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|  Quantitative assay of targeted proteome in trichome glandular cells using large-scale selected reaction monitoring strategy | Solanum lycopersicum | QTRAP 5500 | No | 2 | Tomato type VI trichome glandular cell | Takemori A, Nakashima T, Ômura H, Tanaka Y, Nak... | PXD012250 |
| Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates | Corynebacterium glutamicum ATCC 13032 | 6460 Triple Quadrupole LC/MS | No | 1 | C. glutamicum, isoprenoid pathway, targeted proteomics | Sasaki Yusuke and Eng T and HRA and TJ and CY a... | PXD012293 |
| Juvenile geoduck ctenidia tissue after summer deployment in Puget Sound, WA | Pacific geoduck | TSQ Vantage,Orbitrap Fusion Lumos | No | 2 | Panopea generosa, geoduck, ocean acidification, oxidative stress proteins | Spencer LH, Horwith M, Lowe AT, Venkataraman YR... | PXD012294 |
| A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cells | Homo sapiens | Q Exactive HF,Orbitrap Fusion Lumos | Yes | 17 | PRM, high resolution, low abundant proteins, UPR, signalling proteins | Nguyen CDL, Malchow S, Reich S, Steltgens S, Sh... | |
| Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 1 | Synthetic biology, Metabolic engineering, Protoemics, Metabolomics, Machine Learning | Opgenorth P, Costello Z, Okada T, Goyal G, Chen... | PXD012312 |
| Measurement of Nrf2-Regulated Antioxidant Response Proteins as Potential Biomarkers for Radiation Injury Assessment | Mus musculus | Q Exactive | Yes | 4 | radiation, biomarker, parallel reaction monitoring | Liu K, Singer E, Cohn W, Micewicz ED, McBride W... | |
| Pharmacokinetic analysis of a novel human EGFRvIII:CD3 bispecific antibody in plasma and whole blood using a high-resolution targeted mass spectroscopy approach | Mus musculus, Homo sapiens | Q Exactive HF-X | Yes | 2 | PRM, pharmacokinetics, biotherapeutic antibody, stable isotope-labeled protein, whole blood, HF-X | Schaller TH, Foster MW, Thompson JW, Spasojevic... | PXD012472 |
| Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differences | Crassostrea gigas | Orbitrap Fusion Lumos,TSQ Vantage | No | 3 | proteomics, oysters, in situ measurements, estuarine systems, antioxidant enzymes, molecular chaperones | Venkataraman YR, Timmins-Schiffman E, Horwith M... | PXD012569 |
| Lysine & Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease | Mus musculus | Orbitrap Fusion Lumos,TripleTOF 6600 | No | 9 | Mass spectrometry, methylation, precursor mass window, DIA-MS, methylome, succinylation, acetylation | | PXD012621 |
| Exploring Non-Canonical Terpene Space With a Heterologous Lepidopteran Mevalonate Pathway | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 1 | Mevalonate Pathway, Terpenes, Juvenile Hormones, homoisopentenyl pyrophosphate, HIPP, homodimethylallyl pyrophosphate, HDMAPP | Eiben CB, de Rond T, Bloszies C, Gin J, Chiniqu... | PXD012697 |
| Targeted Mass Spectrometry of Brain and Pancreatic tissues | Homo sapiens | Q Exactive HF | Yes | 2 | Targeted Mass Spectrometry, QPrEST, PRM, Brain, Pancreas, CZI | | PXD012931 |
| N-terminal amino acid identification using targeted mass spectrometry | Escherichia coli | Q Exactive | No | 2 | Parallel reaction monitoring, amber initiator tRNA, nanoluciferase, N-terminal amino acid | Vincent, R. M., Wright, B., & Jaschke, P. R. (2... | PXD012390 |
| Target Expression Profiling Identifies FLT3 as a BiTE® Target for Acute Myeloid Leukemia | Homo sapiens | LTQ Orbitrap Velos | No | 1 | FLT3, cerebellum, acute myeloid leukemia | Brauchle B, Goldstein RL, Karbowski CM, Henn A,... | |
| Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping | Homo sapiens, Sus scrofa, Bos taurus | Velos Plus | No | 15 | Glycomics, Protein Glycosylation, normalisation, LC-MS | Standardization of PGC-LC-MS-based glycomics fo... | |
