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|  Selected reaction monitoring of dysregulated proteins in gut tissue of Labeo rohita infected with Aeromonas hydrophila | Labeo rohita | TSQ Altis | Yes | 2 | Aeromonas hydrophila, extracellular matrix, gut proteomics, mass spectrometry, rohu, SRM | | PXD048261 |
| Gamete Bundle Proteomics for the Stony Rice Coral, Montipora capitata | Montipora capitata | Orbitrap Fusion Lumos | No | 2 | skyline, coral, gametes | Timmins-Schiffman et al. 2025.Proteomic Plastic... | PXD048391 |
| Plasma proteomics identify biomarkers predicting Parkinson's disease up to 7 years before symptom onset | Homo sapiens | Xevo TQ MS,ACQUITY UPLC | No | 3 | LC-MS, MRM, Targeted proteomics, Biomarkers, Parkinson's disease, Neurodegeneration | Plasma proteomics identify biomarkers predictin... | PXD041419 |
| Mouse Skeletal Muscle Sarcopenia | Mus musculus | Orbitrap Eclipse | No | 4 | sarcopenia, aging, skeletal muscle, DIA | Kerr HL, Krumm K, Anderson B, Christiani A, Str... | PXD048723 |
| Loss of POGLUT2 and 3 eliminates O-glucose at predicted sites but does not alter other modifications on EGFs | Mus musculus | Q Exactive Plus | No | 5 | POGLUT2, POGLUT3, O-glycosylation, mouse, primary fibroblasts, fibrillin-1, extracellular | Neupane S, Williamson DB, Roth RA, Halabi CM, H... | PXD043827 |
| Fecal Microbiota Transplant_Bile Acid | Homo sapiens | 6560 Q-TOF LC/MS | No | 2 | Bile Acid | Metagenomic, metabolomic, and lipidomic shifts ... | |
| Analysis of N-Glycosylation for SARS-CoV-2 expressed receptor-binding domain VOCs and membrane protein with LC-MS. | Severe acute respiratory syndrome coronavirus 2 | SYNAPT G2-Si | No | 1 | SARS-CoV-2, N-Glycosylation, HD-DDA, ESI-IMS-Q-TOF-MS | Schwarze M, Volke D, Rojas Echeverri JC, Schick... | PXD048930 |
| IO3 immunoMRM panel experimental data | Homo sapiens | QTRAP 5500 | Yes | 5 | immunotherapy, immunomodulation, mutliplexing | Publication pending | PXD049020 |
| Development of a fit-for-purpose multi-marker panel for early diagnosis of pancreatic ductal adenocarcinoma | Homo sapiens | QTRAP 5500 | Yes | 1 | PDAC, early diagnosis, serum biomarker, multiple-reaction monitoring, analytical validation | Kim H, Huh S, Park J, Han Y, Ahn KG, Noh Y, Lee... | |
| AD-BXD Mouse PreFrontal Cortex Proteomics | Mus musculus | Orbitrap Fusion,Orbitrap Fusion Lumos | No | 50 | DIA, Alzheimer's Disease, resilience, BXD genometypes | | PXD045403 |
| Brain Creatine Kinase as a biomarker for Alzheimer’s disease | Homo sapiens | Q Exactive HF | Yes | 1 | brain creatine kinase, CKB, Alzeheimer's disease, Dementia, energy-deficit | Zheng T, Kotol D, Sjöberg R, Mitsios N, Uhlén M... | PXD050060 |
| Selective autophagy monitoring by PRM | Homo sapiens | Q Exactive HF-X | Yes | 4 | Autophagy, Selective autophagy, Mitophagy, PRM | Leytens A, Benítez-Fernández R, Jiménez-García ... | |
| Effect of burn wound treatment with fish skin on mouse skin proteome | Mus musculus | impact II | No | 1 | tilapia, fish skin, burn injury, DIA, epidermal proteome | Garrity C, Garcia-Rovetta C, Rivas I, Delatorre... | PXD050514 |
| Targeted MS assay to evaluate Cereblon neosubstrate changes in rabbit embryos following maternal administration of IMiDs | Oryctolagus cuniculus | Orbitrap Eclipse | No | 6 | CRBN, IMiD, PRM, IA, Neosubstrate | Federspiel JD, Catlin NR, Nowland WS, Stethem C... | PXD050568 |
| The proline-rich antimicrobial peptide Api137 disrupts assembly of the large ribosomal subunit inducing immature dead-end particles | Escherichia coli | LTQ Orbitrap XL | No | 1 | In-Gel Digest, Api137, 70S ribosome, antimicrobial peptide | Lauer, S.M., Gasse, J., Krizsan, A. et al. The ... | PXD051066 |
