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|  FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standards | Homo sapiens | Q Exactive HF | Yes | 1 | absolute quantification of proteins, MS Western, QconCAT, targeted quantitative proteomics, cerebrospinal fluid, neurodegeneration, neuroinflammation | publication pending | PXD030762 |
| Quantitative XL-MS Analysis of HHARI in the presence or absence of 4EHP | Homo sapiens | Q Exactive | No | 1 | Cross-linking Mass Spectrometry Kojak ProXL Skyline Cullin HHARI RBR E3 ligase ubiquitin | Reiter KH, Zelter A, Janowska MK, Riffle M, Shu... | PXD030871 |
| One-Pot Isotope Dilution PRM for Quantitative Protein Heterogeneity in Red Blood Cells | Homo sapiens | Orbitrap Fusion ETD,Orbitrap Exploris 480,6495B Triple Quadrupole LC/MS | Yes | 14 | Single cell proteomics, quantitative, One-pot, hemoglobin, erythrocyte, red blood cell, HbA1c, glycated hemoglobin, carboxymethyl hemoglobin. | Eshghi A, Xie X, Hardie D, Chen MX, Izaguirre F... | PXD030875 |
| The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5 | Homo sapiens | TSQ Quantiva | Yes | 1 | SRM, cardiomyocytes, transcription factors | Maven et al., The multi-lineage transcription f... | PXD031059 |
| Imetelstat Is a Potent Inducer of Ferroptosis That Effectively Diminishes Acute Myeloid Leukemia Burden and Delays Relapse Following Pro-Oxidant Therapy | Homo sapiens | 6470A Triple Quadrupole LC/MS | No | 2 | Imetelstat, acute myeloid leukemia, ferroptosis, patient-derived xenograft, telomerase, lipid metabolism, LAMTOR2, FADS2, reactive oxygen species, phosphorothioate oligonucleotide, G-quadruplex | Bruedigam C, Porter AH, Song A, Vroeg In de Wei... | |
| Profiling the diversity of agonist-selective effects on the proximal proteome environment of G protein-coupled receptors | Homo sapiens | TSQ Quantiva | No | 1 | SRM, APEX, proximity labeling, GPCR, mu-opioid receptor | Polacco BJ, Lobingier BT, Blythe EE, Abreu N, K... | PXD031393 |
| Cov²MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein | SARS-CoV-2 | Xevo TQ-XS,TripleTOF 6600 | No | 36 | SARS-CoV-2, Covid-19, Mass Spectrometry, Proteomics, Viral proteins, Peptides, Diagnostics | Van Puyvelde B, Van Uytfanghe K, Van Oudenhove ... | PXD031401 |
| Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. | Plasmodium falciparum | Xevo TQ-XS,Xevo G2-XS Tof | No | 6 | Malaria; Plasmodium; RAP; RNA-binding proteins | Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A... | |
| A scalable, targeted mass spectrometry-based assay for monitoring the progression of herpesvirus infections | Human betaherpesvirus 5, Herpes simplex virus 1, Kaposi's sarcoma-associated herpesvirus, Homo sapiens | Q Exactive HF | No | 17 | PRM, herpesvirus, HSV-1, HCMV, KSHV | Kennedy MA, Tyl MD, Betsinger CN, Federspiel JD... | PXD025879 |
| PrP concentration in the central nervous system: regional variability, genotypic effects, and pharmacodynamic impact | Homo sapiens, Rattus norvegicus | TSQ Quantiva | Yes | 2 | cerebrospinal fluid, LC-MRM-MS, TSQ Quantiva, Skyline, antisense oligonucleotide, prion protein | Mortberg MA, Zhao HT, Reidenbach AG, Gentile JE... | PXD031432 |
| Skin cancer-associated S. aureus downregulates DNA repair mechanisms, and promotes oxidative stress and DNA damage in human keratinocytes | Staphylococcus capitis, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus | 6470A Triple Quadrupole LC/MS | No | 1 | Skin, S. aureus secretome, multiomics, actinic keratosis, squamous cell carcinoma, DNA damage | Krueger A, Mohamed A, Kolka CM, Stoll T, Zaugg ... | PXD031676 |