| Homeostatic and Interferon-induced gene expression represent different states of promoter-associated transcription factor ISGF3 | Mus musculus | Q Exactive HF-X | No | 1 | Targeted MS, PRM, quantification, BioID | Platanitis E, Demiroz D, Schneller A, Fischer K... | PXD013251 |
| Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability | Homo sapiens | TSQ Vantage | Yes | 6 | kinase-substrate pair, phosphopeptide SRM | Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMi... | |
| IFI16 pyrin oligomerization mediates antiviral actions | Homo sapiens | Q Exactive HF | No | 1 | IFI16, oligomerization, innate immunity, herpesvirus, IP-MS | | |
| Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast | Saccharomyces cerevisiae | 6460 Triple Quadrupole LC/MS | No | 2 | Metabolic engineering, polyketides, S. cerevisiae, Targeted proteomics | Jakociunas T, Klitgaard AK, Kontou EE, Nielsen ... | PXD013388 |
| Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor | Xanthomonas oryzae pv. oryzae | 6460 Triple Quadrupole LC/MS | No | 1 | RaxX, X. oryzae, XA21 immune receptor, Tyrosine sulfation, RiPPs | Luu DD, Joe A, Chen Y, Parys K, Bahar O, Pruitt... | PXD013389 |
| Endo-Lysosomal Proteins and Ubiquitin CSF Concentrations in Alzheimer’s and Parkinson’s Disease | Homo sapiens | Q Exactive | Yes | 12 | Biomarker, CSF, Mass Spectrometry, Alzheimer’s disease, Parkinson’s disease | Sjodin S, Brinkmalm G, Ohrfelt A, Parnetti L, P... | PXD013451 |
| In vitro kinase assay of human FLNc domain 18-21 with Akt and PKC alpha | Homo sapiens | LTQ Orbitrap Elite | No | 1 | FLNc, in vitro kinase assay, AKT, PKCa | | PXD008893 |
| International Ring Trial of a Broad-Spectrum Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis [System Suitability Files] | Homo sapiens | Q Exactive HF,Q Exactive Plus,Q Exactive | Yes | 2 | p400HR, targeted, metabolomics, Q Exactive, Biocrates | Thompson JW, Adams KJ, Adamski J, Asad Y, Borts... | |
| Validation of N-terminal Labeling Mass Spectrometry for Characterization of Partially Hydrolyzed Gluten Proteins | wheat | Q Exactive Plus | No | 7 | LC-MS/MS; Hydrolyzed gluten; gluten; N-terminal Labeling; mass spectrometry; TAILS | Cao W, Baumert JL, Downs ML. Evaluation of N-te... | PXD013679 |
| Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages | Saccharomyces cerevisiae | Q Exactive HF | No | 1 | Proteome Discoverer, MaxQuant, Proteomics, Mitogen-activated protein kinase (MAPK), Hyperosmotic stress response, High-osmolarity glycerol (HOG), Hog1, Kic1, Orm2, ORMDL, p38 | Janschitz M, Romanov N, Varnavides G, Hollenste... | PXD013789 |
| Rebuilding core abscisic acid signaling pathways of Arabidopsis in yeast | Saccharomyces cerevisiae, Arabidopsis thaliana | Orbitrap Fusion Lumos | No | 1 | SnRK2, ABA, phosphorylation | Ruschhaupt M, Mergner J, Mucha S, Papacek M, Do... | PXD013849 |
| Milk glycopeptide across lactation | Homo sapiens | Orbitrap Fusion Lumos | Yes | 1 | Human milk; Glycoproteomics | Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Hec... | PXD022415 |
| Light-dependent N-terminal phosphorylation of LHCSR3 and LHCB4 are interlinked in Chlamydomonas reinhardtii | Chlamydomonas reinhardtii | Q Exactive Plus | No | 4 | Photosynthesis, Light Harvesting, High Light Stress, Protein Phosphorylation | Scholz M, Gäbelein P, Xue H, Mosebach L, Bergne... | |
| Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics | Homo sapiens | Q Exactive HF | Yes | 1 | SIL, Recombiant protein fragment, Plasma | | |
| Developing a robust assay to monitor and quantify key players of metabolic pathways during adipogenesis by targeted proteomics | Mus musculus | TSQ Vantage | Yes | 2 | Absolute quantification, adipogenesis, metabolic pathways, targeted proteomics | Hentschel A, Ahrends R. Developing a Robust Ass... | |
