-04 Regulation of electrogenic Na+/HCO3- cotransporter 1 (NBCe1) in mouse cortical astrocytes and its dependence on m-TOR mediated phosphorylation of Ser245.Mus musculusQ Exactive HF-XGiannaki M, Ludwig C, Heermann S, Roussa E. Reg...No1PXD024529
2021-02-26 Utilizing Skyline to Analyze Lipidomics Data Containing Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry DimensionsHomo sapiens6560 Q-TOF LC/MSKirkwood KI, Pratt BS, Shulman N, Tamura K, Mac...No6 
2021-02-25 ACONITASE 3 is part of the ANAC017 transcription factor-dependent mitochondrial dysfunction responseArabidopsis thalianaQ Exactive,Q Exactive HFPascual J, Rahikainen M, Angeleri M, Alegre S, ...No15PXD018881
2021-02-23 PRMT6 substrate specificity analysisHomo sapiensOrbitrap Fusion LumosHamey JJ, Rakow S, Bouchard C, Senst JM, Kolb P...No95PXD016711
2021-02-18 Mouse Heart SS31 Targeted ProteomicsMus musculusOrbitrap Fusion LumosWhitson JA, Martín-Pérez M, Zhang T, Gaffrey MJ...No1PXD024247
2021-02-17 Role of Epigenetics in Unicellular to Multicellular Transition in DictyosteliumDictyostelium discoideum AX2Q Exactive HF,Orbitrap FusionWang SY, Pollina EA, Wang IH, Pino LK, Bushnell...No1PXD024225
2021-02-16 Identification of proteins deregulated by platinum-based chemotherapy as novel biomarkers and therapeutic targets in non-small cell lung cancerHomo sapiensTripleTOF 5600Ryan SL, Dave KA, Beard S, Gyimesi M, McTaggart...No1PXD024209
2021-02-10 Endogenous THBS1 is C-mannosylated by human induced pluripotent stem cells.Homo sapiensQTRAP 5500Cirksena K, Hütte HJ, Shcherbakova A, Thumberge...Yes1PXD024117
2021-02-09 Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring in vivo Arginine Isotope Incorporation in Alzheimer’s Disease Mouse ModelsMus musculusQ Exactive HFAdams KJ, Wilson JG, Millington DS, Moseley MA,...No8 
2021-02-07 Spotlight on alternative frame coding: two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selectionPseudomonas aeruginosaQ Exactive HF-Xpublication pendingYes1PXD024029
2021-01-29 Smoothened Transduces Hedgehog Signals via Activity-Dependent Sequestration of PKA Catalytic SubunitsHomo sapiensOrbitrap Exploris 480Arveseth CD, Happ JT, Hedeen DS, Zhu JF, Capene...No1PXD023893
2021-01-28 Grizzly Bear Serum DIA Proteomicsgrizzly bearQ Exactive HF,nanoACQUITY UPLCSaxton MW, Perry BW, Evans Hutzenbiler BD, Troj...No1PXD023555
2021-01-10 Tracking Gluten throughout Brewing Using N-Terminal Labeling Mass SpectrometryTriticum aestivum, Hordeum vulgare, Humulus lupulus, Saccharomyces cerevisiaeQ Exactive PlusCao W, Baumert JL, Downs ML. Tracking Gluten th...No18PXD023495
2021-01-07 Factor H and related proteins in AMDHomo sapiens6495A Triple Quadrupole LC/MSCipriani V, Tierney A, Griffiths JR, Zuber V, S...Yes2PXD023466
2020-12-24 Lysosomal targetomics in ghrKO mice reveals a role for chaperone-mediated autophagy in shaping the nucleocytosolic acetyl-coA production pathwayMus musculusQ Exactive HFpublication pendingNo2PXD023309
2020-12-18 Tissue plasminogen activator effects on fibrin volume and the ocular proteome in a juvenile rabbit model of lensectomyNew Zealand rabbitOrbitrap Fusion LumosNo1PXD023232
2020-12-14 Targeted quantification of phosphorylation sites in S. macrospora wildtype and STRIPAK-mutantsSordaria macrosporaQ Exactive HFDataset with publication pendingYes4PXD023130
2020-12-13 Validation of detected viral and host peptides from COVID-19 nasopharyngeal swab samplesSARS-CoV-2, Homo sapiensTSQ AltisBankar R, Suvarna K, Ghantasala S, Banerjee A, ...Yes2PXD021845
2020-12-07 IgG M-protein quantification by PRM in blood of multiple myeloma patientHomo sapiensOrbitrap Fusion LumosMcDonald Z, Taylor P, Liyasova M, Liu Q, Ma B. ...No3PXD022980
2020-12-02 The reproductive toxicant acrylamide modulates the mouse epididymal proteome to drive alterations to the sperm epigenome and dysregulate embryo development.Mus musculusOrbitrap Exploris 480Trigg NA, Skerrett-Byrne DA, Xavier MJ, Zhou W,...No1PXD022876
2020-11-30 Surfactant-assisted one-pot sample preparation for label-free single-cell proteomicsHomo sapiensTSQ VantageTsai CF, Zhang P, Scholten D, Martin K, Wang YT...Yes1PXD022827
2020-11-22 Improving SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradationHomo sapiensQ Exactive HF-X,TripleTOF 6600Pino LK, Baeza J, Lauman R, Schilling B, Garcia...No4PXD022659
2020-11-21 Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patientsSARS-CoV-2, Homo sapiensXevo TQ-S,Xevo TQ-XS,TripleTOF 6600,TSQ Altis,Triple Quad 5500,6495A Triple Quadrupole LC/MS,Triple Quad 6500,Xevo TQDIn preparation (preprint on medRxiv)No34 
2020-11-19 Targeted mass spectrometry quantification of total soy protein residues from commercially processed ingredients for food allergen managementGlycine maxQ Exactive PlusChen S, Yang C, Downs M. Targeted mass spectrom...No1PXD022639
2020-11-11 Validation of host proteins differentially expressed between COVID severe and non-severe plasma samplesHomo sapiensTSQ AltisDataset with publication pending - 10.3389/fphy...Yes1PXD022475
2020-11-11 A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signalingPseudomonas aeruginosa PAO1Q Exactive PlusAllihn PWA, Hackl MW, Ludwig C, Hacker SM, Sieb...Yes2PXD022470
2020-11-10 Microwave oven-assisted derivatization of histone proteoforms using trimethylacetic anhydrideHomo sapiensOrbitrap Fusion LumosKuchaříková H, Dobrovolná P, Lochmanová G, Zdrá...No1PXD022454
2020-11-07 Targeted MRM assay Complement System for Complement deficienciesHomo sapiensXevo TQ-SWillems E, Lorés-Motta L, Zanichelli A, Suffrit...Yes4PXD022416
2020-10-27 Assessment of streptavidin peptide shedding in streptavidin-based enrichment strategies  Berg Luecke L, Gundry RL. Assessment of Strepta...No1 
2020-10-24 ‘The long tail of Covid 19’ - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patientsHomo sapiensXevo TQ-SDoykov I, Hällqvist J, Gilmour KC, Grandjean L,...No3PXD022159
2020-10-19 The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistanceHomo sapiensTSQ AltisJoshi, Sunil and Nechiporuk, Tamilla and Bottom...Yes1PXD022083
2020-10-12 Targeted mass spectrometry-based assays for multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signalingHomo sapiensTSQ Quantiva,QTRAP 5500Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zha...No4 
2020-10-08 Quantification of HER2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) and Frozen Breast Cancer TissuesHomo sapiensQTRAP 6500Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE,...Yes4PXD021893
2020-10-06 Proteomic characterization of human neural stem cells during in vitro differentiationHomo sapiensTripleTOF 5600+Červenka J, Tylečková J, Kupcová Skalníková H, ...No1PXD021860
2020-09-18 Genome-scale metabolic rewiring to improve titers, rates and yields of the non-native non-ribosomal peptide product indigoidine at scalePseudomonas putida KT24406460 Triple Quadrupole LC/MSBanerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Ch...No1PXD021570
2020-09-15 BAC-DROP: Rapid digestion of proteome fractionated via dissolvable polyacrylamide gel electrophoresis and its application to bottom-up proteomics workflowHomo sapiens, Bos taurus, Hepatitis B virusQTRAP 5500Takemori A, Ishizaki J, Nakashima K, Shibata T,...No7PXD021489