| Absolute Protein Quantitation of the Mouse Macrophage Toll-Like Receptor and Chemotaxis Pathways | Mus musculus | Q Exactive HF | Yes | 1 | macrophage, chemotaxis pathway, Toll-like receptor pathway, parallel reaction monitoring | Manes NP, Calzola JM, Kaplan PR, Fraser IDC, Ge... | PXD031697 |
| IFI16-mediated suppression of HSV-1 protein expression | Homo sapiens, Human herpesvirus 1 | Q Exactive HF | No | 1 | HSV-1, innate immunity, DNA sensing, IFI16 | Publication pending | PXD031850 |
| HDL Proteomics in Coronary Artery Calcification in Type 1 Diabetes (CACTI) Study | Homo sapiens | Orbitrap Fusion Lumos | No | 6 | HDL proteomics, CACTI, Diabetes, incident CVD, parallel reaction monitoring, quantification, Orbitrap Fusion Lumos, Skyline | Shao B, Snell-Bergeon JK, Pyle LL, Thomas KE, d... | PXD031854 |
| Prediction and experimental validation of a new salinity-responsive cis-regulatory element (CRE) in tilapia | Oreochromis mossambicus | impact II | No | 1 | tilapia, OmB cell line, cellular osmoregulation, CRE, transcription factor, data-independent acquisition, quantitative proteomics | Kim C, Wang X, Kültz D. Prediction and Experime... | PXD032181 |
| The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor Biopsies | Homo sapiens | Orbitrap Fusion Lumos | Yes | 5 | FAIMS PRM HER2 | Sweet S, Chain D, Yu W, Martin P, Rebelatto M, ... | PXD027134 |
| Mouse apolipoproteome study - hyperlipidemic mouse models | Mus musculus | TSQ Altis | Yes | 8 | MRM plasma mouse | Steffensen LB, Larsen JH, Hansen DR, Tha TML, L... | PXD032868 |
| Targeted proteomics of diel cycle of copepod Pleuromamma xiphias | Pleuromamma xiphias | TSQ Altis | No | 3 | copepod, selected reaction monitoring, diel vertical migration, circadian rhythm | Timmins-Schiffman E, Maas AE, Khanna R, Blanco-... | PXD033033 |
| Elevation of fatty acid desaturase 2 in esophageal adenocarcinoma increases polyunsaturated lipids and may exacerbate bile acid-induced genotoxicity | Homo sapiens | 6470A Triple Quadrupole LC/MS | No | 2 | Barrett’s Esophagus, esophageal adenocarcinoma, polyunsaturated lipids, desaturase, FADS2, reactive oxygen species | Molendijk J, Kolka CM, Cairns H, Brosda S, Moha... | |
| Discovery and validation of serum glycoprotein biomarker panel for detection of high grade serous ovarian cancer | Homo sapiens | 6490 Triple Quadrupole LC/MS | Yes | 3 | glycosylation, LeMBA, lectin, ovarian cancer screening, STL | Dutt M, Hartel G, Richards RS, Shah AK, Mohamed... | PXD033108 |
| An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia | Homo sapiens | TripleTOF 6600,TripleTOF 5600 | No | 1 | Leukemia, T-ALL, Epigenetics, Histone post-translational modifications, LC-MS | | PXD031500 |
| Targeted proteomics (parallel reaction monitoring) to quantify starch-biosynthetic proteins in yeast | Saccharomyces cerevisiae, Arabidopsis thaliana | Q Exactive | Yes | 2 | starch, heterologous expression, starch synthase, branching enzyme, debranching enzyme, isoamylase | Publication pending | PXD033364 |
| Iron-Regulated Assembly of the Cytosolic Iron-Sulfur Cluster Biogenesis Machinery | Homo sapiens | Orbitrap Fusion Lumos | No | 3 | PRM, iron-sulfur cluster, protein interactions | Fan X, Barshop WD, Vashisht AA, Pandey V, Leal ... | PXD033557 |
| A proteomics investigation of cigarette smoke exposed Wistar rats revealed improved anti-inflammatory effects of the cysteamine nanoemulsions delivered via inhalation | Rattus norvegicus | TSQ Altis | No | 1 | Rat, COPD, cysteamine, MRM, proteomics | Sharma G, Pund S, Govindan R, Nissa MU, Biswas ... | PXD033559 |
