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|  Degradation kinetics of lignocellulolytic enzymes in a biogas reactor by quanti-tative mass spectrometry | Lentinula edodes | timsTOF Pro | No | 3 | Mass spectrometry, Biogas production, Fungal enzymes, lignocellulose conversion, Lentinula edodes | Küchler, J.; Willenbücher, K.; Reiß, E.; Nuß, L... | |
| Validation of protein expression in kidney tissue of Labeo rohita during Edwardsiella tarda infection | Labeo rohita, Edwardsiella tarda | TSQ Altis | No | 1 | Edwardsiella tarda, kidney proteomics, mass spectrometry, rohu, SRM | Pinto N, Nissa MU, Yashwanth BS, Sathiyanarayan... | PXD039749 |
| MED6-189: An effective Antimalarial Kalihinol Analog Targets Plasmodium falciparum Apicoplast and Membrane Biogenesis | Plasmodium falciparum | Xevo G2-XS QTof,Xevo TQ MS | No | 4 | Malaria, Plasmodium, Drug mechanisms, Kalihinol. | Nature | |
| PeakDecoder enables machine learning-1 based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements | Pseudomonas putida KT2440 | TSQ Altis | Yes | 1 | metabolomics, mass spectrometry, ion mobility spectrometry, data-independent acquisition, synthetic biology, HILIC, algorithm, machine learning. | Nature Communications | |
| 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 sapiens | QTRAP 5500 | No | 2 | immunotherapy, MRM, enrichment, correlative biomarkers | Whiteaker JR, Zhao L, Schoenherr RM, Huang D, L... | |
| Metrologically traceable quantification of three apolipoprotein E isoforms in cerebrospinal fluid | Homo sapiens | Xevo TQ-S | No | 27 | apolipoprotein E, isoform, Alzheimer’s disease, single-point calibration, neurodegenerative disorders | Huynh HH, Kuch K, Orquillas A, Forrest K, Barah... | PXD038803 |
| A strategy to characterize the global histone PTM landscape within tissues of non-model organisms | Oreochromis mossambicus | impact II | No | 9 | Mass spectrometry, epigenetics, histone post-translational modifications, Mozambique tilapia, tissue specificity | Mojica EA, Kültz D. A Strategy to Characterize ... | PXD040536 |
| Salinity-responsive histone PTMs identified in Mozambique tilapia tissues | Oreochromis mossambicus | impact II | No | 18 | Epigenetics, Stress-induced evolution, Osmoregulation, Euryhalinity, Mass spectrometry | Mojica EA, Fu Y, Kültz D. Salinity-responsive h... | PXD040557 |
| Development and validation of a matrix independent calibration strategy for targeted mass spectrometry-based quantification of milk protein allergens from complex food matrices | Bos taurus | Q Exactive Plus | No | 15 | food allergens, milk, casein, whey | Ramachandran, B. and M.L. Downs, Development an... | PXD040564 |
| PRM quantification of MCS proteins and viral proteins in HCMV virus microenvironment | Homo sapiens, HHV-5 | Q Exactive HF | No | 2 | virus microenvironment, HCMV, membrane contact site, PRM | Song B, Sheng X, Justice JL, Lum KK, Metzger PJ... | PXD038466 |
| Targeted Proteomics of Lung Squamous Cell Carcinomas | Homo sapiens | TSQ Altis | Yes | 1 | Lung Squamous Cell Carcinoma, multiple reaction monitoring | Putty Reddy S, Alontaga AY, Welsh EA, Haura EB,... | PXD040680 |
| Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer | Homo sapiens | QTRAP 6500 | Yes | 4 | Human, FFPE, HGSOC, MRM | Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, H... | PXD040742 |
| Dysregulations in the levels of lactate dehydrogenase and pyruvate kinase upon IL-17A and echinomycin treatments in human primary keratinocytes | Homo sapiens | TSQ Altis | No | 1 | keratinocytes, Interleukin-17A, echinomycin, lactate dehydrogenase, pyruvate kinase | Dhamija B, Marathe S, Sawant V, Basu M, Attrish... | PXD040678 |
| Global response of Octopus berrima to ocean warming | Octopus berrima | impact II | No | 1 | octopus, global warming, thermal stress, embryo, DIA | Hua QQH, Kültz D, Wiltshire K, Doubleday ZA, Gi... | PXD040795 |
| PRM data for "Functional analysis of a common BAG3 allele associated with protection from heart failure" | Homo sapiens | Q Exactive Plus | No | 1 | iPS-CM cardiomyocytes PRM BAG3 | Functional analysis of a common BAG3 allele ass... | PXD041228 |
| Tapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral Factor | Homo sapiens, Human herpesvirus 8 strain GK18 | Q Exactive HF | No | 1 | TPCA, IP, PRM, KSHV | Publication pending | PXD041269 |
| S-Adenosylmethionine Negatively Regulates the Mitochondrial Respiratory Chain Repressor MCJ in the Liver | Mus musculus | Orbitrap Fusion Lumos | No | 1 | MCJ methylation liver | | PXD042309 |
| Assessing the role of trypsin in quantitative plasma- and single-cell
proteomics towards clinical application | Homo sapiens | TSQ Altis,Orbitrap Eclipse,Q Exactive HF | Yes | 2 | Trypsin, bottom-up proteomics, single-cell proteomics, plasma proteomics, absolute quantification, targeted proteomics | Woessmann J, Petrosius V, Üresin N, Kotol D, Ar... | PXD042450 |
| Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition | Homo sapiens | Orbitrap Fusion Lumos,Orbitrap Astral | No | 15 | plasma, DIA, Astral, Orbitrap, limit of quantification | Heil LR, Damoc E, Arrey TN, Pashkova A, Denisov... | PXD042704 |
| Environmental Conditions Elicit a Slow but Enduring Response of Histone Post-Translational Modifications in Mozambique Tilapia | Oreochromis mossambicus | impact II | No | 2 | salinity, DIA, tilapia, gill, histone, PTM | Mojica EA, Petcu KA, Kültz D. Environmental con... | PXD042718 |
| In-vitro differential redox-labeling of NTRC | Chlamydomonas reinhardtii | Q Exactive Plus | No | 1 | Chlamydomonas, NTRC, chloroplast | | PXD042813 |
| Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome | Homo sapiens | Orbitrap Eclipse | No | 5 | extracellular vesicles, DIA mass spectrometry, plasma proteomics, quantitative proteomics, neurodegenerative disease | Publication pending | PXD042947 |
| Deep quantitative proteomics of North American Pacific coast star tunicate | Botryllus schlosseri | impact II | No | 1 | tunicates, DIA, protein quantitation, network analysis, LCMS, ecological proteomics, evolutionary proteomics | Kültz D, Gardell AM, DeTomaso A, Stoney G, Rink... | PXD043046 |
| 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 spectrometry | Homo sapiens | TSQ Altis | Yes | 24 | HIV-1; Mycobacterium tuberculosis; p24; CFP10; mass spectrometry | Li L, Lyon CJ, LaCourse SM, Zheng W, Stern J, E... | PXD043191 |
| Targeted Proteomics Quantitation of NRF2 and Predictive Biomarkers in HNSCC | Homo sapiens | Orbitrap Eclipse | No | 4 | HNSCC, NRF2, IS-PRM | | |
| Comparing peptide identifications by FAIMS versus quadrupole gas phase fractionation | Homo sapiens | Orbitrap Eclipse | No | 4 | high-field asymmetric waveform ion mobility spectrometry, gas phase fractionation | Publication pending | PXD043458 |
| Development and analytical validation of a multiplexed targeted mass spectrometry assay to detect ovarian cancer protein biomarkers in sera | Homo sapiens | Q Exactive Plus | Yes | 8 | Targeted mass spectrometry, parallel reaction monitoring (PRM) | Ryu J, Boylan KLM, Twigg CAI, Evans R, Skubitz ... | |
| Gut Microbiome IMS-MS Experiments | Homo sapiens, Mus musculus | 6560 Q-TOF LC/MS | No | 2 | Ion Mobility, FMT, MCBA, bile acids | | |
| Multiple reaction monitoring based targeted validation of over-expressed proteins of high-grade gliomas | Homo sapiens | TSQ Altis | Yes | 2 | High-grade gliomas, glioblastoma, mass spectrometry, over-expressed protein markers, brain tumor | Verma A, Patel R, Mahale A, Thorat RV, Rath SL,... | PXD043621 |
| A novel overlapping gene azyx-1 affects the translation of zyxin in C. elegans | Caenorhabditis elegans | Q Exactive HF-X | Yes | 2 | overlapping gene, non-canonical, PRM, targeted proteomics | Publication pending | PXD034878 |
| Label-free Parallel Reaction Monitoring (PRM) analysis of selected novel potential targets of IFNg stimulation in Hela cells. | Homo sapiens | Q Exactive HF | No | 1 | QuaNPA, IFNg, PRM | Borteçen T, Müller T, Krijgsveld J. An integrat... | PXD043967 |