2020-09-13 SARS-CoV-2_PRM_SRM_targeted_acquisitionsSARS-CoV2Q Exactive HF-X,TSQ AltisCardozo KHM, Lebkuchen A, Okai GG, Schuch RA, V...No18PXD019300
2020-09-11 A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimensHomo sapiens, SARS-CoV-2Orbitrap Exploris 480Renuse S, Vanderboom PM, Maus AD, Kemp JV, Gurt...Yes2 
2020-09-10 The calcium-permeable channel OSCA1.3 regulates plant stomatal immunityArabidopsis thalianaXevo TQ-SThor K, Jiang S, Michard E, George J, Scherzer ...No1PXD020852
2020-09-01 High throughput targeted proteomics assays for quantifying large-scale pathway proteins in Pseudomonas putida KT2440Pseudomonas putida KT2440TSQ AltisGao Y, Fillmore TL, Munoz Munoz N, Bentley GJ, ...Yes4 
2020-09-01 A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticusOreochromis niloticusimpact IIRoot L, Campo A, MacNiven L, Con P, Cnaani A, K...No1 
2020-08-30 Data used to demonstrate Peptide Correlation Analysis (PeCorA)Mus musculusQ ExactiveNo1 
2020-08-26 IP-MS Analysis of ESX-5 and ESX-1 Substrates Enables Mycobacterial Species IdentificationMycobacteriaQ Exactive HF-XShu Q, Rajagopal M, Fan J, Zhan L, Kong X, He Y...Yes1PXD021148
2020-08-17 Dynamic glycoproteomics identifies a role of N-glycosylation and Galectin-1 on myogenesis and muscle developmentRattus norvegicus6330 Ion Trap LC/MSBlazev R, Ashwood C, Abrahams JL, Chung LH, Fra...No4 
2020-08-17 Characterization and statistical modeling of glycosylation changes in sickle cell disease and traitHomo sapiensLTQ Orbitrap VelosAshwood HE, Ashwood C, Schmidt AP, Gundry RL, H...No2 
2020-08-16 Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissuesMus musculus6495B Triple Quadrupole LC/MS,6495A Triple Quadrupole LC/MS,6490 Triple Quadrupole LC/MSMichaud SA, Pětrošová H, Sinclair NJ, Kinnear A...Yes45PXD020930
2020-08-12 In vitro synthesis of 32 translation-factor proteins from a single template reveals impaired ribosomal processivityEscherichia coli6460 Triple Quadrupole LC/MSDoerr A, Foschepoth D, Forster AC, Danelon C. I...No12PXD020877
2020-08-07 Longitudinal Protein Profiling using Targeted Proteomics and Recombinant StandardsHomo sapiensQ Exactive HFKotol D, Hunt H, Hober A, Karlsson MJ, Forsströ...Yes2PXD020797
2020-08-06 Temporal quantitative proteomics of mGluR-induced protein translation and phosphorylation in neuronsRattus norvegicusTSQ Altisvan Gelder CA, Penning R, Veth T, Catsburg LA, ...Yes1PXD020777
2020-08-03 Comparative quantitative LC-MS/MS analysis of 13 amylase/trypsin inhibitors in ancient and modern Triticum speciesTriticumTSQ VantageGeisslitz S, Longin CFH, Koehler P, Scherf KA. ...Yes8PXD020714
2020-07-31 Combining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects.Bos taurusTripleTOF 6600,Q Exactive Plus,TSQ VantageBons J, Husson G, Chion M, Bonnet M, Maumy-Bert...Yes10PXD020680
2020-07-22 An Optimised Proteomics Workflow for the Detection of Small Proteins.Bacillus subtilisQ ExactiveBartel J, Varadarajan AR, Sura T, Ahrens CH, Ma...No1PXD020514
2020-07-20 Detection of flg22 peptide upon treatment with different Arabidopsis root-derived bacterial supernatantArabidopsis thalianaQ ExactiveDataset with its publication pendingNo1PXD020452
2020-07-20 Rat nerve axoplasm RBPsRattus norvegicusQ Exactive PlusPatel P, Buchanan C, Kar AN, Lee SJ, Urisman A,...No1 
2020-07-16 Targeted proteomics measurements for Genetically controlled membrane synthesis in liposomesEscherichia coli6460 Triple Quadrupole LC/MSBlanken D, Foschepoth D, Serrão AC, Danelon C. ...No2PXD020399
2020-07-11 Validation of the MiXCR/HIGH-VQUEST pipeline for the selection of clonotypic peptides in MM cell linesHomo sapiensXevo TQ-SLangerhorst P, Brinkman AB, VanDuijn MM, Wessel...Yes1 
2020-07-08 Development of a potential salivary biomarker panel for Oral Squamous Cell Carcinoma using a proteomics-based approach.Homo sapiensOrbitrap FusionJain A, Kotimoole CN, Ghoshal S, Bakshi J, Chat...Yes2PXD020263
2020-07-07 Combined Peptidomic and Proteomic analysis of OSCC SalivaHomo sapiensXevo TQ-XS,ACQUITY UPLCNeves LX, Granato DC, Busso-Lopes AF, Carnielli...Yes1PXD020237
2020-06-25 ADAM17 cytoplasmic domain modulates Thioredoxin-1Homo sapiensXevo TQ-XSE Costa RAP, Granato DC, Trino LD, Yokoo S, Car...Yes1PXD020016
2020-06-24 S-Adenosylmethionine Depletion Activates La Ribonucleoprotein Domain
Family Member 1 to Induce Protein Translation		Homo sapiens, Mus musculusOrbitrap Fusion Lumos,TripleTOF 6600No3PXD020015
2020-06-23 Identification of candidate circulating glucocorticoid response biomarkers in humans using a proteomic approachHomo sapiensLCMS-8050Inder WJ, Mohamed A, Keshvari S, Barclay JL, Ru...No1PXD019972
2020-06-22 Seasonally relevant changes in UV-A alter neurohormone levels and behavior via cOpsin1Platynereis dumeriliiQ Exactive HF-XVeedin Rajan VB, Häfker NS, Arboleda E, Poehn B...No3PXD014682
2020-06-11 PRM Quantification of TET2, GATA3 and ERHomo sapiensQ Exactive HFYes6PXD019726
2020-06-11 Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma.Homo sapiens4000 QTRAPMultiplexed MRM-based protein quantification of...Yes13 
2020-06-09 Phage Phix174 - Wildtype and engineered proteomeEscherichia virus phiX174, phiX174.1fQ ExactiveWright BW, Ruan J, Molloy MP, Jaschke PR. Genom...No1PXD019681
2020-06-09 Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testingSARS-CoV-2, Homo sapiensOrbitrap Fusion LumosZecha J, Lee CY, Bayer FP, Meng C, Grass V, Zer...Yes7PXD019680
2020-06-03 Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic AnalysisMus musculus6495B Triple Quadrupole LC/MSMichaud SA, Pětrošová H, Jackson AM, McGuire JC...Yes45PXD019539
2020-06-02 Phosphoproteomic Effects of Acute Depletion of PP2A Regulatory Subunit Cdc55Saccharomyces cerevisiaeOrbitrap FusionPlank M, Berti M, Loewith R. Phosphoproteomic E...No3PXD019534
2020-06-01 Discovery of biomarker candidates associated with the risk of short- and long-term relapse after infliximab withdrawal in Crohn’s patients: a proteomics-based studyHomo sapiensXevo TQ-SPierre N, Baiwir D, Huynh-Thu VA, Mazzucchelli ...No4PXD019434
2020-05-27 Marked increased production of acute phase reactants by skeletal muscle during cancer cachexiaMus musculusXevo TQ-S,nanoACQUITY UPLC System with 1D TechnologyMassart IS, Paulissen G, Loumaye A, Lause P, Pö...Yes2PXD019433
2020-05-25 Antibody RING-Mediated Destruction (ARMeD) of endogenous proteinsHomo sapiensQ ExactiveIbrahim AFM, Shen L, Tatham MH, Dickerson D, Pr...No1PXD016193
2020-05-21 Translation Error Clusters Induced by Aminoglycoside AntibioticsEscherichia coliQ Exactive HF-X,Q Exactive Plus,Q Exactive HFWohlgemuth I, Garofalo R, Samatova E, Günenç AN...Yes75PXD019328
2020-05-11 Proteomic Tissue-based Classifier for Early Prediction of Prostate Cancer ProgressionHomo sapiensTSQ VantageGao Y, Wang Y-T, Chen Y, Wang H, Young D, Shi T...Yes381 
2020-05-08 Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung CancerHomo sapiensOrbitrap Fusion LumosLiebler DC, Holzer TR, Haragan A, Morrison RD, ...Yes4PXD019061
