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| Demo Experiment | | | Example Data |
| Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma | | | Schilling - main_Study_9 |
| Protein acetylation in response to carbon overflow: detecting dynamic acetylation changes by mass spectrometry | | | Schilling - Ecoli_Glucose_Acetylome |
| Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptides | | | ALF-SWATH_anchor_proteins_absolute_quantification |
| Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantification | | | ALF-SWATH_anchor_proteins_dilution_series |
| Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using Skyline | | | ALF-SWATH_Top21_Mtb_proteins_manual |
| Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptides | | | Ludwig_Mtb_anchors |
| Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantification | | | Ludwig_Mtb_dilutions |
| Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using Skyline | | | Ludwig_Mtb_requant |
| Analytical protein standards | | | Searle_PREGO_manuscript |
| Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomics | | | Neuronal Development SRM |
| Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomics | | | Dunkley - Neuronal Development SRM |
| Renal proteomes of marine and FW sticklebacks | | | Kültz et al. (2016) J. Proteomics |
| Ariadne’s thread: a robust software solution leading to automated absolute and relative quantification of SRM data | | | Goetze - Ariadne |
| Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissues | | | Steiner - HER2 quantification in FFPE breast cancer tissues |
| MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments | | | MS1_MS2_SWATH |
| MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments | | | Schilling - MS1_MS2_SWATH |
| Multiplexed, scheduled high resolution sMRM-HR acquisition on full scan MS/MS instruments integrating data dependent and targeted, quantitative mass spectrometric workflows. | | | Schilling - MRM_HR_TripleTOF_MS2_FullScanFiltering |
| Evaluation of multi-tRNA synthetase complex by multiple reaction monitoring mass spectrometry coupled with size exclusion chromatography | | | ARS_SEC_AP_MRM |
| Evaluation of multi-tRNA synthetase complex by multiple reaction monitoring mass spectrometry coupled with size exclusion chromatography | | | Heesung - ARS_SEC_AP_MRM |
| Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks | | | Kültz et. al (2015) Proteomics |
| Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks | | | Kultz et al. (2015) Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks. Proteomics |
| Application of a quantitative SRM-based proteomics method to study iron starvation in Synechocystis sp. PCC 6803 | | | Muth-Pawlak - SRM_irondepr_2015 |
| Renal proteomes of marine and FW sticklebacks | | | Kultz et al. (2015) Renal proteomes of marine and FW sticklebacks. J Proteomics |
| Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. | | | Parker - CiRT_Peptides |
| Assembly dynamics and stoichiometry of the apoptosis signal-regulating kinase (ASK) signalosome in response to electrophile stress | | | Liebler - ASK manuscript |
| A quantitative tagless co-purification method to validate and identify protein-protein interactions | | | Biggin - Tagless_analysis_of_protein-protein_interactions_in_Desulfovibrio_vulgaris |
| Proteomic profile of deleted in breast cancer 1 (DBC1) protein-protein interactions | | | Greco - DBC1 SRM |
| Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reported | | | Witkowska_DVH_TAP |
| Differential light-dependent phosphorylation of Ser and Thr residues regulates plant STN7 kinase | | | UTurku-STN7 |
| Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective | | | Kockmann - MSQC1 |
| Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissues | | | Paulovich - FFPE_MRM_optimization |
| Annexin A5 is the Most-Abundant Membrane-Associated Protein in Stereocilia but is Dispensable | | | Barr-Gillespie - Annexin A5 |
| Conserved protein abundance pattern of the EGFR-MAPK pathway reveals its regulatory architecture | | | PNNL_EGFR_pathway |
| In vitro kinase assay of human and mouse FLNc domain 23-24 | | | Warscheid Lab - FLNc d23-24 in vitro kinase assay |
| In vivo kinase assay of mouse FLNc | | | Warscheid Lab - C-terminal FLNc in vivo kinase assays |