| Addressing the Protease Bias in Quantitative Proteomics | Homo sapiens | TSQ Altis | Yes | 12 | Multiple proteases, SRM, Targeted proteomics, Absolute quantification, Plasma proteomics | Woessmann J, Kotol D, Hober A, Uhlén M, Edfors ... | PXD033574 |
| SARS-CoV-2 PRM-MS Assay with Clinical Patient Samples | Homo sapiens | Q Exactive HF | No | 1 | COVID-19, SARS-CoV-2, Proteomics, PRM, LC-MS, mass spectrometry, parallel reaction monitoring | Gajbhiye A, Nalbant A, Heunis T, Sidgwick F, Po... | PXD033790 |
| Rapid assessment of lipidomics sample purity and quantity using attenuated total reflectance Fourier-transform infrared spectroscopy | Homo sapiens | 6470A Triple Quadrupole LC/MS | No | 1 | lipidomics, lipids, phospholipids, sphingolipids, triglycerides, exosomes, FTIR, mass spectrometry, extracellular vesicles, chemical contaminants | Robinson, H.; Molendijk, J.; Shah, A.K.; Rahman... | |
| Multiple phosphorylation combinatorially regulates IFI16 antiviral immune signaling | Homo sapiens | Q Exactive HF | No | 2 | Innate immune sensing, herpesvirus, phosphorylation | | |
| Retrospective longitudinal monitoring of multiple myeloma patients by mass spectrometry using archived serum protein electrophoresis gels and de novo sequence analysis | Homo sapiens | Q Exactive HF | No | 10 | Minimal Residual Disease, Serum protein Electrophoresis, Mass Spectrometry, Multiple Myeloma | Noori S, Zajec M, Russcher H, Tintu AN, Broijl ... | PXD034406 |
| Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipids | Homo sapiens | Q Exactive HF | Yes | 1 | CD1d, NKT cell, Sortase A, Shotgun lipidomics, Sphingomyelin | Sortase A-cleavable CD1d identifies sphingomyel... | PXD034495 |
| A Peptide-Centric Quantitative Proteomics Dataset for the Phenotypic Assessment of Alzheimer’s Disease | Homo sapiens | Orbitrap Fusion Lumos | No | 27 | Quantitative Proteomics, DIA Mass Spectrometry, Alzheimer’s disease, peptide-centric, human brain tissue | Merrihew GE, Park J, Plubell D, Searle BC, Keen... | PXD034525 |
| Mass spectrometry-driven discovery of neuropeptides mediating nictation behavior of nematodes | Caenorhabditis elegans | Q Exactive HF-X | No | 2 | Caenorhabditis elegans, dauer, L3, nictation, LC-MS/MS, parallel reaction monitoring, neuropeptidomics | Cockx B, Van Bael S, Boelen R, Vandewyer E, Yan... | |
| Tandem Mass Tag-Based Quantitative Proteomic Profiling Identifies Novel Serum Biomarkers of Drug-Induced Liver Injury in Humans | Homo sapiens | Orbitrap Exploris 480 | No | 3 | DILI, Biomarker, Liver Disease | Ravindra KC, Vaidya VS, Wang Z, Federspiel JD, ... | PXD034882 |
| Longitudinal evaluation of biomarkers in wound fluids of venous leg ulcers treated with a protease-modulating wound dressing | Homo sapiens | Orbitrap Exploris 480 | Yes | 4 | protease-modulating wound dressing, protein biomarker, SureQuant, venous leg ulcer, wound fluid | Mikosiński J, Kalogeropoulos K, Bundgaard L, La... | PXD025748 |
| NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency | Homo sapiens | TripleTOF 5600+,TripleTOF 5600 | No | 1 | iPSC, Proteomics, DIA, SWATH, LINCS, multi-omic | | PXD021497 |
| MRM based validation of target antigen expression in Pituitary Adenoma patients | Homo sapiens | TSQ Altis | No | 1 | MRM, Pituitary Adenoma, Antibody, HuProt array | Evaluation of autoantibody signatures in Pituit... | PXD035165 |
| Kinase activity profiling in breast cancer samples | Homo sapiens | TSQ Altis | Yes | 1 | Breast cancer, clinical, kinase activity, phosphorylation, treatment prediction | | PXD035186 |
| PRM targeted mass spectrometry reveals the phosphorylation regulation of human bile acid transporter ASBT | Homo sapiens | Q Exactive HF | Yes | 11 | ASBT, PRM, Phosphorylation stochiometry | | PXD035472 |