2020-04-20 Insights in the molecular kinetics and dynamics of the furin-cleaved form of PCSK9Homo sapiensLTQ VelosOleaga C, Hay J, Gurcan E, David LL, Mueller PA...No1PXD018700
2020-04-20 Highly Multiplex Targeted Proteomics Enabled by Real-Time Chromatographic AlignmentHomo sapiensOrbitrap Fusion LumosRemes PM, Yip P, MacCoss MJ. Highly Multiplex T...No1PXD018675
2020-04-17 Antibody-free targeted proteomics assay for absolute measurement of α-tubulin acetylationHomo sapiens, Mus musculus6490 Triple Quadrupole LC/MSShah AK, Wali G, Sue CM, Mackay-Sim A, Hill MM....Yes2PXD018626
2020-04-09 Malignant pleural mesothelioma targeted proteomics signature from bloodHomo sapiensXevo TQ-SCerciello F, Choi M, Sinicropi-Yao SL, Lomeo K,...No57PXD018457
2020-03-19 Accurate MS-based Rab10 phosphorylation stoichiometry determination as a readout for LRRK2 activity in Parkinson’s diseaseHomo sapiens, Mus musculusQ Exactive HF,Q Exactive HF-XKarayel O, Tonelli F, Virreira Winter S, et al....Yes4 
2020-03-04 MitoPlex: A Targeted Multiple Reaction Monitoring Assay for Quantification of a Curated Set of Mitochondrial ProteinsMus musculusQTRAP 6500+,TripleTOF 5600+Stotland AB, Spivia W, Orosco A, Andres AM, Got...Yes7PXD017884
2020-03-04 Targeted FLNc S2233 S2236 phosphorylation assayHomo sapiens, Mus musculusQ Exactive PlusYes3 
2020-02-24 Acarbose improves late-life physical function in mice of both sexes, but rejuvenates cardiac structure and lipid profile in males onlyMus musculusOrbitrap Fusion LumosHerrera JJ, Louzon S, Pifer K, Leander D, Merri...No2PXD017706
2020-02-23 Clinical application of multiple reaction monitoring-mass spectrometry to HER2 measurements as a potential diagnostic tool for breast cancer therapyHomo sapiens6490 Triple Quadrupole LC/MSDo M, Kim H, Yeo I, Lee J, Park IA, Ryu HS, Kim...No7PXD017691
2020-02-19 Proteomics of osmoregulatory versus general stress responses in threespine stickleback gillsGasterosteus aculeatusimpact IILi J, Kültz D. Proteomics of Osmoregulatory Res...No6PXD017662
2020-02-07 Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological BackgroundsHomo sapiensQ Exactive HFDataset with its publication pendingYes28PXD017458
2020-02-07 Global Chromatin Profiling Dataset of Chemical Perturbations in Multiple Biological BackgroundsHomo sapiensQ Exactive PlusDele-Oni DO, Christianson KE, Egri SB, Vaca Jac...Yes28PXD017459
2020-02-06 Interspecies assertiveness of Lactobacillus curvatus and Lactobacillus sakei in sausage fermentationsLactobacillus curvatus subsp. curvatusQ Exactive HF-XJanßen D, Dworschak L, Ludwig C, Ehrmann MA, Vo...No1PXD017183
2020-02-05 Mapping of the multiple myeloma cell surface N-glycoproteome and targeted validation
in patient samples uncovers immunotherapy targets		Homo sapiensOrbitrap Fusion LumosOldham RAA, Faber ML, Keppel TR, Buchberger AR,...No3PXD017692
2020-01-29 LipidCreator: A workbench to probe the lipidomic landscapeHomo sapiensQ Exactive HF,QTRAP 6500Peng B, Kopczynski D, Pratt BS, Ejsing CS, Burl...Yes4 
2020-01-29 PINE: An Automation Tool to Extract & Visualize Functionally Enriched Networks from Mass Spectrometry-Based Proteomics DatasetsMus musculusOrbitrap Fusion LumosSundararaman N, Go J, Robinson AE, Mato JM, Lu ...No1PXD017324
2020-01-28 Identification of Isopeptides Between Human Tissue Transglutaminase and Wheat, Rye, and Barley Gluten Peptidescommon wheat, rye, barley, Homo sapiensQ Exactive HFLexhaller B, Ludwig C, Scherf KA. Identificatio...No11PXD017693
2020-01-24 Parallel reaction monitoring assay development for multiple sclerosis biomarkers in cerebrospinal fluid.Homo sapiens, Rattus norvegicusQ Exactive HFGuldbrandsen A, Lereim RR, Jacobsen M, Garberg ...Yes8PXD017281
2020-01-24 A mouse brain-based multi-omics integrative approach reveals potential blood biomarkers for ischemic strokeMus musculusLTQ Orbitrap VelosSimats A, Ramiro L, García-Berrocoso T, Briansó...No1PXD017280
2020-01-22 From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditionsEscherichia coliTripleTOF 5600Mori M, Zhang Z, Banaei-Esfahani A, Lalanne JB,...Yes1PXD017258
2020-01-22 Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype DeterminationHomo sapiensOrbitrap Fusion LumosOtto JJ, Correll VL, Engstroem HA, Hitefield NL...Yes1PXD017257
2020-01-19 Inter-ViSTA: Targeted validation of temporal pUL37 interactorsHomo sapiensQ Exactive HFFederspiel JD, Cook KC, Kennedy MA, Venkatesh S...No6PXD013848
2020-01-15 Identification of cGAS post-translational modificationsHomo sapiensQ Exactive HFSong B, Greco TM, Lum KK, Taber CE, Cristea IM....No2PXD017133
2020-01-15 Detection of head and neck cancer based on longitudinal changes in serum protein abundanceHomo sapiensTSQ AltisCancer Epidemiology, Biomarkers & PreventionYes14 
2020-01-06 Mass Spectrometry-GUided Immunoassay DEvelopment (MS-GUIDE)Homo sapiensOrbitrap Fusion ETD,Q Exactive Pluspublication pendingYes2PXD016976
2019-12-20 Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass SpectrometryHomo sapiens, Escherichia coliSYNAPT G2-SiBritt HM, Cragnolini T, Khatun S, Hatimy A, Jam...Yes23 
2019-12-20 Quantitative proteomics analysis of Angiostrongylus vasorum-induced alterations in dog serumCanis lupus familiarisQ Exactive HF-XTritten L, Gillis-Germitsch N, Kockmann T, Schn...Yes2PXD016887
2019-12-19 Signaling proteins of a chemosensory pathway from sperm of Arbacia punctulataArbacia punctulataTSQ VantageTrotschel C, Hamzeh H, Alvarez L, Pascal R, Lav...Yes2PXD015502
2019-12-12 Identification of Putative Early Atherosclerosis Biomarkers by Unsupervised Deconvolution of Heterogeneous Vascular ProteomesHomo sapiensTripleTOF 6600,QTRAP 6500+Parker SJ, Chen L, Spivia W, Saylor G, Mao C, V...No4PXD016730
2019-12-11 CRK2-mediated control of ROS production by phosphorylation of the RBOHD C-terminus in ArabidopsisArabidopsis thalianaQ Exactive PlusKimura S, Hunter K, Vaahtera L, Tran HC, Citter...No4PXD013525
2019-12-04 Assessment of Serological Early Biomarker Candidates for Lung Adenocarcinoma by using Multiple Reaction Monitoring-Mass SpectrometryHomo sapiens6495A Triple Quadrupole LC/MSWu HY, Pan YY, Kopylov AT, Zgoda V, Ma MC, Wang...No18PXD014683
2019-12-02 Targeted metabolomics profiling of acute myocardial infarction risk human seraHomo sapiens6490 Triple Quadrupole LC/MSKhan A, Choi Y, Back JH, Lee S, Jee SH, Park YH...No6 
2019-12-01 PRM method for detection of both casein and whey milk allergens from baked food matrixBos taurusQ Exactive PlusRamachandran B, Yang CT, Downs ML. Parallel Rea...No6PXD016539
2019-11-21 Characterization of signaling pathways associated with pancreatic β-cell adaptive flexibility in compensation of obesity-linked diabetes in db/db miceMus musculusQ Exactive HFKang T, Boland BB, Jensen P, Alarcon C, Nawrock...Yes1PXD016392
2019-11-19 Mass spectrometry of in-gel digests reveals differences in amino acid sequences of high-molecular-weight glutenin subunits in spelt and emmer compared to common wheatTriticum aestivum, Triticum spelta, Triticum dicoccoidesQTRAP 6500+Geisslitz S, America AHP, Scherf KA. Mass spect...No2PXD016342
2019-11-14 ACE over expression in myeloid cells increases oxidative metabolism and cellular ATPMus musculusQTRAP 6500+Cao DY, Spivia WR, Veiras LC, Khan Z, Peng Z, J...Yes1 
