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|  Targeted Proteomics of HDL in People With Type 2 Diabetes | Homo sapiens | TSQ Vantage | No | 2 | | Vaisar T, Couzens E, Hwang A, Russell M, Barlow... | |
| 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 taurus | TSQ Quantum,TSQ Vantage,4000 QTRAP,QTRAP 5500,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ-XS | No | 15 | mass spectrometry, quantification, selected reaction monitoring, system suitability, skyline | Abbatiello SE, Mani DR, Schilling B, Maclean B,... | PXD010535 |
| Global, site-resolved, quantitative analysis of the yeast redoxome | Saccharomyces cerevisiae | LTQ Orbitrap Elite | No | 5 | | Ulrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ... | |
| Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cells | Mus musculus | Q Exactive HF | No | 3 | | | |
| Monitoring molecular contaminants and interferences in proteomic data sets | | | No | 1 | | Rardin MJ. Rapid assessment of contaminants and... | |
| Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damage | Homo sapiens | QTRAP 6500 | No | 5 | | Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla ... | |
| Discovery of a testis-specific complex TEX101-DPEP3 and selection of its disrupting antibodies | Homo sapiens | TSQ Quantiva | Yes | 4 | | Schiza, C., Korbakis, D., Panteleli, E., Jarvi,... | |
| Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. Journal of The American Society for Mass Spectrometry | Bos taurus, Saccharomyces cerevisiae | 6560 Q-TOF LC/MS | Yes | 5 | ion mobility spectrometry, Skyline, data independent acquisition, proteomics | MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, ... | PXD010650 |
| PknG physiological substrates | Mycobacterium bovis BCG | Q Exactive | No | 1 | | Kehilwe C Nakedi, Bridget Calder, Mousumi Barne... | |
| Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway | Homo sapiens | TSQ Vantage,nanoACQUITY UPLC | Yes | 4 | | Yi L, Shi T, Gritsenko MA, X'avia Chan CY, Fill... | |
| Serum glycoprotein biomarker validation for esophageal adenocarcinoma - Ochsner cohort dataset | Homo sapiens | 6490 Triple Quadrupole LC/MS | Yes | 4 | | Shah AK, Hartel G, Brown I, Winterford C, Na R,... | |
| Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort dataset | Homo sapiens | 6490 Triple Quadrupole LC/MS | Yes | 4 | | Shah AK, Hartel G, Brown I, Winterford C, Na R,... | |
| Identification of functional TEX101 interactome through proteomic profiling of human spermatozoa homozygous for a missense variant rs35033974 | Homo sapiens | TSQ Quantiva,Q Exactive Plus | Yes | 5 | | Schiza C, Korbakis D, Jarvi K, Diamandis EP, Dr... | |
| Targeted Quantification of the Peroxisome Proteome during Human Cytomegalovirus Infection | Human Cytomegalovirus, Homo sapiens | Q Exactive HF | No | 1 | | Infection-Induced Peroxisome Biogenesis Is a Me... | |
| Global Characterization of Human IgG1 under Oxidative Stresses—Combining dual independent protease digestions and LC-HRMS Data Independent Acquisition (DIA) | Homo sapiens | Q Exactive Plus | No | 8 | | Chen Y, Doud E, Stone T, Xin L, Hong W, Li Y. R... | |
| Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer | Homo sapiens | Xevo TQ-XS | Yes | 2 | | | |
| Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells | Homo sapiens | TSQ Vantage | No | 12 | | | |
| Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements | Escherichia coli | Q Exactive HF | No | 5 | | Taumer C, Griesbaum L, Kovacevic A, Soufi B, Na... | |
| HR-SRM-baseds analysis of mouse/human SGLT2 in kidney and heart tissue. | Mus musculus, Homo sapiens | TripleTOF 5600+ | No | 1 | | Mustroph et al., ESC Heart Failure, in revision... | |
| Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine Learning | Homo sapiens | QTRAP 5500 | Yes | 3 | | Toghi Eshghi S, Auger P, Mathews WR. Quality as... | |
| Modular Engineering of L-Tyrosine Production in Escherichia coli | Escherichia coli | 4000 QTRAP | No | 1 | | Juminaga, Darmawi, et al. "Modular engineering ... | |
| Viscous control of cellular respiration by membrane lipid composition | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 1 | | Budin I, de Rond T, Chen Y, Chan LJ, Petzold CJ... | |
| Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production | Escherichia coli | QTRAP 5500 | No | 1 | | Alonso-Gutierrez, Jorge, et al. "Metabolic engi... | |
| A Kinetic-Based Approach to Understanding Heterologous Mevalonate Pathway Function in E. Coli | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 1 | | Weaver, Lane J., et al. "A kinetic‐based approa... | |
| targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins | Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 45 | | Batth, Tanveer S., et al. "A targeted proteomic... | |
| Streptococcus pyogenes evades adaptive immunity through specific modification of host IgG glycosylation | Homo sapiens, Mus musculus | TSQ Vantage | No | 8 | | Naegeli, A., Bratanis, E., Karlsson, C., Shanno... | |
| Identification of novel protein lysine acetyltransferases in Escherichia coli | Escherichia coli | TripleTOF 6600 | No | 2 | | D.G. Christensen, J.G. Meyer, J.T. Baumgartner,... | |
| Mass spectrometry-based absolute quantification of 20S proteasome status for controlled ex-vivo expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells | Homo sapiens | QTRAP 5500,QTRAP 6500 | No | 24 | | Menneteau T, Fabre B, Garrigues L, Stella A, Zi... | |
| Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible Succinylation | Mus musculus | TripleTOF 5600 | No | 1 | Succinylation, data-independent acquisition, proteomics, brown fat, mitochondria, UCP1 | submission to cell | PXD010205 |
| Mechanical force induces rapid phosphorylation dependent signaling in Xenopus embryos | Xenopus laevis | Q Exactive HF | No | 6 | Phosphorylation, Signaling | | |
| Incorporation of fluoritnated tryptophan into RV1187 | Mycobacterium tuberculosis | Xevo TQ-S | No | 1 | Mycobacterium tuberculosis, Fluoro-W | Nurul Islam M, Hitchings R, Kumar S, Fontes FL,... | PXD010703 |
| Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS | Sus scrofa, Bos taurus, Homo sapiens | Velos Plus,HCTultra | No | 7 | Diagnostic ions; Glycomics; MS/MS; Skyline | Ashwood C, Lin CH, Thaysen-Andersen M, Packer N... | |
| Enhanced validation of antibodies for research applications | Homo sapiens | Q Exactive HF | Yes | 2 | western blot, targeted proteomics, parallel reaction monitoring, prm, qprest, quantification | Edfors F, Hober A, Linderbäck K, Maddalo G, Azi... | |
| Detection of Six Commercially Processed Soy ingredients in an Incurred Food Matrix Using Parallel Reaction Monitoring | Glycine max | Q Exactive Plus | No | 4 | Soybean, food allergen, parallel reaction monitoring | Chen S, Yang CT, Downs ML. Detection of Six Com... | PXD010843 |
| Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnostics | Homo sapiens | Q Exactive HF | No | 1 | FFPE; cancer; DIA; | Kim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, W... | PXD010934 |
| Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae | Saccharomyces cerevisiae | Q Exactive Plus | Yes | 4 | yeast, transcription factor, time-course | Kelliher CM, Foster MW, Motta FC, Deckard A, So... | PXD010937 |
| A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification | Homo sapiens | TSQ Vantage | Yes | 3 | Targeted proteomics, hepcidin-25, quantifications, mass spectrometry | Moghieb A, Tesfay L, Nie S, Gritsenko M, Fillmo... | |
| Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells | Homo sapiens | TSQ Vantage | Yes | 3 | Carrier-assisted, cLC-SRM, sensitivity, single-cell proteomics, targeted proteomics | | |
| Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics | Vitis vinifera, Grapevine leafroll-associated virus | Q Exactive HF | Yes | 4 | grapevine, Grapevine red blotch virus, Proteomics, shotgun LC-MS/MS, parallel reaction monitoring, absolute quantification | Buchs N, Braga-Lagache S, Uldry AC, Brodard J, ... | PXD011138 |
| 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 efficacy | Homo sapiens | LTQ Orbitrap Velos | No | 1 | atherosclerosis, limited proteolysis, ApoB-100 | Benitez-Amaro A, Pallara C, Nasarre L, Rivas-Ur... | PXD011261 |
| Plasmalogen Quantification during Human Cytomegalovirus Infection | Human Cytomegalovirus, Homo sapiens | LTQ Orbitrap XL | No | 3 | | Infection-Induced Peroxisome Biogenesis Is a Me... | |