| An automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbes | Escherichia coli, Saccharomyces cerevisiae, Pseudomonas putida KT2440, Rhodosporidium toruloides | 6460 Triple Quadrupole LC/MS | No | 8 | Automation, Sample preparation, Proteomics, Bacteria, Fungi, Microbes, Biotechnology, High-throughput | Chen Y, Guenther JM, Gin JW, Chan LJG, Costello... | PXD014182 |
| Cell cycle validation | Mus musculus, Sus scrofa, Xenopus laevis, Xenopus tropicalis | Q Exactive HF | No | 3 | | Federspiel JD, Tandon P, Wilczewski CM, Wasson ... | |
| Targeted MRM assay Complement System in Health and Infectious Disease | Homo sapiens | Xevo TQ-S | Yes | 1 | targeted mass spectrometry, multiple reaction monitoring (MRM), complement system, infectious disease, C-reactive protein (CRP), clusterin | Willems E, Alkema W, Keizer-Garritsen J, Supper... | PXD014264 |
| A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships | Listeria monocytogenes | Q Exactive | No | 2 | Listeria, proteotype, proteogenomics, smORFs, DIA, PRM, EGD-e, ScottA | Varadarajan AR, Goetze S, Pavlou MP, Grosboillo... | PXD014294 |
| ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection | Human immunodeficiency virus 1, Homo sapiens | TSQ Quantiva | No | 4 | Host-virus interactions, ARIH2, HIV, vif, CUL5, AP-MS, APOBEC3G | Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultq... | |
| A targeted strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancer | Homo sapiens | TSQ Vantage,QTRAP 5500,4000 QTRAP | No | 3 | Cancer biomarker, Ovarian cancer, Plasma | Huttenhain R, Choi M, de la Fuente L, Oehl K, C... | PXD014474 |
| Analysis of endogenous peptides released from osteoarthritic cartilage unravels novel pathogenic markers | Homo sapiens | QTRAP 5500 | Yes | 1 | osteoarthritis, cartilage, secretome, peptidomics, neopeptides, biomarkers | Fernandez-Puente P, González-Rodríguez L, Calam... | |
| Light-dependent dynamics of phosphorylation of the thylakoid structural protein CURT1B | Arabidopsis thaliana | TSQ Vantage | No | 7 | Arabidopsis thaliana, Thylakoids, grana margins, LHCII, CURT1, | Trotta A, Bajwa AA, Mancini I, Paakkarinen V, P... | PXD014562 |
| Unique-region phosphorylation targets LynA for rapid degradation, tuning its expression and signaling in myeloid cells | Mus musculus | Orbitrap Fusion | No | 6 | SFK LYN A, Degadation, macrophage, Kinase, phosphoprotein | Brian BF, Jolicoeur AS, Guerrero CR, Nunez MG, ... | PXD014621 |
| Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells | Homo sapiens | TSQ Vantage | Yes | 2 | Systems pharmacology, targeted therapy, adaptive resistance, BRAFV600E cancers, ERK/MAPK pathway, kinetic modeling | Gerosa L, Chidley C, Fröhlich F, Sanchez G, Lim... | |
| Matrix-matched calibration curves | Saccharomyces cerevisiae, Homo sapiens | Q Exactive HF,Orbitrap Fusion Lumos,TSQ Quantiva | No | 5 | loq, calibration curve, matrix matched | Pino LK, Searle BC, Yang HY, Hoofnagle AN, Nobl... | PXD014815 |
| Prion MRM assay development and clinical study | Homo sapiens, Mus musculus, Rattus norvegicus, Macaca cynomolgus | TSQ Quantiva,Q Exactive | Yes | 16 | targeted mass spectrometry; multiple reaction monitoring mass spectrometry; prion; cerebrospinal fluid; biomarker | Minikel EV, Kuhn E, Cocco AR, Vallabh SM, Harti... | PXD014781 |
| Absolute Quantification of Schistosoma mansoni Esophageal Gland Products | Schistosoma mansoni | Xevo TQ-S | Yes | 1 | Schistosoma mansoni, esophageal gland, gastrodermis, microexon genes, quantitative proteomics, QconCAT | Neves LX, Wilson RA, Brownridge P, Harman VM, H... | PXD014899 |
| Peptide signature for the fast detection of bacterial species in Urinary Tract infections using LC-MS | Escherichia coli K-12, Klebsiella pneumoniae subsp. pneumoniae ATCC 700721, Enterococcus faecalis V583, Streptococcus agalactiae 2603V/R | Orbitrap Fusion ETD,Q Exactive HF-X | No | 4 | Bacterial identification; Peptide signature; Urine | Roux-Dalvai F, Gotti C, Leclercq M, Helie M-C, ... | PXD014970 |
| Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow Cytometry | Homo sapiens | Orbitrap Fusion Lumos | Yes | 1 | quality control, flow cytometry, troponin, cardiomyocytes, mass spectrometry, standard operating protocol | Waas M, Weerasekera R, Kropp EM, Romero-Tejeda ... | PXD014971 |
| HDL proteome remodeling post-stroke | Homo sapiens | Q Exactive HF | No | 1 | parallel reaction monitoring, HDL, stroke | Plubell DL, Fenton AM, Rosario S, Bergstrom P, ... | PXD015001 |
| Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 3 | Ppant ejection assay | Blake-Hedges JM, Pereira JH, Cruz-Morales P, Th... | |
| Urinary PRM analysis of early type 1 diabetes | Homo sapiens | Q Exactive HF-X | Yes | 1 | urine, peptidomics, type 1 diabetes, kidney disease | Van JAD, Clotet-Freixas S, Zhou J, Batruch I, S... | PXD012389 |
| Multiplexed MRM concentration measurements of >200 endogenous proteins in dried blood spots for biomarker discovery and validation | Homo sapiens | 6490 Triple Quadrupole LC/MS | Yes | 13 | MRM, DBS, protein, concentration, spike in | Eshghi A, Pistawka AJ, Liu J, Chen M, Sinclair ... | PXD015118 |
| Personalized human milk proteome | Homo sapiens | Q Exactive HF-X | Yes | 2 | Endogenous Peptides/ Human Milk/ Immunity/ Personalized Nutrition/ Proteins | | PXD015119 |
| Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics | Homo sapiens, Mus musculus | Xevo TQ-S,Triple Quad 5500,Synapt G2 HDMS | Yes | 6 | Skyline, Small Molecules, Metabolomics, Pharmacokinetics, Quantification, Mass Spectrometry, Selected Reaction Monitoring, Targeted Mass Spectrometry, High-Resolution, Untargeted Mass Spectrometry | Adams KJ, Pratt B, Bose N, Dubois LG, St.John-W... | |
| Chemical and phosphoproteomics illuminate the cellular mode of action of AKT inhibitors | Homo sapiens | Orbitrap Fusion Lumos | No | 1 | AKT inhibitor, phosphorylation | Wiechmann S, Ruprecht B, Siekmann T, Zheng R, F... | PXD015188 |
| Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes | Homo sapiens | LTQ Orbitrap Velos | No | 5 | N-glycan, glycomics, O-glycan, cardiac, heart, stem-cell | Ashwood C, Waas M, Weerasekera R, Gundry RL. Re... | |
| FeS protein levels in Arabidopsis plants expressing a mutated NEET protein | Arabidopsis thaliana | TSQ Quantiva | No | 1 | Arabidopsis, NEET, Fe-S | Zandalinas SI, Song L, Sengupta S, McInturf SA,... | PXD015447 |
| Antibody-free multiplex measurement of 23 human cytokines in primary cell culture secretome using targeted multiple reaction monitoring mass spectrometry | Homo sapiens | 6490 Triple Quadrupole LC/MS | Yes | 26 | Cytokine, Cell secretome, Targeted mass spectrometry | Krueger A, Stoll T, Shah AK, Sinha R, Frazer IH... | PXD015448 |
| Comprehensive Detection of Isopeptides between Human Tissue Transglutaminase and Gluten Peptides | Triticum, human | Q Exactive HF | No | 4 | celiac disease; crosslink; deamidation; gliadin; gluten; isopeptides; LC-MS/MS; tissue transglutaminase; transamidation | Lexhaller B, Ludwig C, Scherf KA. Comprehensive... | |
| Min protein in vitro protein expression kinetics | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 2 | Min system, CFPS, in vitro gene expression, MRM, SRM, | Godino E, López JN, Foschepoth D, Cleij C, Doer... | PXD015686 |
| 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 Assay | Homo sapiens | 6490 Triple Quadrupole LC/MS | Yes | 8 | human, apolipoprotein, omega-3, fenofibrate, hypertriglyceridemia | Hober A, Edfors F, Ryaboshapkina M, Malmqvist J... | PXD013314 |
| PRM of Nth1 phospho-peptides in response to AGC-kinase inhibition | Saccharomyces cerevisiae | Orbitrap Fusion ETD | No | 1 | AGC-kinases, Sch9, Ypk1, PKA, chemical genetics | Plank M, Perepelkina M, Müller M, Vaga S, Zou X... | PXD015760 |