| Development, Validation, and Application of a MRM with SIS Peptide Strategy to Quantify Multiplexed Panels of Proteins in Mouse Plasma and Heart Tissues | | | Development, Validation, and Application of a MRM with SIS Peptide Strategy to Quantify Multiplexed Panels of Proteins in Mouse Plasma and Heart Tissues |
| Development, Validation, and Application of a MRM with SIS Peptide Strategy to Quantify Multiplexed Panels of Proteins in Mouse Plasma and Heart Tissues | | | Genome BC Proteomics Centre - PC Mouse uEiHq2 |
| Quantifiable peptide tags for targeted proteomics. | | | Staes - PQS_peptides |
| Plastin-1 Controls Stereocilia Diameter by Transforming Actin Filament Packing from Hexagonal to Liquid | | | Stereocilia Crosslinker Targeted Data |
| PRM analysis of EC uterine aspirate | | | Domon - EC |
| Robust temporal profiling of GRB2 protein complexes in primary T cells using SWATH mass spectrometry | | | Aebersold - GRB2 interactome by AP-SWATH |
| Identification and characterization of protein acetylation in Neisseria gonorrhoeae | | | Schilling - NGackA |
| Gadd45a Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4 | | | Chris Adams_Gadd45a |
| Gadd45a Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4 | | | Schilling - Chris Adams_Gadd45a |
| SELECTIVE AND SENSITIVE QUANTIFICATION OF THE CYTOCHROME P450 3A4 PROTEIN IN HUMAN LIVER HOMOGENATES THROUGH MULTIPLE REACTION MONITORING MASS SPECTROMETRY | | | CRCHUL - CYP3A4_microsomes_homogenates |
| Detection of Low Abundance Ocean Bacteria Peptides | | | Nunn - Detection of Low Abundance Ocean Bacteria Peptides |
| Osmolality/ salinity responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish | | | Wang and Kültz (2017) PNAS |
| A general method for targeted quantitative cross-linking mass spectrometry | | | Bruce - PRM_XL_manuscript |
| Dynamic phosphorylation of apoptosis signal regulating kinase 1 (ASK1) in response to oxidative and electrophilic stress | | | Liebler - ASK PTM |
| ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments | | | iPRG 2015 |
| FLNc Calpain GluC SRM Analysis | | | Warscheid Lab - FLNc Calpain GluC SRM |
| Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteria | | | UTurku - IsaR1 |
| Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated Proteins | | | Lagache - N1OHMk |
| PECAN - A Library Free Peptide Detection Tool for DIA Data | | | PECAN - A Library Free Peptide Detection Tool for DIA Data |
| Osmolality/ salinity responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish | | | Kueltz - Wang and Kultz - 2016_1 |
| Plastin-1 Controls Stereocilia Diameter by Transforming Actin Filament Packing from Hexagonal to Liquid | | | Barr-Gillespie - Stereocilia Crosslinker Targeted Data |
| Protein Translation Study Comparing Ribosome Occupancy and Protein Synthesis During Chemotherapeutic Response | | | Wiita - Protein Translation Model SRM data |
| Impact of cystinosin glycosylation on protein stability by differential dynamic SILAC | | | Guerrera - 3SDXiS |
| Photosynthesis-related phosphopeptides in Synechocystis 6803 | | | UTurku - Angeleri_JProtRes_2016 |
| An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinases | | | MIB-PRM paper |
| An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinases | | | UCSF-MSF MIB-PRM paper |
| Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanoma | | | Liebler - Melanoma Paper |
| Rtoichiometric surface density model | | | Lund U. IMP - Stoichiometric Density Model |
| Enzyme-level response to the inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 | | | UTurku - SufR-SRM |
| Spatially and temporally resolved protein interaction networks in living cells. | | | Krogan - GPCR-APEX |
| Protein quantification in Synechocystis sp. PCC 6803 mutant lacking type 2 NAD(P)H dehydrogenase ndbC. | | | Muth - Synechocystis sp. PCC 68031 |
| Quantitative Proteomics Method Comparison | | | Koomen - Quant Method Comparison - H1993 Tx |
| Multiplexed MRM-based Protein Quantitation Using Two Different Stable Isotope Labeled Peptides for Calibration | | | Borchers Lab - Double SIS-JPR |
| Proteomic assay development for reproductive maturation state determination in Geoduck: towards a non-invasive proteomic assay for improving aquaculture | | | Nunn - Geoduck Reproduction |