| Sampling the proteome by emerging single-molecule and mass-spectrometry based methods | Homo sapiens | Orbitrap Eclipse | No | 1 | data independent acquisition, plasma, extracellular vesicles, bioinformatics | MacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu... | PXD035637 |
| Validation of known and novel AKT, S6K and RSK targets by targeted MS | Mus musculus | Q Exactive Plus | Yes | 1 | Mouse, Skeletal muscle, Phosphoproteomics, PRM, AKT, S6K, RSK | Fricke AL, Mühlhäuser WWD, Reimann L, Zimmerman... | PXD035962 |
| Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei | Syntrophomonas wolfei | Orbitrap Exploris 480 | No | 1 | lysine acylation, post-translational modifications, Syntrophs, Syntrophomonas wolfei | | PXD036088 |
| Absolute and relative quantitation of ATI in modified wheat | Triticum aestivum subsp. aestivum, Triticum turgidum subsp. durum | TSQ Vantage,Q Exactive Plus | Yes | 3 | wheat, CRIPSR-Cas9, mRNAi, ATI reduction, wheat sensitivity | Geisslitz S, Islam S, Buck L, Grunwald-Gruber C... | |
| Multisite proteome provides insights into the biology and prognostic markers for head and neck cancer | Homo sapiens | Orbitrap Exploris 240 | No | 1 | Head and Neck Squamous Cell Carcinoma, Mouth Neoplasms, Proteomics, Lymph Node Metastasis, Buffy coat, Saliva, Biomarkers, Prognosis, Immune System, Machine Learning | Busso-Lopes AF, Neves LX, Câmara GA, Granato DC... | PXD036311 |
| Reduction of MRM protein target list using correlation analysis | Bos taurus | 6495A Triple Quadrupole LC/MS | No | 1 | dairy, quantitative proteomics, correlation analysis, MRM, MFGM | Ebhardt HA, Ponchon P, Theodosiadis K, Fuerer C... | PXD036543 |
| Activity-dependent regulation of SLK phosphorylation | Mus musculus | Q Exactive | No | 2 | parallel reaction monitoring, Ste20-like kinase, neurons | Publication pending | PXD036547 |
| The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector | Arabidopsis thaliana | Orbitrap Fusion | No | 1 | Plant immunity, phosphorylation, effector | accepted for publication in EMBO | PXD036761 |
| Differential isotope labelling by amino acids (DILAC) reveals metabolic cross-feeding and phenotypic heterogeneity in a clonal cell population | Saccharomyces cerevisiae | TripleTOF 6600 | No | 7 | 13C, yeast, heterogeneity, subpopulations, PRM, DILAC | Stephan Kamrad, Clara Correia-Melo, Lukasz Szyr... | PXD036959 |
| Targeting tumor-intrinsic neural vulnerabilities of glioblastoma | Homo sapiens | Q Exactive HF-X | No | 2 | pharmacoscopy, glioblastoma, TP53, BTG1 | | PXD037015 |
| Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetes | Homo sapiens | TSQ Vantage | Yes | 6 | Type 1 diabetes, targeted proteomics, serum, markers | Hirvonen MK, Lietzén N, Moulder R, Bhosale SD, ... | PXD033946 |
| Analysis of the effect of ClpC1 directed antibiotics on ClpC1, ClpC2 and ClpC3 protein levels. | Mycolicibacterium smegmatis | Q Exactive HF-X,Orbitrap Exploris 480 | Yes | 3 | BacPROTAC, PROTAC, protein degradation, TPD, antibiotics | Hoi DM, Junker S, Junk L, Schwechel K, Fischel ... | PXD037198 |
| Characterizing the origin of blood plasma proteins from organ tissues in rainbow trout (Oncorhynchus mykiss) using a comparative non-targeted proteomics approach | Oncorhynchus mykiss | 6545 Q-TOF LC/MS,1200 series LC/MSD SL | No | 24 | proteomics, blood plasma, rainbow trout, fish, tissue or origin | Tannouri N, Simmons DBD. Characterizing the ori... | PXD037782 |