| Single-point Calibration | Saccharomyces cerevisiae | Q Exactive HF,TSQ Altis | No | 2 | signal calibration, harmonization, external reference | Pino LK, Searle BC, Huang EL, Noble WS, Hoofnag... | PXD011297 |
| In vitro phosphorylation of ASY1 by CDKA;1 | Arabidopsis thaliana | Q Exactive Plus | No | 1 | phosphorylation, PRM, Arabidopsis thaliana, meiosis | Yang C, Sofroni K, Wijnker E, Hamamura Y, Carst... | PXD011335 |
| ATI in Ancient Wheats | Triticum | TSQ Vantage,LTQ Orbitrap Velos | Yes | 7 | Amylase/trypsin-inhibitor, wheat, spelt, emmer, einkorn | Geisslitz S, Ludwig C, Scherf KA, Koehler P. Ta... | |
| A rapid methods development workflow for high-throughput quantitative proteomic applications | Saccharomyces cerevisiae, Pseudomonas putida KT2440, Escherichia coli | 6460 Triple Quadrupole LC/MS | No | 17 | discovery proteomics, targeted proteomics, iRT calculator, methods development | Chen Y, Vu J, Thompson MG, Sharpless WA, Chan L... | |
| Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism | Pseudomonas putida KT2440 | 6460 Triple Quadrupole LC/MS | No | 1 | targeted proteomics | Thompson MG, Blake-Hedges JM, Cruz-Morales P, B... | PXD011350 |
| Discovery and quantification of non-human proteins in human milk | Bos taurus, Gallus gallus, Oryza sativa, Canis familiaris, Felis catus, Equus caballus, Homo sapiens | Q Exactive HF-X | Yes | 2 | non-human peptides, non-human proteins, shotgun proteomics, parallel reaction monitoring, mass spectrometry, human milk | Zhu J, Garrigues L, Van den Toorn H, Stahl B, H... | |
| Protein-based Cardiogenic Shock Patient Classifier | Homo sapiens | Orbitrap Fusion Lumos | Yes | 1 | Cardiogenic Shock, PRM | Rueda F, Borràs E, García-García C, Iborra-Egea... | PXD011593 |
| Improving Precursor Selectivity in Data Independent Acquisition Using Overlapping Windows | Saccharomyces cerevisiae, Bos taurus | Q Exactive | Yes | 11 | yeast, rapamycin, proteasome, multiplexing, data independent acquisition, Q-Exactive, orbitrap, spike-in, quantification, bovine | Amodei D, Egertson J, MacLean BX, Johnson R, Me... | PXD011910 |
| Multiplex assay for quantification of acute phase proteins and immunoglobulin A in dried blood spots | Homo sapiens | 6495B Triple Quadrupole LC/MS,6495A Triple Quadrupole LC/MS | Yes | 12 | inflammation markers, acute phase proteins, immune response, dried blood spots, targeted quantitative proteomics, selected reaction monitoring | Vidova, V., Stuchlikova, E., Vrbova, M., Almasi... | PXD011944 |
| Discovery and qualification of serum protein biomarkers for cholangiocarcinoma diagnosis | Homo sapiens | LCMS-8050 | Yes | 1 | cholangiocarcinoma; proteomics; mass spectrometry; multiple reaction monitoring; serum biomarker discovery pipeline | Duangkumpha K, Stoll T, Phetcharaburanin J, Yon... | |
| Isotopologue multi-point calibration for proteomics biomarker quantification in clinical practice | Homo sapiens | QTRAP 5500 | Yes | 4 | targeted proteomics, SRM, clinical proteomics, HER2, isotopologues, internal calibration | Chiva C, Pastor O, Trilla-Fuertes L, Gámez-Pozo... | PXD012035 |
| High throughput generation of a resource of the human secretome in mammalian cells | Homo sapiens | Q Exactive HF | No | 1 | dia, human secretome, assay development, plasma | Tegel H, Dannemeyer M, Kanje S, Sivertsson Å, B... | PXD012054 |
| Search for synaptic biomarkers of Alzheimer’s disease | Homo sapiens | QTRAP 5500 | Yes | 4 | Alzheimer’s disease, cerebrospinal fluid, synapse, biomarkers, selected reaction monitoring | Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Bal... | PXD012138 |
| A dataset describing a suite of novel antibody reagents for the RAS signaling network | Homo sapiens | QTRAP 5500,QTRAP 6500 | Yes | 117 | RAS proteins, peptide-based immuno-MRM, monoclonal antibodies | Schoenherr RM, Huang D, Voytovich UJ, Ivey RG, ... | PXD012604 |
| Comparative phosphoproteomic analysis reveals a decay of ABA signaling in barley grains during after-ripening | Hordeum vulgare | TripleTOF 5600 | No | 1 | phosphoproteome, barley, abscisic acid, ABA, dormancy | Ishikawa S, Barrero JM, Takahashi F, Nakagami H... | |