2019-10-31 Identification of an intronic enhancer in the tilapia glutamine synthetase gene.Oreochromis mossambicusimpact IIKim C, Kültz D. An osmolality/salinity-responsi...No1 
2019-10-29 Characterization and relative quantitation of wheat, rye and barley gluten protein types by LC-MS/MScommon wheat, rye, barleyTripleTOF 6600,QTRAP 6500Lexhaller B, Colgrave ML, Scherf KA. Characteri...No6PXD016065
2019-10-15 Targeted assay for differentiation and monitoring the concentration of GDF 8 (Myostatin) and GDF11 in mouse serumMus musculusOrbitrap Fusion LumosCamparini L, Kollipara L, Sinagra G, Loffredo F...Yes2PXD015838
2019-10-09 PRM of Nth1 phospho-peptides in response to AGC-kinase inhibitionSaccharomyces cerevisiaeOrbitrap Fusion ETDPlank M, Perepelkina M, Müller M, Vaga S, Zou X...No1PXD015760
2019-10-08 Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-Labeled Recombinant Protein Fragments Based SRM AssayHomo sapiens6490 Triple Quadrupole LC/MSHober A, Edfors F, Ryaboshapkina M, Malmqvist J...Yes8PXD013314
2019-10-02 Min protein in vitro protein expression kineticsEscherichia coli6460 Triple Quadrupole LC/MSGodino E, López JN, Foschepoth D, Cleij C, Doer...No2PXD015686
2019-09-28 Comprehensive Detection of Isopeptides between Human Tissue Transglutaminase and Gluten PeptidesTriticum, humanQ Exactive HFLexhaller B, Ludwig C, Scherf KA. Comprehensive...No4 
2019-09-14 Antibody-free multiplex measurement of 23 human cytokines in primary cell culture secretome using targeted multiple reaction monitoring mass spectrometryHomo sapiens6490 Triple Quadrupole LC/MSKrueger A, Stoll T, Shah AK, Sinha R, Frazer IH...Yes26PXD015448
2019-09-13 FeS protein levels in Arabidopsis plants expressing a mutated NEET proteinArabidopsis thalianaTSQ QuantivaZandalinas SI, Song L, Sengupta S, McInturf SA,...No1PXD015447
2019-09-05 Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypesHomo sapiensLTQ Orbitrap VelosAshwood C, Waas M, Weerasekera R, Gundry RL. Re...No5 
2019-08-27 Chemical and phosphoproteomics illuminate the cellular mode of action of AKT inhibitorsHomo sapiensOrbitrap Fusion LumosWiechmann S, Ruprecht B, Siekmann T, Zheng R, F...No1PXD015188
2019-08-22 Skyline for Small Molecules: A Unifying Software Package for Quantitative MetabolomicsHomo sapiens, Mus musculusXevo TQ-S,Triple Quad 5500,Synapt G2 HDMSAdams KJ, Pratt B, Bose N, Dubois LG, St.John-W...Yes6 
2019-08-22 Personalized human milk proteomeHomo sapiensQ Exactive HF-XYes2PXD015119
2019-08-21 Multiplexed MRM concentration measurements of >200 endogenous proteins in dried blood spots for biomarker discovery and validationHomo sapiens6490 Triple Quadrupole LC/MSEshghi A, Pistawka AJ, Liu J, Chen M, Sinclair ...Yes13PXD015118
2019-08-19 Urinary PRM analysis of early type 1 diabetesHomo sapiensQ Exactive HF-XVan JAD, Clotet-Freixas S, Zhou J, Batruch I, S...Yes1PXD012389
2019-08-14 Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenaseEscherichia coli6460 Triple Quadrupole LC/MSBlake-Hedges JM, Pereira JH, Cruz-Morales P, Th...No3 
2019-08-12 HDL proteome remodeling post-strokeHomo sapiensQ Exactive HFPlubell DL, Fenton AM, Rosario S, Bergstrom P, ...No1PXD015001
2019-08-09 Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow CytometryHomo sapiensOrbitrap Fusion LumosWaas M, Weerasekera R, Kropp EM, Romero-Tejeda ...Yes1PXD014971
2019-08-09 Peptide signature for the fast detection of bacterial species in Urinary Tract infections using LC-MSEscherichia coli K-12, Klebsiella pneumoniae subsp. pneumoniae ATCC 700721, Enterococcus faecalis V583, Streptococcus agalactiae 2603V/ROrbitrap Fusion ETD,Q Exactive HF-XRoux-Dalvai F, Gotti C, Leclercq M, Helie M-C, ...No4PXD014970
2019-08-02 Absolute Quantification of Schistosoma mansoni Esophageal Gland ProductsSchistosoma mansoniXevo TQ-SNeves LX, Wilson RA, Brownridge P, Harman VM, H...Yes1PXD014899
2019-07-29 Prion MRM assay development and clinical studyHomo sapiens, Mus musculus, Rattus norvegicus, Macaca cynomolgusTSQ Quantiva,Q ExactiveMinikel EV, Kuhn E, Cocco AR, Vallabh SM, Harti...Yes16PXD014781
2019-07-26 Matrix-matched calibration curvesSaccharomyces cerevisiae, Homo sapiensQ Exactive HF,Orbitrap Fusion Lumos,TSQ QuantivaPino LK, Searle BC, Yang HY, Hoofnagle AN, Nobl...No5PXD014815
2019-07-16 Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cellsHomo sapiensTSQ VantageGerosa L, Chidley C, Fröhlich F, Sanchez G, Lim...Yes2 
2019-07-15 Unique-region phosphorylation targets LynA for rapid degradation, tuning its expression and signaling in myeloid cellsMus musculusOrbitrap FusionBrian BF, Jolicoeur AS, Guerrero CR, Nunez MG, ...No6PXD014621
2019-07-10 Light-dependent dynamics of phosphorylation of the thylakoid structural protein CURT1BArabidopsis thalianaTSQ VantageTrotta A, Bajwa AA, Mancini I, Paakkarinen V, P...No7PXD014562
2019-07-04 Analysis of endogenous peptides released from osteoarthritic cartilage unravels novel pathogenic markersHomo sapiensQTRAP 5500Fernandez-Puente P, González-Rodríguez L, Calam...Yes1 
2019-07-03 A targeted strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancerHomo sapiensTSQ Vantage,QTRAP 5500,4000 QTRAPHuttenhain R, Choi M, de la Fuente L, Oehl K, C...No3PXD014474
2019-06-28 ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infectionHuman immunodeficiency virus 1, Homo sapiensTSQ QuantivaHüttenhain R, Xu J, Burton LA, Gordon DE, Hultq...No4 
2019-06-18 A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationshipsListeria monocytogenesQ ExactiveVaradarajan AR, Goetze S, Pavlou MP, Grosboillo...No2PXD014294
2019-06-16 Targeted MRM assay Complement System in Health and Infectious DiseaseHomo sapiensXevo TQ-SWillems E, Alkema W, Keizer-Garritsen J, Supper...Yes1PXD014264
2019-06-13 Cell cycle validationMus musculus, Sus scrofa, Xenopus laevis, Xenopus tropicalisQ Exactive HFFederspiel JD, Tandon P, Wilczewski CM, Wasson ...No3 
2019-06-07 An automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbesEscherichia coli, Saccharomyces cerevisiae, Pseudomonas putida KT2440, Rhodosporidium toruloides6460 Triple Quadrupole LC/MSChen Y, Guenther JM, Gin JW, Chan LJG, Costello...No8PXD014182
2019-06-07 Developing a robust assay to monitor and quantify key players of metabolic pathways during adipogenesis by targeted proteomicsMus musculusTSQ VantageHentschel A, Ahrends R. Developing a Robust Ass...Yes2 
2019-05-31 Screening a Resource of Recombinant Protein Fragments for Targeted ProteomicsHomo sapiensQ Exactive HFYes1 
2019-05-29 Light-dependent N-terminal phosphorylation of LHCSR3 and LHCB4 are interlinked in Chlamydomonas reinhardtiiChlamydomonas reinhardtiiQ Exactive PlusScholz M, Gäbelein P, Xue H, Mosebach L, Bergne...No4 
2019-05-27 Milk glycopeptide across lactationHomo sapiensOrbitrap Fusion LumosZhu J, Lin YH, Dingess KA, Mank M, Stahl B, Hec...Yes1PXD022415
2019-05-14 Rebuilding core abscisic acid signaling pathways of Arabidopsis in yeastSaccharomyces cerevisiae, Arabidopsis thalianaOrbitrap Fusion LumosRuschhaupt M, Mergner J, Mucha S, Papacek M, Do...No1PXD013849