| Sirtuin 5 Reduces Malonylation in Non-mitochondrial Metabolic Pathways in Diabetic Kidney Disease | Mus musculus | Q Exactive | Yes | 1 | Diabetic kidney disease, metabolomics, nutrient utilization, proteomics, sirtuin 5 | Baek J, Sas K, He C, Nair V, Giblin W, Inoki A,... | PXD037819 |
| Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define putative diagnostic biosignatures for Parkinson’s disease | Homo sapiens | Q Exactive HF-X | No | 1 | Biomarker discovery, Parkinson's disease, Extracellular vesicles, Exosomes, Proteomics, Phosphoproteomics, LC-MS | Hadisurya M, Li L, Kuwaranancharoen K, Wu X, Le... | PXD032175 |
| Pan-cancer plasma proteome profiling using SIS recombinant protein fragments reveals downregulation of proteins interacting with immunoglobulins in multiple myeloma | Homo sapiens | Q Exactive HF | Yes | 1 | Targeted Proteomics, Cancer, Plasma Profiling, Multiple Myeloma | Kotol D, Woessmann J, Hober A, Álvez MB, Tran M... | PXD037946 |
| Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkers | Homo sapiens | Q Exactive HF | Yes | 2 | targeted proteomics, biomarker validation, duchenne muscular dystrophy | Johansson C, Hunt H, Signorelli M, Edfors F, Ho... | PXD038089 |
| Effects of alpha-crystallin gene knockout on zebrafish lens development | Danio rerio | Q Exactive HF | No | 1 | zebrafish, alpha-crystallin, lens, development, cataract, knockout | Posner M, Murray KL, Andrew B, Brdicka S, Rober... | PXD030918 |
| Dynamic monitoring of myeloma minimal residual disease with targeted mass spectrometry | Homo sapiens | Orbitrap Exploris 120 | No | 47 | multiple myeloma, minimal residual disease, M-protein, clonotypic peptides, targeted mass spectrometry | Noori S, Wijnands C, Langerhorst P, Bonifay V, ... | PXD038370 |
| Control of intracellular pH and bicarbonate by CO2 diffusion into human sperm | Homo sapiens | Orbitrap Exploris 480 | Yes | 16 | Absolute Quantification, Limit-of-Detection, human sperm cells | Grahn E, Kaufmann SV, Askarova M, Ninov M, Welp... | |
| Monitoring extended stable isotope-labeled synthetic peptides as a quality control for protease digestion in targeted, multiplexed mass spectrometry-based assays | Homo sapiens | QTRAP 6500,QTRAP 5500 | Yes | 5 | MRM, immuno-affinity enrichment, quantification, human cell line, sample processing, QC | | PXD038465 |
| Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment | Homo sapiens | Orbitrap Fusion Lumos | No | 2 | DIA, data independent acquisition | Heil LR, Remes PM, Canterbury JD, Yip P, Barsho... | PXD038508 |
| HIC1 interacts with FOXP3 multi protein complex: a novel mechanism to regulate human regulatory T cell differentiation and function | Homo sapiens | TSQ Vantage | Yes | 1 | FOXP3+ regulatory T cells, hypermethylated in cancer 1 (HIC1), interactome | Andrabi SBA, Batkulwar K, Bhosale SD, Moulder R... | PXD038532 |
| Relative complement deficiency predicts development of islet autoimmunity and type 1 diabetes | Homo sapiens | TSQ Altis | Yes | 12 | T1D, biomarkers, autoimmunity, complement proteins | Webb-Robertson BM, Nakayasu ES, Dong F, Waugh K... | |
| Synergistic targeting of DNA-PK and KIT signaling pathways in KIT mutant acute myeloid leukemia | Mus musculus | Orbitrap Exploris 480 | No | 6 | Phosphoproteomics, AML, KIT | Murray HC, Miller K, Brzozowski JS, Kahl RGS, S... | PXD030214 |
| Elucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modeling | Homo sapiens | TSQ Altis | Yes | 6 | Phosphoproteomics; kinase; targeted mass spectrometry; kinase dynamics; fibroblast growth factors; dynamic modeling; fibroblast growth factor receptor; breast cancer. | Veth TS, Francavilla C, Heck AJR, Altelaar M. E... | PXD039005 |