| Targeted MS validation of huntingtin protein interaction signatures in Huntington's disease mouse models | Mus musculus | Q Exactive HF | No | 1 | IP-MS, PRM, HTT, S-Trap | Justice JL, Greco TM, Hutton JE, Reed TJ, Mair ... | PXD051407 |
| optiPRM: A targeted immunopeptidomics LC-MS workflow with ultra-high sensitivity for the detection of mutation-derived tumor neoepitopes from limited input material | Homo sapiens | Orbitrap Exploris 480 | No | 7 | PRM, immunopeptidomics, neoepitope | Salek M, Förster JD, Becker JP, Meyer M, Charoe... | |
| Defective pgsA contributes to increased membrane fluidity and cell wall thickening in S. aureus with high-level daptomycin resistance | Staphylococcus aureus | Synapt XS | No | 9 | lipidomics, staphylococcus aureus, branched fatty acids | | |
| Lost in translation? Proteomic evidence for a muted molecular response to thermal stress in a stenothermal Antarctic fish and possible evolutionary mechanisms | Trematomus bernacchii | impact II | No | 3 | Ecological proteomics, Thermal stress, Cellular stress response, Heat shock response, Integrative stress response, DIA, Quantitative proteomics, Stenothermy | Dowd WW, Kültz D. Lost in translation? Evidence... | PXD051983 |
| A Novel High-Throughput Immunoaffinity LC-MS/MS Assay for P III-NP and other Fragments of Type III Procollagen in Human Serum | Homo sapiens | Xevo TQ-S | No | 30 | P-III-NP, collagen turnover, single-point calibrator | Huynh HH, Barahona-Carrillo L, Moncrieffe D, Co... | PXD052245 |
| GlyCombo enables rapid, complete glycan composition identification across diverse glycomic sample types | Homo sapiens | LTQ Orbitrap XL,LTQ Orbitrap Velos,Orbitrap Fusion Lumos,Velos Plus,LTQ XL,amaZon Speed | No | 12 | glycomics, computation, N-glycan, O-glycan, GSL, glycolipid | GlyCombo enables rapid, complete glycan composi... | |
| DIA Proteomics of Coho Salmon Ovaries Across 4 Stages | Oncorhynchus kisutch | Orbitrap Fusion Lumos | No | 1 | coho, salmon, gametogenesis, reproduction | Timmins-Schiffman E, Telish J, Field C, Monson ... | PXD052361 |
| Coho ovarian tissue response to gonadotropins | Oncorhynchus kisutch | TSQ Altis | No | 1 | coho, salmon, gonadotropins, gametogenesis | | PXD052463 |
| Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pigmentosa | Mus musculus | Q Exactive | No | 1 | Inherited retinal degenerations, retinitis pigmentosa, retinal proteome, retinal degeneration P23H | Montaser AB, Gao F, Peters D, Vainionpää K, Zhi... | PXD052598 |
| Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pigmentosa | Mus musculus | Q Exactive | No | 1 | Inherited retinal degenerations, retinitis pigmentosa, retinal proteome, retinal degeneration, rd10, P23H, Rpe65-/- | Montaser AB, Gao F, Peters D, Vainionpää K, Zhi... | PXD052698 |
| Tutorials on How to Use PRM Conductor, a Skyline External Tool | | | No | 21 | targeted, PRM, Conductor, tutorial, Thermo, Stellar | Remes, P. M.; Jacob, C. C.; Heil, L. R.; Shulma... | |
| Characterization of Stellar MS | Homo sapiens, Gallus gallus, Escherichia coli | Stellar | Yes | 17 | Stellar, PRM, Targeted, matrix-matched, E. coli, HeLa, chicken, plasma, label-free, PQ500, absolute, quantitation | Remes PM, Jacob CC, Heil LR, Shulman N, MacLean... | PXD052734 |
| Linear Ion Trap Global to Targeted Proteomics: A workflow for targeted proteomics assay development using a versatile linear ion trap | Mus musculus | Stellar | No | 6 | Ion Trap, Stellar MS, DIA, Data-independent acquisition, DDA, High pH reverse phase fractionation, offline fractionation, global proteomics, targeted proteomics, parallel reaction monitoring, prm | | PXD052847 |
| Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling Across Diverse Sample Types | Bos taurus, Chinese hamster, Homo sapiens | Orbitrap Fusion Lumos | No | 1 | Glycomics, N-glycans, flow injection, high throughput | | |
| An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS | Homo sapiens, Mus musculus | Q Exactive,Q Exactive HF,Orbitrap Fusion | Yes | 12 | Histones, post-translational modifications, ubiquitination, epigenetics, LC-MS/MS | Lopes M, Lund PJ, Garcia BA. Optimized and Robu... | PXD053212 |
| A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data | Homo sapiens, Mus musculus | Orbitrap Astral,Q Exactive HF-X | No | 2 | de novo, data independent acquisition, sequence variant, extracellular vesicles, Mag-Net | Justin Sanders, Bo Wen, Paul Rudnick, Rich John... | PXD053291 |
| External validation of serum biomarkers predicting short-term and mid/long-term relapse in Crohn’s disease patients stopping infliximab | Homo sapiens | Xevo TQ-S | No | 2 | Crohn’s disease, infliximab withdrawal, relapse prediction, biomarkers | Pierre N, Huynh-Thu VA, Baiwir D, Mazzucchelli ... | PXD051233 |
| Calcium-triggered (de)ubiquitination events in synapses | Rattus norvegicus, Homo sapiens | Orbitrap Exploris 480 | Yes | 5 | synapse, ubiquitination, CaMKIIα, phosphorylation | Ainatzi S, Kaufmann SV, Silbern I, Georgiev SV,... | PXD053470 |
| Reproducible protein quantitation of 270 human proteins at increased depth using nanoparticle-based fractionation and reaction monitoring mass spectrometry with stable isotope-labelled internal standards | Homo sapiens | 6495C Triple Quadrupole LC/MS | Yes | 1 | plasma proteomics, LC/MRM-MS, fractionation, absolute quantitation, Seer Proteograph | Gaither C, Popp R, Gajadhar AS, Borchers CH. Re... | PXD053704 |
| Absolute abundance of human crystallins in lens | Homo sapiens, Mus musculus | Orbitrap Eclipse | Yes | 4 | Crystallin, lens, cataract, stable isotope labeling, mass spectrometry | Halverson-Kolkind KA, Caputo N, Lampi KJ, Sriva... | PXD053890 |
| Serum Alpha-2-Macroglobulin Links Type 1 Diabetes Status and Incident Cardiovascular Disease | Homo sapiens | Orbitrap Fusion Lumos | No | 2 | Alpha-2-macroglobulin, atherosclerosis, case-cohort design, incident cardiovascular disease, Cox proportional regression, MS, parallel reaction monitoring, proteomics. | Shao B, Snell-Bergeon JK, de Boer IH, Davidson ... | PXD054039 |
| Detection and Quantification of Drug-Protein Adducts in Human Liver | Homo sapiens, fall armyworm | Orbitrap Exploris 480,Orbitrap Eclipse | No | 4 | Raloxifene, P450, CYP, CYP3A4, CYP3A5, CYP2C8, CYP2C9, CYP2C19, P450-Reductase, Xenobiotic, Adduct, Reactive Metabolite, comet, Magnum, Limelight, PeptideProphet, VMC | Zelter A, Riffle M, Shteynberg DD, Zhong G, Rid... | PXD054246 |
| A framework for quality control in quantitative proteomics | Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Bos taurus | Orbitrap Eclipse,Orbitrap Fusion Lumos,Orbitrap Fusion | No | 9 | quality control, proteomics, mass spectrometry, liquid chromatography, sample preparation, system suitability, quantitative results, PRM, DIA, DDA | Tsantilas KA, Merrihew GE, Robbins JE, Johnson ... | PXD051318 |
| Label-free Multiple Reaction Monitoring-Mass Spectrometry for Quantifying Phosphopeptides from Extracellular Vesicles | Homo sapiens | QTRAP 6500 | No | 13 | PCa, phosphopeptide, local normalization | | |