2019-05-09 Novel interconnections of HOG signaling revealed by combined use of two proteomic software packagesSaccharomyces cerevisiaeQ Exactive HFJanschitz M, Romanov N, Varnavides G, Hollenste...No1PXD013789
2019-04-30 Validation of N-terminal Labeling Mass Spectrometry for Characterization of Partially Hydrolyzed Gluten ProteinswheatQ Exactive PlusCao W, Baumert JL, Downs ML. Evaluation of N-te...No7PXD013679
2019-04-12 International Ring Trial of a Broad-Spectrum Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis [System Suitability Files]Homo sapiensQ Exactive HF,Q Exactive Plus,Q ExactiveThompson JW, Adams KJ, Adamski J, Asad Y, Borts...Yes2 
2019-04-10 In vitro kinase assay of human FLNc domain 18-21 with Akt and PKC alphaHomo sapiensLTQ Orbitrap EliteNo1PXD008893
2019-04-10 Endo-Lysosomal Proteins and Ubiquitin CSF Concentrations in Alzheimer’s and Parkinson’s DiseaseHomo sapiensQ ExactiveSjodin S, Brinkmalm G, Ohrfelt A, Parnetti L, P...Yes12PXD013451
2019-04-06 Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptorXanthomonas oryzae pv. oryzae6460 Triple Quadrupole LC/MSLuu DD, Joe A, Chen Y, Parys K, Bahar O, Pruitt...No1PXD013389
2019-04-06 Programmable polyketide biosynthesis platform for production of aromatic compounds in yeastSaccharomyces cerevisiae6460 Triple Quadrupole LC/MSJakociunas T, Klitgaard AK, Kontou EE, Nielsen ...No2PXD013388
2019-04-01 IFI16 pyrin oligomerization mediates antiviral actionsHomo sapiensQ Exactive HFNo1 
2019-03-30 Regulated Phosphosignaling Associated with Breast Cancer Subtypes and DruggabilityHomo sapiensTSQ VantageHuang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMi...Yes6 
2019-03-26 Homeostatic and Interferon-induced gene expression represent different states of promoter-associated transcription factor ISGF3Mus musculusQ Exactive HF-XPlatanitis E, Demiroz D, Schneller A, Fischer K...No1PXD013251
2019-03-08 Standardization of PGC-LC-MS-based glycomics for sample specific glycotypingHomo sapiens, Sus scrofa, Bos taurusVelos PlusStandardization of PGC-LC-MS-based glycomics fo...No15 
2019-03-06 Target Expression Profiling Identifies FLT3 as a BiTE® Target for Acute Myeloid LeukemiaHomo sapiensLTQ Orbitrap VelosBrauchle B, Goldstein RL, Karbowski CM, Henn A,...No1 
2019-03-05 N-terminal amino acid identification using targeted mass spectrometryEscherichia coliQ ExactiveVincent, R. M., Wright, B., & Jaschke, P. R. (2...No2PXD012390
2019-03-01 Targeted Mass Spectrometry of Brain and Pancreatic tissuesHomo sapiensQ Exactive HFYes2PXD012931
2019-02-13 Exploring Non-Canonical Terpene Space With a Heterologous Lepidopteran Mevalonate PathwayEscherichia coli6460 Triple Quadrupole LC/MSEiben CB, de Rond T, Bloszies C, Gin J, Chiniqu...No1PXD012697
2019-02-07 Lysine & Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver DiseaseMus musculusOrbitrap Fusion Lumos,TripleTOF 6600No9PXD012621
2019-01-30 Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differencesCrassostrea gigasOrbitrap Fusion Lumos,TSQ VantageVenkataraman YR, Timmins-Schiffman E, Horwith M...No3PXD012569
2019-01-22 Pharmacokinetic analysis of a novel human EGFRvIII:CD3 bispecific antibody in plasma and whole blood using a high-resolution targeted mass spectroscopy approachMus musculus, Homo sapiensQ Exactive HF-XSchaller TH, Foster MW, Thompson JW, Spasojevic...Yes2PXD012472
2019-01-15 Measurement of Nrf2-Regulated Antioxidant Response Proteins as Potential Biomarkers for Radiation Injury AssessmentMus musculusQ ExactiveLiu K, Singer E, Cohn W, Micewicz ED, McBride W...Yes4 
2019-01-11 Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine LearningEscherichia coli6460 Triple Quadrupole LC/MSOpgenorth P, Costello Z, Okada T, Goyal G, Chen...No1PXD012312
2019-01-10 A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cellsHomo sapiensQ Exactive HF,Orbitrap Fusion LumosNguyen CDL, Malchow S, Reich S, Steltgens S, Sh...Yes17 
2019-01-09 Juvenile geoduck ctenidia tissue after summer deployment in Puget Sound, WAPacific geoduckTSQ Vantage,Orbitrap Fusion LumosSpencer LH, Horwith M, Lowe AT, Venkataraman YR...No2PXD012294
2019-01-08 Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysatesCorynebacterium glutamicum ATCC 130326460 Triple Quadrupole LC/MSSasaki Yusuke and Eng T and HRA and TJ and CY a...No1PXD012293
2019-01-07 Quantitative assay of targeted proteome in trichome glandular cells using large-scale selected reaction monitoring strategySolanum lycopersicumQTRAP 5500Takemori A, Nakashima T, Ômura H, Tanaka Y, Nak...No2PXD012250
2018-12-26 Comparative phosphoproteomic analysis reveals a decay of ABA signaling in barley grains during after-ripeningHordeum vulgareTripleTOF 5600Ishikawa S, Barrero JM, Takahashi F, Nakagami H...No1 
2018-12-21 A dataset describing a suite of novel antibody reagents for the RAS signaling networkHomo sapiensQTRAP 5500,QTRAP 6500Schoenherr RM, Huang D, Voytovich UJ, Ivey RG, ...Yes117PXD012604
2018-12-20 Search for synaptic biomarkers of Alzheimer’s diseaseHomo sapiensQTRAP 5500Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Bal...Yes4PXD012138
2018-12-13 High throughput generation of a resource of the human secretome in mammalian cellsHomo sapiensQ Exactive HFTegel H, Dannemeyer M, Kanje S, Sivertsson Å, B...No1PXD012054
2018-12-13 Isotopologue multi-point calibration for proteomics biomarker quantification in clinical practiceHomo sapiensQTRAP 5500Chiva C, Pastor O, Trilla-Fuertes L, Gámez-Pozo...Yes4PXD012035
2018-12-05 Discovery and qualification of serum protein biomarkers for cholangiocarcinoma diagnosisHomo sapiensLCMS-8050Duangkumpha K, Stoll T, Phetcharaburanin J, Yon...Yes1 
2018-12-05 Multiplex assay for quantification of acute phase proteins and immunoglobulin A in dried blood spotsHomo sapiens6495B Triple Quadrupole LC/MS,6495A Triple Quadrupole LC/MSVidova, V., Stuchlikova, E., Vrbova, M., Almasi...Yes12PXD011944
2018-11-30 Improving Precursor Selectivity in Data Independent Acquisition Using Overlapping WindowsSaccharomyces cerevisiae, Bos taurusQ ExactiveAmodei D, Egertson J, MacLean BX, Johnson R, Me...Yes11PXD011910
2018-11-06 Protein-based Cardiogenic Shock Patient ClassifierHomo sapiensOrbitrap Fusion LumosRueda F, Borràs E, García-García C, Iborra-Egea...Yes1PXD011593
2018-10-24 Discovery and quantification of non-human proteins in human milkBos taurus, Gallus gallus, Oryza sativa, Canis familiaris, Felis catus, Equus caballus, Homo sapiensQ Exactive HF-XZhu J, Garrigues L, Van den Toorn H, Stahl B, H...Yes2 
2018-10-12 Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolismPseudomonas putida KT24406460 Triple Quadrupole LC/MSThompson MG, Blake-Hedges JM, Cruz-Morales P, B...No1PXD011350
2018-10-11 A rapid methods development workflow for high-throughput quantitative proteomic applicationsSaccharomyces cerevisiae, Pseudomonas putida KT2440, Escherichia coli6460 Triple Quadrupole LC/MSChen Y, Vu J, Thompson MG, Sharpless WA, Chan L...No17 
2018-10-10 ATI in Ancient WheatsTriticumTSQ Vantage,LTQ Orbitrap VelosGeisslitz S, Ludwig C, Scherf KA, Koehler P. Ta...Yes7 
2018-10-10 In vitro phosphorylation of ASY1 by CDKA;1Arabidopsis thalianaQ Exactive PlusYang C, Sofroni K, Wijnker E, Hamamura Y, Carst...No1PXD011335