| Targeted assay for differentiation and monitoring the concentration of GDF 8 (Myostatin) and GDF11 in mouse serum | Mus musculus | Orbitrap Fusion Lumos | Yes | 2 | Parallel Reaction Monitoring (PRM), targeted, quantitative proteomics, Myostatin/GDF8, GDF11 | Camparini L, Kollipara L, Sinagra G, Loffredo F... | PXD015838 |
| Characterization and relative quantitation of wheat, rye and barley gluten protein types by LC-MS/MS | common wheat, rye, barley | TripleTOF 6600,QTRAP 6500 | No | 6 | allergy, amylase/trypsin-inhibitor (ATI), celiac disease, gliadin, gluten, mass spectrometry, non-celiac gluten sensitivity (NCGS), proteomics | Lexhaller B, Colgrave ML, Scherf KA. Characteri... | PXD016065 |
| Identification of an intronic enhancer in the tilapia glutamine synthetase gene. | Oreochromis mossambicus | impact II | No | 1 | Ecological Proteomics, Euryhaline fish, DIA assay, Tilapia cell line | Kim C, Kültz D. An osmolality/salinity-responsi... | |
| ACE over expression in myeloid cells increases oxidative metabolism and cellular ATP | Mus musculus | QTRAP 6500+ | Yes | 1 | ACE overexpression, Mouse Monocyte Metabolism, Mitoplex | Cao DY, Spivia WR, Veiras LC, Khan Z, Peng Z, J... | |
| 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 wheat | Triticum aestivum, Triticum spelta, Triticum dicoccoides | QTRAP 6500+ | No | 2 | High-molecular weight glutenin subunits, spelt, emmer, einkorn, LC-MS/MS, SDS-PAGE | Geisslitz S, America AHP, Scherf KA. Mass spect... | PXD016342 |
| Characterization of signaling pathways associated with pancreatic β-cell adaptive flexibility in compensation of obesity-linked diabetes in db/db mice | Mus musculus | Q Exactive HF | Yes | 1 | PRM, db/db, islet | Kang T, Boland BB, Jensen P, Alarcon C, Nawrock... | PXD016392 |
| PRM method for detection of both casein and whey milk allergens from baked food matrix | Bos taurus | Q Exactive Plus | No | 6 | Targeted mass spectrometry; PRM; Milk allergen detection; casein and whey proteins; baked food matrix | Ramachandran B, Yang CT, Downs ML. Parallel Rea... | PXD016539 |
| Targeted metabolomics profiling of acute myocardial infarction risk human sera | Homo sapiens | 6490 Triple Quadrupole LC/MS | No | 6 | metabolomics, Acute myocardial infarction. | Khan A, Choi Y, Back JH, Lee S, Jee SH, Park YH... | |
| Assessment of Serological Early Biomarker Candidates for Lung Adenocarcinoma by using Multiple Reaction Monitoring-Mass Spectrometry | Homo sapiens | 6495A Triple Quadrupole LC/MS | No | 18 | early biomarkers, lung adenocarcinoma, LC-MRM-MS, plasma | Wu HY, Pan YY, Kopylov AT, Zgoda V, Ma MC, Wang... | PXD014683 |
| CRK2-mediated control of ROS production by phosphorylation of the RBOHD C-terminus in Arabidopsis | Arabidopsis thaliana | Q Exactive Plus | No | 4 | Phosphoproteomics, Reactive-oxygen species, receptor-like protein kinases, Arabidopsis thaliana | Kimura S, Hunter K, Vaahtera L, Tran HC, Citter... | PXD013525 |
| Identification of Putative Early Atherosclerosis Biomarkers by Unsupervised Deconvolution of Heterogeneous Vascular Proteomes | Homo sapiens | TripleTOF 6600,QTRAP 6500+ | No | 4 | Atherosclerosis, Tissue Fibrous Plaque proteome | Parker SJ, Chen L, Spivia W, Saylor G, Mao C, V... | PXD016730 |
| Signaling proteins of a chemosensory pathway from sperm of Arbacia punctulata | Arbacia punctulata | TSQ Vantage | Yes | 2 | sperm chemosensation, protein copy number, membrane protein | Trotschel C, Hamzeh H, Alvarez L, Pascal R, Lav... | PXD015502 |
| Quantitative proteomics analysis of Angiostrongylus vasorum-induced alterations in dog serum | Canis lupus familiaris | Q Exactive HF-X | Yes | 2 | Angiostrongylus vasorum | Tritten L, Gillis-Germitsch N, Kockmann T, Schn... | PXD016887 |
| Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass Spectrometry | Homo sapiens, Escherichia coli | SYNAPT G2-Si | Yes | 23 | quantitation, cross linking, ion mobility | Britt HM, Cragnolini T, Khatun S, Hatimy A, Jam... | |