| Breeding from 1891 to 2010 did not increase the content of amylase/trypsin-inhibitors in wheat (Triticum aestivum L.) | Triticum aestivum | TSQ Vantage | Yes | 25 | Amylase/trypsin-inhibitors (ATIs), Heritability, non-celiac gluten sensitivity (NCGS), non-celiac wheat sensitivity (NCWS), stable isotope dilution assay (SIDA), wheat allergy | Geisslitz S, Pronin D, Neerukonda M, Curella V,... | PXD043968 |
| Quantitative Measurement of Secretory Protein Mistargeting by Proximity Labeling and Parallel Reaction Monitoring | Homo sapiens | LTQ Orbitrap Velos Pro,LTQ Orbitrap Velos | No | 2 | Proximity Labeling, Parallel Reaction Monitoring, ER Pre-Emptive Quality Control | | PXD044008 |
| Validation of a proteomic signature of lung cancer risk from bronchial specimens of risk-stratified individuals | Homo sapiens | TSQ Altis,TSQ Vantage | Yes | 5 | Early detection, Lung cancer, High risk, Proteomics, Bronchial epithelium | Cancers 2023, 15(18), 4504; https://doi.org/10.... | |
| Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis. | Arabidopsis thaliana | Q Exactive HF-X,Orbitrap Fusion Lumos | No | 6 | TRAPPII, shaggy-like kinases, BRASSINOSTEROID INSENSITIVE 2 (BIN2), decision-making, growth trade-offs, light responses, water stress, adaptation, osmotic stress, additive stress, TGN, Arabidopsis | | PXD044142 |
| The phosphorylation landscape of infection-related development by the rice blast fungus | Magnaporthe oryzae | Orbitrap Fusion | No | 1 | Fungus, Appressorium, Pmk1 pathway, protein phosphorylation, phosphoproteomics | Cruz-Mireles N, Osés-Ruiz M, Derbyshire P, Jégo... | PXD044865 |
| Antimicrobial peptides of the apidaecin family inhibit the bacterial ribosome by multimodal mechanisms involving three different sites on the large ribosomal subunit | Escherichia coli | SYNAPT G2-Si | No | 3 | PrAMPs, 70S ribosome | Lauer SM, Reepmeyer M, Berendes O, Klepacki D, ... | PXD044892 |
| Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses | | 6560 Q-TOF LC/MS | Yes | 1 | Bioaccumulation, Lepomis, consumption advisory, mass spectrometry, ion mobility spectrometry | | |
| Proteomic characterization of extracellular matrix (ECM) produced by human fibroblast activation protein (FAP)-positive pericyte-like cells and glioma cells | Homo sapiens | TripleTOF 5600+ | No | 1 | Glioblastoma, Collagen I, Fibronectin, Fibroblast activation protein, Extracellular matrix, SWATH-MS | Vymola P, Garcia-Borja E, Cervenka J, Balaziova... | PXD045057 |
| Skeletal Muscle TFEB Signaling Promotes Central Nervous System Function and Reduces Neuroinflammation during Aging and Neurodegenerative Disease | Mus musculus | Orbitrap Fusion Lumos | No | 1 | DIA, skeletal muscle, transcription factor, aging, neurodegenerative disease | Matthews I, Birnbaum A, Gromova A, Huang AW, Li... | PXD045241 |
| Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease | Homo sapiens | Xevo TQ-S | No | 2 | Crohn’s disease, disease location, serum proteomics | N. Pierre, V.A. Huynh-Thu, D. Baiwir, et al., S... | PXD045278 |
| AD-BXD Mouse Hippocampus Proteomics | Mus musculus | Orbitrap Fusion Lumos | No | 49 | DIA, Alzheimer's Disease, resilience, BXD genometypes | | PXD045425 |
| Cognitive Functions, Neurotransmitter Alterations, and Hippocampal Microstructural Changes in Mice Caused by Feeding on Western Diet | Mus musculus | Q Exactive | No | 3 | MASH, neuroinflammation, liver-brain axis, astrogliosis, microgliosis | Custodio RJ, Hobloss Z, Myllys M, Hassan R, Gon... | |
| In-Gel digest and filter-aided sample preparation to identify Dermatophagoides - and yeast protein antigens in severe equine asthma. | Saccharomyces cerevisiae, Dermatophagoides pteronyssinus | SYNAPT G2-Si | No | 3 | Immunoglobulin isotypes, proteomics, 2D immunoblot, LC-MS, asthma, COPD, RAO, heaves | Schnabel CL, Jentsch MC, Lübke S, Kaiser-Thom S... | PXD045568 |
| HAMSAB modified gut microbiota signature in human type 1 diabetes delays disease after transfer into gnotobiotic mice | Mus musculus | 6470A Triple Quadrupole LC/MS | No | 2 | aryl-hydrocarbon receptor, autoimmunity, fecal microbiota transfer, metabolites, microbiome, multiomics, prebiotic, short-chain fatty acids, tryptophan, type 1 diabetes | | |