2018-10-05 Single-point CalibrationSaccharomyces cerevisiaeQ Exactive HF,TSQ AltisPino LK, Searle BC, Huang EL, Noble WS, Hoofnag...No2PXD011297
2018-10-04 Plasmalogen Quantification during Human Cytomegalovirus InfectionHuman Cytomegalovirus, Homo sapiensLTQ Orbitrap XLInfection-Induced Peroxisome Biogenesis Is a Me...No3 
2018-10-02 Low-density lipoprotein receptor-related protein 1 (LRP1)-derived peptides protect against aggregation of LDL and cholesterol loading of vascular cells. Molecular and Cellular basis for antiatherosclerotic efficacyHomo sapiensLTQ Orbitrap VelosBenitez-Amaro A, Pallara C, Nasarre L, Rivas-Ur...No1PXD011261
2018-09-18 Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by ProteomicsVitis vinifera, Grapevine leafroll-associated virusQ Exactive HFBuchs N, Braga-Lagache S, Uldry AC, Brodard J, ...Yes4PXD011138
2018-09-17 Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cellsHomo sapiensTSQ VantageYes3 
2018-09-07 A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin QuantificationHomo sapiensTSQ VantageMoghieb A, Tesfay L, Nie S, Gritsenko M, Fillmo...Yes3 
2018-08-30 Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiaeSaccharomyces cerevisiaeQ Exactive PlusKelliher CM, Foster MW, Motta FC, Deckard A, So...Yes4PXD010937
2018-08-29 Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnosticsHomo sapiensQ Exactive HFKim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, W...No1PXD010934
2018-08-22 Detection of Six Commercially Processed Soy ingredients in an Incurred Food Matrix Using Parallel Reaction MonitoringGlycine maxQ Exactive PlusChen S, Yang CT, Downs ML. Detection of Six Com...No4PXD010843
2018-08-22 Enhanced validation of antibodies for research applicationsHomo sapiensQ Exactive HFEdfors F, Hober A, Linderbäck K, Maddalo G, Azi...Yes2 
2018-08-17 Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MSSus scrofa, Bos taurus, Homo sapiensVelos Plus,HCTultraAshwood C, Lin CH, Thaysen-Andersen M, Packer N...No7 
2018-08-06 Incorporation of fluoritnated tryptophan into RV1187Mycobacterium tuberculosisXevo TQ-SNurul Islam M, Hitchings R, Kumar S, Fontes FL,...No1PXD010703
2018-08-06 Mechanical force induces rapid phosphorylation dependent signaling in Xenopus embryosXenopus laevisQ Exactive HFNo6 
2018-08-01 Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible SuccinylationMus musculusTripleTOF 5600submission to cellNo1PXD010205
2018-07-12 Mass spectrometry-based absolute quantification of 20S proteasome status for controlled ex-vivo expansion of Human Adipose-derived Mesenchymal Stromal/Stem CellsHomo sapiensQTRAP 5500,QTRAP 6500Menneteau T, Fabre B, Garrigues L, Stella A, Zi...No24 
2018-07-05 Identification of novel protein lysine acetyltransferases in Escherichia coliEscherichia coliTripleTOF 6600D.G. Christensen, J.G. Meyer, J.T. Baumgartner,...No2 
2018-07-05 Streptococcus pyogenes evades adaptive immunity through specific modification of host IgG glycosylationHomo sapiens, Mus musculusTSQ VantageNaegeli, A., Bratanis, E., Karlsson, C., Shanno...No8 
2018-06-11 targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteinsEscherichia coli6460 Triple Quadrupole LC/MSBatth, Tanveer S., et al. "A targeted proteomic...No45 
2018-06-11 A Kinetic-Based Approach to Understanding Heterologous Mevalonate Pathway Function in E. ColiEscherichia coli6460 Triple Quadrupole LC/MSWeaver, Lane J., et al. "A kinetic‐based approa...No1 
2018-06-11 Metabolic engineering of Escherichia coli for limonene and perillyl alcohol productionEscherichia coliQTRAP 5500Alonso-Gutierrez, Jorge, et al. "Metabolic engi...No1 
2018-06-11 Viscous control of cellular respiration by membrane lipid compositionEscherichia coli6460 Triple Quadrupole LC/MSBudin I, de Rond T, Chen Y, Chan LJ, Petzold CJ...No1 
2018-06-11 Modular Engineering of L-Tyrosine Production in Escherichia coliEscherichia coli4000 QTRAPJuminaga, Darmawi, et al. "Modular engineering ...No1 
2018-05-25 Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine LearningHomo sapiensQTRAP 5500Toghi Eshghi S, Auger P, Mathews WR. Quality as...Yes3 
2018-05-22 HR-SRM-baseds analysis of mouse/human SGLT2 in kidney and heart tissue.Mus musculus, Homo sapiensTripleTOF 5600+Mustroph et al., ESC Heart Failure, in revision...No1 
2018-04-19 Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics MeasurementsEscherichia coliQ Exactive HFTaumer C, Griesbaum L, Kovacevic A, Soufi B, Na...No5 
2018-04-17 Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cellsHomo sapiensTSQ VantageNo12 
2018-03-27 Combining discovery and targeted proteomics reveals a prognostic signature in oral cancerHomo sapiensXevo TQ-XSYes2 
2018-03-26 Global Characterization of Human IgG1 under Oxidative Stresses—Combining dual independent protease digestions and LC-HRMS Data Independent Acquisition (DIA)Homo sapiensQ Exactive PlusChen Y, Doud E, Stone T, Xin L, Hong W, Li Y. R...No8 
2018-03-22 Targeted Quantification of the Peroxisome Proteome during Human Cytomegalovirus InfectionHuman Cytomegalovirus, Homo sapiensQ Exactive HFInfection-Induced Peroxisome Biogenesis Is a Me...No1 
2018-03-22 Identification of functional TEX101 interactome through proteomic profiling of human spermatozoa homozygous for a missense variant rs35033974Homo sapiensTSQ Quantiva,Q Exactive PlusSchiza C, Korbakis D, Jarvi K, Diamandis EP, Dr...Yes5 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort datasetHomo sapiens6490 Triple Quadrupole LC/MSShah AK, Hartel G, Brown I, Winterford C, Na R,...Yes4 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - Ochsner cohort datasetHomo sapiens6490 Triple Quadrupole LC/MSShah AK, Hartel G, Brown I, Winterford C, Na R,...Yes4 
2018-03-16 Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK PathwayHomo sapiensTSQ Vantage,nanoACQUITY UPLCYi L, Shi T, Gritsenko MA, X'avia Chan CY, Fill...Yes4 
2018-03-15 PknG physiological substratesMycobacterium bovis BCGQ ExactiveKehilwe C Nakedi, Bridget Calder, Mousumi Barne...No1 
2018-03-08 Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. Journal of The American Society for Mass SpectrometryBos taurus, Saccharomyces cerevisiae6560 Q-TOF LC/MSMacLean BX, Pratt BS, Egertson JD, MacCoss MJ, ...Yes5PXD010650
2018-03-05 Discovery of a testis-specific complex TEX101-DPEP3 and selection of its disrupting antibodiesHomo sapiensTSQ QuantivaSchiza, C., Korbakis, D., Panteleli, E., Jarvi,...Yes4 
2018-02-02 Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damageHomo sapiensQTRAP 6500Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla ...No5 
2018-01-31 Monitoring molecular contaminants and interferences in proteomic data sets  Rardin MJ. Rapid assessment of contaminants and...No1 
2018-01-26 Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cellsMus musculusQ Exactive HFNo3 
2018-01-23 Global, site-resolved, quantitative analysis of the yeast redoxomeSaccharomyces cerevisiaeLTQ Orbitrap EliteUlrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ...No5 
2018-01-22 Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)Bos taurusTSQ Quantum,TSQ Vantage,4000 QTRAP,QTRAP 5500,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ-XSAbbatiello SE, Mani DR, Schilling B, Maclean B,...No15PXD010535