| Meta-Analysis and DIA-MS-based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian population | Homo sapiens | Orbitrap Fusion | No | 1 | COPD, smokers, asymptomatic smokers, healthy subjects, DIA, proteomics, Indian population | Sharma G, Gupta DP, Ganguly K, Anand MP, Srivas... | PXD055103 |
| Automated sequential derivatization for Gas Chromatography-[Orbitrap] Mass Spectrometry based metabolite profiling of human blood-based samples | Homo sapiens | Orbitrap Exploris GC 240 | No | 3 | Automation, derivatization, Thermo Scientific™ TriPlus™ RSH, metabolite profiling, gas chromatography–mass spectrometry (GC-MS) | Jbebli A, Coufalíková K, Zanaboni M, Bergna M, ... | |
| RPLC-IM-MS of S. aureus Branched Lipids | Staphylococcus aureus | Synapt XS | No | 2 | staphylococcus aureus, branched, lipids, s. aureus, rplc | | |
| High-resolution metaproteomic analysis of an ocean microbiome preceding a Chaetoceros bloom | marine metagenome | Orbitrap Fusion Lumos | No | 3 | ocean microbiome, bacterial fraction, matrix-matched calibration curve, time series, Chaetoceros, harmful algal bloom, data independent acquisition, parallel reaction monitoring | | PXD052911 |
| RPL40 methyltransferase discovery and characterisation | Homo sapiens | Orbitrap Fusion Lumos,Q Exactive Plus,LTQ Orbitrap Velos Pro | No | 21 | Protein methylation, ribosome, translation, methyltransferase | Hamey JJ, Shah M, Wade JD, Bartolec TK, Wettenh... | PXD056489 |
| Streamlining Workflows in Ion Mobility Data Acquisition, Calibration and Processing: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies | | 6560 Q-TOF LC/MS | Yes | 2 | DTIMS, MOBILion, MOBIE, TWIMS, CCS | | |
| Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics | Homo sapiens, Saccharomyces cerevisiae | Orbitrap Fusion Lumos,Orbitrap Exploris 480,Orbitrap Astral | No | 6 | spectral library generation, Carafe, deep learning, DIA | Wen, Bo, Chris Hsu, Wen-Feng Zeng, Michael Riff... | PXD056793 |
| SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome | Mus musculus, Homo sapiens | 6495C Triple Quadrupole LC/MS | Yes | 1 | absolute quantitation; targeted and untargeted quantitation; stable isotope labeling; SILAC mice; multiplexing | doi: https://doi.org/10.1101/2024.11.05.622109 | PXD057580 |
| Effect of Host Telomerase Inhibition on Human Cytomegalovirus | Cytomegalovirus humanbeta5 | Q Exactive HF,Dionex instrument model | No | 1 | Cytomegalovirus, telomerase, telomerase inhibition. | | PXD058198 |
| A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxyacids | Streptomyces | 6460 Triple Quadrupole LC/MS | No | 1 | Metabolic engineering, polyketide synthase, PKS, 1,3-butanediol, P-pant ejection assay, Streptomyces albus | Pending publication | PXD047663 |
| Marfan syndrome variation of the POGLUT2 and POGLUT3 consensus sequence can produce aberrant fibrillin-1 O-glucosylation | Homo sapiens | Q Exactive Plus | No | 28 | extracellular matrix, fibrillin, glycoprotein, glycosyltransferase, mass spectrometry, Marfan syndrome, O-glucose, POGLUT2, POGLUT3 | Kegley, N. R., Ito, A., Williamson, D. B., McAr... | PXD058951 |
| Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding | Escherichia coli BL21(DE3) | Orbitrap Fusion Lumos,Orbitrap Exploris 480 | No | 11 | barcoding, peptide, size exclusion chromatography, SEC, protein design, RFDiffusion, generative design, deep learning, machine learning, DL, ML | Massively parallel assessment of designed prote... | PXD059224 |
| A histone PTM Skyline template with spectral library and iRT calculator | Homo sapiens | Q Exactive HF | No | 2 | histone modification, histone PTM, PTM, epigenetics, chromatin | | |