| In-Gel Digest to identify Aspergillus fumigatus protein antigens in severe equine asthma (SEA) | Aspergillus fumigatus | SYNAPT G2-Si | No | 3 | recurrent airway obstruction, COPD, proteomics, immunoglobulin isotype, serum, antibody, immunoblot | Jentsch MC, Lübke S, Schrödl W, Volke D, Krizsa... | PXD045869 |
| Acoustic Ejection Mass Spectrometry Empowers Ultra-Fast Peptide Biomarker Quantification... A Paradigm shift | Homo sapiens, SARS-CoV-2 | Triple Quad 6500+ | No | 29 | Mass Spectrometry, SARS-CoV-2, Biomarkers, Acoustic Ejection Mass Spectrometry, Inflammation | Van Puyvelde B, Hunter CL, Zhgamadze M, Savant ... | PXD046249 |
| METLIN-CCS: an ion mobility spectrometry
collision cross-section database | | | No | 1 | small molecule, collision cross-section, CCS, ion mobility spectrometry, IMS | Baker ES, Hoang C, Uritboonthai W, Heyman HM, P... | |
| TFAM Tg Mice skeletal muscle_iMPAQT | Mus musculus | QTRAP 6500 | No | 1 | TFAM; iMPAQT; skeletal muscle | Igami K, Kittaka H, Yagi M, Gotoh K, Matsushima... | |
| Metabolic, Neurotoxic and Immunotoxic Effects of PFAAs and their
Mixtures on the Proteome of Plasma and Head Kidney from Rainbow
Trout | Oncorhynchus mykiss | 6545 Q-TOF LC/MS | No | 2 | proteomics, blood plasma, head kidney, rainbow trout, PFAAs, Perfluoroalkyl acids | Pollard S, De Silva AO, Simmons DBD. Metabolic,... | PXD046517 |
| Assessment of Kinome-wide Rewiring Upon Picornavirus Infection | Homo sapiens | TSQ Altis | Yes | 2 | Picornavirus, kinome, phosphorylation, kinase activation loop, phosphoproteomics, CVB3, EMCV, 2A, L protein, Viral life cycle | Veth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wieren... | PXD046598 |
| PRM quantification of interferon-induced proteins upon Type I IFN-beta, Type II IFN-gamma, and LPS stimulation of differentiated THP-1 cells | Homo sapiens | Q Exactive HF | No | 1 | Interferon, ISG, Interferon beta, Interferon gamma, LPS, THP-1 | | |
| Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk | Homo sapiens | TSQ Vantage | Yes | 1 | Serum proteomics, age-trends, dietary intervention, type-1 diabetes, beta-cell autoimmunity | Bhosale SD, Moulder R, Suomi T, et al (2024) Se... | PXD047235 |
| Peptide centric detection of cross-linked peptides using PASEF, MeroX, and Skyline | Bos taurus | timsTOF Pro | No | 4 | XL-MS, PASEF, DDA, DIA, Peptide-centric | Rojas Echeverri JC, Hause F, Iacobucci C, Ihlin... | PXD047307 |
| Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics | Homo sapiens | Orbitrap Eclipse | Yes | 1 | Chemical proteomics, acetylation, phosphorylation, lysine deacetylase inhibitors, HDACs, proteomic pharmacology | Publication pending | PXD047419 |
| 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/MS | No | 3 | PFAS, Ion Mobility, Mass Spectrometry | Expected in the near future. | |
| It’s a trap: ClpP substrates caught in action | Staphylococcus aureus | Orbitrap Fusion | No | 1 | S. aureus, ClpP, protease substrate trapping, ClpP substrates, parallel reaction monitoring | Angew. Chem. Int. Ed. 2024, e202409220 | PXD047469 |
| Evidence for an RNAi-independent role of DICER-LIKE2 in conferring growth inhibition and basal antiviral resistance | Arabidopsis thaliana | Orbitrap Eclipse | No | 1 | DCL2 | Nielsen CPS, Arribas-Hernández L, Han L, Reiche... | PXD046163 |
| Modeling the simultaneous dynamics of proteins in blood plasma and the cerebrospinal fluid in human in vivo | Homo sapiens | timsTOF Pro 2 | No | 8 | Proteomics, SILK, kinetic | Publication pending | PXD047851 |
| Development of a Mass Spectrometry-Based Method for Quantification of Total Cashew Protein in Roasting Oil | Anacardium occidentale | Q Exactive,Q Exactive Plus | Yes | 9 | Cashew, Oil, Frying, Roasting, Food Allergen | Chen S, Downs ML. Development of a Mass Spectro... | PXD047985 |
| Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation | Homo sapiens | QTRAP 5500,nanoACQUITY UPLC,TSQ Vantage | Yes | 6 | N-glycosylation, glycosylation, endoplasmic reticulum, Congenital disorders of glycosylation | Sakson R, Beedgen L, Bernhard P, Alp KM, Lübbeh... | PXD048072 |