2018-01-03 Targeted Proteomics of HDL in People With Type 2 DiabetesHomo sapiensTSQ VantageVaisar T, Couzens E, Hwang A, Russell M, Barlow...No2 
2017-12-18 Curated DIA assay for consistent ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus)Gasterosteus aculeatusImpactHD UHR-QTOFJ. Li, B.B. Levitan, S. Gomez-Jimenez and D. Kü...No4 
2017-11-29 Measurement by a Novel LC-MS/MS Methodology of Vitamin D–Binding ProteinHomo sapiensQ Exactive PlusHenderson CM, Lutsey PL, Misialek JR, Laha TJ, ...Yes1 
2017-11-20 Quantification of Site-Specific Protein Lysine Acetylation and Succinylation Stoichiometry using Data-Independent Acquisitions (DIA) Mass Spectrometry --Protocol ExampleBos taurusTripleTOF 5600Wei L, Meyer JG, Schilling B. Quantification of...No1 
2017-11-02 Nitric oxide prevents Aft1 activation and metabolic remodeling in Frataxin-deficient yeastSaccharomyces cerevisiae6420 Triple Quadrupole LC/MSAlsina D, Ros J, Tamarit J. Redox Biology. Vo...Yes1 
2017-11-02 SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageAngeleri M, Zorina A, Aro EM, Battchikova N. In...No1 
2017-10-25 Targeted proteomics in triple negative breast cancer on FFPE samplesHomo sapiensOrbitrap Fusion LumosGámez-Pozo, A. et al. Prediction of adjuvant ch...Yes2 
2017-10-17 DDR panel radiation responseHomo sapiensQTRAP 6500Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, S...No3 
2017-10-09 MEERCAT: MULTIPLEXED EFFICIENT CELL FREE EXPRESSION OF RECOMBINANT QconCATS FOR LARGE SCALE ABSOLUTE PROTEOME QUANTIFICATION QTRAP 5500Yes6 
2017-09-27 The conservation of sirtuin lipoamidase activity in bacteria as a regulator of metabolic enzyme complexesEscherichia coliQ Exactive,LTQ Orbitrap VelosRowland EA, Greco TM, Snowden CK, McCabe AL, Si...No5 
2017-09-21 Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeSHomo sapiens, Streptococcus pyogenesTSQ Vantage,TSQ QuantivaChristofer A. Q. Karlsson, Sofia Järnum, Lena W...No2 
2017-09-21 Cellular signaling underlying GSIS in pancreatic β-cellsRattus norvegicusQ Exactive HFKang T, Jensen P, Huang H, Lund Christensen G, ...No1 
2017-09-15 Quantification of Plasma proteins using PlasmaDive kit on nanoflow LC-MS system and standard flow LC-MS systemHomo sapiensTSQ Vantage,6495A Triple Quadrupole LC/MSYin X, Baig F, Haudebourg E, Blankley RT, Gandh...Yes2 
2017-08-29 A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen PeroxideSalmonella typhimuriumBruker Amazon SL ion trap and Shimadzu 8050 QQQ,LCMS-8050Karash S, Liyanage R, Qassab A, Lay JO Jr, Kwon...No3 
2017-08-03 Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagarTMSTEC media.Escherichia coliQ ExactiveKalule JB, Fortuin S, Calder B, Robberts L, Ked...No2 
2017-07-05 A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brainMus musculusLTQ Orbitrap Elite,TSQ QuantivaScott P. Goulding, Karen K. Szumlinski, Candice...No3 
2017-06-21 MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experimentsHomo sapiens, Bos taurus4000 QTRAP,QTRAP 5500,TSQ Vantage,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ MSDogu, E, Mohammad-Taheri, S, Abbatiello, SE et ...No8 
2017-06-14 An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomicsBartonella henselae str. Houston-1Orbitrap FusionUlrich Omasits, Adithi R. Varadarajan, Michael ...No2 
2017-05-18 Quantification of Mutant SPOP Proteins in Prostate CancerHomo sapiensTSQ Vantage,nanoACQUITY UPLCYes16 
2017-05-03 Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and TissuesHomo sapiensTSQ Vantage,nanoACQUITY UPLCNie S, Shi T, Fillmore TL, Schepmoes AA, Brewer...No8 
2017-05-03 Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancerHomo sapiensTSQ Vantage,nanoACQUITY UPLCNo70 
2017-05-03 PSB33 sustains Photosystem II D1 protein under fluctuating light conditionsArabidopsis thalianaTSQ VantageNo1 
2017-04-20 Proteomics analysis identifies orthologs of human chitinase-like proteins as inducers of tube-morphogenesis defects in DrosophilaDrosophila melanogasterTSQ VantageSandra G. Zimmerman, Gennifer E. Merrihew, Mich...No2 
2017-04-17 Proteomic assay development for reproductive maturation state determination in Geoduck: towards a non-invasive proteomic assay for improving aquaculturePanopea generosaTSQ VantageEmma B. Timmins-Schiffman, Grace A Crandall, Br...No2 
2017-04-13 Multiplexed MRM-based Protein Quantitation Using Two Different Stable Isotope Labeled Peptides for Calibration  André LeBlanc, Sarah A. Michaud, Andrew J. Perc...No16 
2017-03-29 Quantitative Proteomics Method ComparisonHomo sapiensTSQ Quantiva,Q Exactive PlusHoffman MA, Fang B, Haura EB, Rix U, Koomen JM....No2 
2017-03-21 Role of type 2 NAD(P)H dehydrogenase NdbC in redox regulation of carbon allocation in Synechocystis sp. PCC 68031Synechocystis sp. PCC 6803TSQ VantageHuokko T, Muth-Pawlak D, Battchikova N, Allahve...No1 
2017-03-03 Spatially and temporally resolved protein interaction networks in living cells.Homo sapiensTSQ QuantivaLobingier BT, Hüttenhain R, Eichel K, Miller KB...No2 
2017-02-17 Inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 induces unique iron-dependent protein-level responsesSynechocystis sp. PCC 6803TSQ VantageLinda Vuorijoki, Arjun Tiwari, Pauli Kallio, Ev...No1 
2017-02-13 Stoichiometric surface density modelStreptococcus pyogenesTSQ QuantivaKristoffer Sjöholm, Ola Kilsgård, Johan Teleman...Yes2 
2017-01-25 Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanomaHomo sapiensQ Exactive PlusMorales-Betanzos CA, Lee H, Gonzalez-Ericsson P...Yes5 
2017-01-10 An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinasesHomo sapiensQ Exactive PlusUrisman A, Levin RS, Gordan JD, Webber JT, Hern...No2 
2016-12-01 Photosynthesis-related phosphopeptides in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageMartina Angeleri, Dorota Muth-Pawlak, Eva-Mari ...Yes3 
2016-11-16 Impact of cystinosin glycosylation on protein stability by differential dynamic SILACHomo sapiensQ Exactive PlusNathalie Nevo, Lucie Thomas, Cerina Chhuon, Zuz...No6 
2016-11-15 Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stressHomo sapiensQTRAP 5500Tzu-Yu Liu, Hector H. Huang, Diamond Wheeler, ...No9 
2016-10-31 Plastin 1 widens stereocilia by transforming actin filament packing from hexagonal to liquidMus musculusOrbitrap FusionKrey JF, Krystofiak ES, Dumont RA, Vijayakumar ...Yes3 
2016-10-26 Osmolality/ salinity responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fishOreochromis mossambicusImpactHD UHR-QTOFWang X. and Kültz DNo2 
2016-10-20 PECAN - A Library Free Peptide Detection Tool for DIA DataHomo sapiens, Saccharomyces cerevisiaeQ Exactive,Q Exactive HF,TSQ Vantage,TSQ QuantivaNo5 
2016-10-18 Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated ProteinsHomo sapiensQ ExactiveBraga-Lagache S, Buchs N, Iacovache MI, Zuber B...No2 
2016-10-17 Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteriaSynechocystis sp. PCC 6803TSQ VantageGeorg J, Kostova G, Vuorijoki L, Schön V, Kadow...No2 
2016-10-07 FLNc Calpain GluC SRM AnalysisHomo sapiensQ Exactive PlusLena Reimann, Heike Wiese, Yvonne Leber, Anja N...No1 
2016-10-03 ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experimentsSaccharomyces cerevisiaeQ ExactiveChoi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS...Yes9 
2016-09-22 Dynamic phosphorylation of apoptosis signal regulating kinase 1 (ASK1) in response to oxidative and electrophilic stress Q Exactive PlusCarlos Morales Betanzos, Joel D. Federspiel, Am...No2 
2016-09-21 A general method for targeted quantitative cross-linking mass spectrometryHomo sapiens, Bos taurusQ-Exactive Plus HF,Q Exactive PlusJuan D. Chavez, Jimmy K. Eng, Devin K. Schweppe...No2 
2016-08-08 Detection of Low Abundance Ocean Bacteria PeptidesRuegeria pomeroyiTSQ VantageNo2 
2016-07-29 SELECTIVE AND SENSITIVE QUANTIFICATION OF THE CYTOCHROME P450 3A4 PROTEIN IN HUMAN LIVER HOMOGENATES THROUGH MULTIPLE REACTION MONITORING MASS SPECTROMETRYHomo sapiensQTRAP 5500Cieślak A, Kelly I, Trottier J, Verreault M, Wu...Yes2 
2016-07-13 Gadd45a Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4Mus musculusTripleTOF 5600Bullard, S.A., Seo, S., Schilling, B., Dyle, M....No1 
2016-06-14 Identification and characterization of protein acetylation in Neisseria gonorrhoeaeNeisseria gonorrhoeaeTripleTOF 5600Post DMB, Schilling B, Reinders LM, D'Souza AK,...No1 
2016-06-08 Robust temporal profiling of GRB2 protein complexes in primary T cells using SWATH mass spectrometryMus musculusTripleTOF 5600Etienne Caron, Romain Roncagalli, Takeshi Hase,...No4 
2016-06-02 PRM analysis of EC uterine aspirateHomo sapiensQ Exactive PlusMartinez-Garcia E, Lesur A, Devis L, Campos AR,...Yes1 
2016-05-25 Quantifiable peptide tags for targeted proteomics.Homo sapiensTSQ VantageGiel Vandemoortele, An Staes, Giulia Gonnelli, ...Yes9 
2016-05-20 Development, Validation, and Application of a MRM with SIS Peptide Strategy to Quantify Multiplexed Panels of Proteins in Mouse Plasma and Heart TissuesMus musculus6490 Triple Quadrupole LC/MSYes2 
2016-05-12 In vivo kinase assay of mouse FLNcC2C12 mouse myotubesThermo Scientific Orbitrap Velos EliteLena Reimann, Heike Wiese, Yvonne Leber, Anja N...No1 
2016-05-12 In vitro kinase assay of human and mouse FLNc domain 23-24Homo sapiens, Mus musculusObritrap Velos Elite,Q Exactive PlusLena Reimann, Heike Wiese, Yvonne Leber, Anja N...No1 
2016-05-06 Conserved protein abundance pattern of the EGFR-MAPK pathway reveals its regulatory architectureHomo sapiensTSQ VantageTujin Shi, Mario Niepel, Jason E. McDermott, Yu...Yes20 
2016-03-23 Annexin A5 is the Most-Abundant Membrane-Associated Protein in Stereocilia but is DispensableMus musculusOrbitrap FusionKrey JF, Drummond M, Foster S, Porsov E, Vijaya...No2 
2016-03-18 Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissuesHomo sapiensQTRAP 5500Kennedy JJ, Whiteaker JR, Schoenherr RM, Yan P,...Yes7 
2016-03-07 Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspectiveHomo sapiensTSQ Vantage,QTRAP 5500,Q Exactive,Q Exactive HF,TripleTOF 5600Tobias Kockmann, Christian Trachsel, Christian ...Yes12 
2016-02-18 Differential light-dependent phosphorylation of Ser and Thr residues regulates plant STN7 kinaseArabidopsis thalianaTSQ VantageTrotta A, Suorsa M, Rantala M, Lundin B, Aro EM...No14 
2016-02-08 Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reportedDesulfovibrio vulgaris str. HildenboroughLTQ Orbitrap Velos,LTQ XL,QSTAR XLM. Shatsky, S. Allen, B.L. Gold, N.L. Liu, T.R....No1 
2015-12-21 Proteomic profile of deleted in breast cancer 1 (DBC1) protein-protein interactionsHomo sapiensLTQ Orbitrap VelosGiguère SS, Guise AJ, Jean Beltran PM, Joshi PM...No1 
2015-12-18 A quantitative tagless co-purification method to validate and identify protein-protein interactionsDesulfovibrio vulgaris str. Hildenborough4800 Plus MALDI TOF/TOF,5800 TOF/TOFMaxim Shatsky, Ming Dong, Haichuan Liu, Lee Lis...No1 
2015-12-07 Assembly dynamics and stoichiometry of the apoptosis signal-regulating kinase (ASK) signalosome in response to electrophile stressHomo sapiensQ Exactive PlusJoel D. Federspiel, Simona G. Codreanu, Amy M. ...No4 
2015-10-27 Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.Homo sapiens, Mus musculus, Saccharomyces cerevisiaeOrbitrap/HCD,TripleTOF 5600Parker SJ, Rost H, Rosenberger G, Collins BC, M...No1 
2015-10-15 Renal proteomes of marine and FW sticklebacksGasterosteus aculeatusImpactHD UHR-QTOFJournal of Proteomics. 2015 Sep;14(9):2331-40. ...No1 
2015-08-10 Development of a quantitative SRM-based proteomics method to study iron metabolism of Synechocystis sp. PCC 6803Synechocystis sp. PCC 6803TSQ VantageDevelopment of a quantitative SRM-based proteom...No3 
2015-08-07 Population-specific plasma proteomes of marine and freshwater three-spined sticklebacksGasterosteus aculeatusimpact HDProteomics Volume 15, Issue 23-24, December 201...No1 
2015-08-06 Evaluation of multi-tRNA synthetase complex by multiple reaction monitoring mass spectrometry coupled with size exclusion chromatographyHomo sapiensQTRAP 5500Park SJ, Ahn HS, Kim JS, Lee C. Evaluation of M...Yes4 
2015-07-17 Multiplexed, scheduled high resolution (sMRM-HR) acquisition on a full scan QqTOF instrument with integrated data-dependent and targeted mass spectrometric workflows.Bos taurus, Saccharomyces cerevisiae, Escherichia coliTripleTOF 5600Schilling B, MacLean B, Held JM, Sahu AK, Rardi...No4 
2015-06-18 MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic ExperimentsMus musculusTripleTOF 5600Rardin MJ, Schilling B, Cheng L, MacLean BX, So...No8 
2015-06-16 Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded Breast Cancer TissuesHomo sapiensTSQ VantageSteiner C, Tille JC, Lamerz J, Kux van Geijtenb...Yes13 
2015-06-14 Ariadne’s thread: a robust software solution leading to automated absolute and relative quantification of SRM datasynthetic peptides, Drosophila melanogasterTSQ Quantum EMRNasso et. al.; Ariadne's Thread: A Robust Softw...Yes3 
2015-06-09 Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomicsHomo sapiensTSQ VantageDunkley T, Costa V, Friedlein A, Lugert S, Aign...Yes3 
2015-04-30 Analytical protein standardsHomo sapiensTSQ VantageSearle BC, Egertson JD, Bollinger JG, Stergachi...No14 
2015-04-28 Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using SkylineMycobacterium tuberculosisTripleTOF 5600Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ...No1 
2015-04-28 Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantificationMycobacterium tuberculosisTripleTOF 5600Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ...Yes1 
2015-04-28 Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptidesMycobacterium tuberculosisTripleTOF 5600Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ...Yes1 
2015-03-09 Protein acetylation in response to carbon overflow: detecting dynamic acetylation changes by mass spectrometryEscherichia coliTripleTOF 6600,TripleTOF 5600Schilling B, Christensen D, Davis R, Sahu AK, H...No4 
2015-02-06 Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasmaHomo sapiens4000 QTRAP,QTRAP 5500,TSQ Vantage,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ MS,Xevo TQ-SAbbatiello SE, Schilling B, Mani DR, Zimmerman ...Yes54