| Idgf paper | | | Berg - Skyline_Analysis_Idgfs |
| PSB33 sustains Photosystem II D1 protein under fluctuating light conditions | | | UTurkuPlantBio - PSB33 |
| Targeted proteomics assays for protein biomarker candidates in ovarian cancer | | | PNNL _ SRM Ovarian Biomarkers |
| Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues | | | PNNL - Deep-Dive Blood Plasma |
| Mutant SPOP Proteins | | | PNNL - Mutant SPOP Proteins |
| An integrative proteogenomics strategy to identify the entire protein coding potential of prokaryotic genomes | | | Wollscheid - Bartonella_Proteogenomics |
| MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experiments | | | Schilling - Longitudinal SSS |
| A Proteomics Analysis of Putative Homer-2a/b Interacting Proteins in the Mouse Brain | | | MacCoss - Homer2 Interactome |
| Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagarTMSTEC media. | | | Blackburn - E.coli_EPEC_STEC |
| A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide | | | U. of A. Mass Spec Facility - Salmonella Typhimurium |
| Quantification of Plasma proteins using PlasmaDive kit on nanoflow LC-MS system and standard flow LC-MS system | | | Kings College London (BHF Center) - PlasmaDive |
| Cellular signaling underlying GSIS in pancreatic β-cells | | | U of So Denmark - MCP-PRM_Skyline |
| Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeS | | | Lund University IMP - IdeS_activity_Human_Samples |
| The conservation of sirtuin lipoamidase activity in bacteria as a regulator of metabolic enzyme complexes | | | Cristea - CobB PRM |
| MEERCAT: MULTIPLEXED EFFICIENT CELL FREE EXPRESSION OF RECOMBINANT QconCATS FOR LARGE SCALE ABSOLUTE PROTEOME QUANTIFICATION | | | EBFP - Meercat |
| DDR panel radiation response | | | Paulovich - DDR_assay_panel_radiation_response |
| Targeted proteomics in triple negative breast cancer on FFPE samples | | | La Paz_TN_Breast_Cancer |
| Targeted proteomics in triple negative breast cancer on FFPE samples | | | Chiva - La Paz_TN_Breast_Cancer |
| SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803 | | | U of Turku - SpkG-Fd5-SYN_GT |
| Nitric Oxide prevents metabolic remodeling in Yfh1-deficient cells. | | | U. of Lleida - Yeast |
| JoVE | | | Schilling - JoVEsuccBSA |
| Measurement by a Novel LC-MS/MS Methodology of Vitamin D–Binding Protein | | | Vitek - Vitamin D |
| Curated DIA assay for consistent ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus) | | | Li et al. (2018) Mol. Cell. Proteomics |
| Curated DIA assay for consistent ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus) | | | KueltzLab - JoLi-01 |
| Targeted proteomics of HDL in T2D | | | Vaisar - HDL_T2D_PlosOne |
| Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (... | | | Study_9S |
| Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (... | | | Study_9S |
| Global, site-resolved, quantitative analysis of the yeast redoxome | | | Warscheid Lab - yeast_oxICAT |
| Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cells | | | Pou4f3-Gfp FACs DIA |
| Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cells | | | Barr-Gillespie - Pou4f3-Gfp FACs DIA |
| Monitoring molecular contaminants and interferences in proteomic data sets | | | Amgen - Molecular Contaminants |
| Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damage | | | Paulovich - FANCD2_immunoMRMassay |
| ARIH2 is a novel Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection | | | CRL5_HIV_interactome |
| Discovery of a testis-specific complex TEX101-DPEP3 and selection of its disrupting antibodies | | | Diamandis Lab - Schiza et al., TEX101-DPEP3 protein complex discovery and validation |
| Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements | | | Ecoli_PRM_Phosphoproteomics |
| Automating Multidimensional Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry Data Analyses Using Skyline | | | MacLean - Baker IMS |
| PknG physiological substrates | | | Blackburn Lab - PknG physiological substrates |
| Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway | | | PNNL - EGFR_MAPK pathway targeted phosphorylation |
| Serum glycoprotein biomarker validation for esophageal adenocarcinoma - Ochsner cohort dataset | | | QIMR Berghofer - EAC LeMBA Validation Ochsner Cohort |
| Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort dataset | | | QIMR Berghofer - EAC LeMBA Validation PROBE-NET Cohort |
| Identification of functional TEX101 interactome through proteomic profiling of human spermatozoa homozygous for a missense variant rs35033974 | | | Diamandis Lab - Schiza et al. TEX101 polymorphism |
| Targeted Quantification of the Peroxisome Proteome during Human Cytomegalovirus Infection | | | Cristea Lab - Peroxisome PRM HCMV |
| Global Characterization of Human IgG1 under Oxidative Stresses—Combining dual independent protease digestions and LC-HRMS Data Independent Acquisition (DIA) | | | Catalent - Tratuzumab Global Characterization |
| Targeted proteomics to map prognostic signature proteins in oral cancer | | | PaesLeme - SRM Saliva |
| Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells | | | PNNL - Carrier-assisted targeted proteomics |
| Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements | | | U of Tuebingen - Ecoli_PRM_Phosphoproteomics |
| HR-SRM-baseds analysis of mouse/human SGLT2 in kidney and heart tissue. | | | IfADo - Mustroph_SGLT2 |
| Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine Learning | | | gRED - Automated QC of Targeted MS Data |
| targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins | | | T.S. Batth et al. Metab. Eng. 2014 - A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins |
| Production of anteiso-branched fatty acids in Escherichia coli | | | B. Haushalter et al. Metab. Eng. 2014 - Production of anteiso-branched fatty acids in Escherichia coli |
| A Kinetic-Based Approach to Understanding Heterologous Mevalonate Pathway Function in E. Coli | | | Kinetic approach proteomic data |
| Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production | | | Limonene Proteomic Data |
| Modular Engineering of L-Tyrosine Production in Escherichia coli | | | Tyrosine pathway engineering proteomic data |
| Modular Engineering of L-Tyrosine Production in Escherichia coli | | | JBEI - Tyrosine pathway engineering proteomic data |
| Viscous control of cellular respiration by membrane lipid composition | | | JBEI - Viscous control of cellular respiration by membrane lipid composition |
| Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production | | | JBEI - Limonene Proteomic Data |
| A Kinetic-Based Approach to Understanding Heterologous Mevalonate Pathway Function in E. Coli | | | JBEI - Kinetic approach proteomic data |
| targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins | | | JBEI - A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins |
| Streptococcus pyogenes evades adaptive immunity through specific modification of host IgG glycosylation | | | Lund University IMP - EndoS |
| Identification of novel protein lysine acetyltransferases in Escherichia coli | | | Schilling - Wolfe_KAT_2018 |
| Mass spectrometry-based absolute quantification of 20S proteasome status for controlled ex-vivo expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells | | | IPBS-CNRS - SRM_Proteasome_2018 |
| Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible Succinylation | | | BrownAdiposeTissue |
| Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible Succinylation | | | Schilling - BrownAdiposeTissue |
| Mechanical force induces rapid phosphorylation dependent signaling in Xenopus embryos | | | Cristea Lab - Xenopus_PRM |
| Monitoring the incorporation of fluoritnated tryptophan | | | Kruh-Garcia Lab - Rv1187 with Fluorinated Tryptophan |
| Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS | | | Macquarie U - Glycan Isomer Discrimination Product Ions |
| Enhanced validation of antibodies for research applications | | | KTH Uhlen Lab - Western blot |
| Detection of Six Commercially Processed Soy ingredients in an Incurred Food Matrix Using Parallel Reaction Monitoring | | | Nebraska U FARRP - Soy Targeted Method Development |
| Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnostics | | | NantOmics - Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnostics |
| Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae | | | Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae |
| Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae | | | Duke Proteomics Core - Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae |
| A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification | | | PNNL - A targeted mass spectrometric assay for hepcidin |
| Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells | | | PNNL - Carrier-assisted LC-SRM |
| Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics | | | U Bern - Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics |
| 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 antiatheros... | | | UPF CRG - ApoB100-2018 |
| Plasmalogen Quantification during Human Cytomegalovirus Infection | | | Cristea Lab - Plasmalogen HCMV |
| Single-point Calibration | | | MacCoss - Single-point Calibration |
| ASY1 in vitro phosphorylation | | | MPIPZ - ASY1 in vitro phosphorylation |
| ATI in Ancient Wheats | | | Leibniz Institute - ATI in Ancient Wheats |
| A rapid methods development workflow for high-throughput quantitative proteomic applications | | | JBEI - Workflow |
| Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism | | | JBEI - Mitch Thompson |
| Discovery and quantification of non-human proteins in human milk | | | Utrecht U - Discovery and quantification of non-human proteins in human milk |
| Protein-based Cardiogenic Shock Patient Classifier | | | UPF CRG - XOC_PRM |
| Improving Precursor Selectivity in Data Independent Acquisition Using Overlapping Windows | | | MacCoss - Improving Precursor Selectivity in Data Independent Acquisition Using Overlapping Windows |
| Multiplex assay for quantification of acute phase proteins and immunoglobulin A in dried blood spots | | | U. Masaryk-Vidova et al. JPR.2018 |
| Discovery and qualification of serum protein biomarkers for cholangiocarcinoma diagnosis | | | QIMRBerghofer - Cholangiocarcinoma serum biomarker MRM-MS |
| Isotopologue multi-point calibration for proteomics biomarker quantification in clinical practice | | | UPF CRG - ImCal |
| The Human Secretome | | | KTH Uhlen Lab - The Human Secretome |
| Search for synaptic biomarkers of Alzheimer’s disease | | | UPF CRG - Sant Pau_AD synaptic |
| A dataset describing a suite of novel antibody reagents for the RAS signaling network | | | Paulovich - RAS_immunoMRM_Antibody_Development |
| Comparative phosphoproteomic analysis reveals a decay of ABA signaling in barley grains during after-ripening | | | TUAT BASE - Comparative phosphoproteomic analysis barley grains_ABA |
| Quantitative assay of targeted proteome in trichome glandular cells using large-scale selected reaction monitoring strategy | | | Ehime HBFP - Tomato TGC |
| Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates | | | JBEI - Thomas Eng et al |
| Juvenile geoduck ctenidia tissue after summer deployment | | | UW Roberts Lab - Geoduck-OA-eelgrass |
| PRM-deep: The absolute quantification of transcription factors and membrane proteins central to the unfolded protein response using multiplexed high-resolution targeted proteomics | | | Ahrends Lab - Signaling targeted proteomics |
| Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning | | | JBEI - Beller DBTL-ML manuscript |
| Measurement of Nrf2-Regulated Antioxidant Response Proteins as Potential Biomarkers for Radiation Injury Assessment | | | UCLA Loo Lab - bone marrow PRM |
| Pharmacokinetic analysis of a novel human EGFRvIII:CD3 bispecific antibody in plasma and whole blood using a high-resolution targeted mass spectroscopy approach | | | Pharmacokinetic analysis of a novel human bispecific antibody |
| Pharmacokinetic analysis of a novel human EGFRvIII:CD3 bispecific antibody in plasma and whole blood using a high-resolution targeted mass spectroscopy approach | | | Duke Proteomics Core - Pharmacokinetic analysis of a novel human bispecific antibody |
| Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differences | | | UW Roberts Lab - gigas-DNR-proteomics |
| Method for Quantifying Protein Methylation Utilizing DIA-MS | | | Van Eyk - Methylation Methods |
| Exploring Non-Canonical Terpene Space With a Heterologous Lepidopteran Mevalonate Pathway | | | JBEI - Exploring Non-Canonical Terpene Space With a Heterologous Lepidopteran Mevalonate Pathway |
| Targeted Mass Spectrometry of Brain and Pancreatic tissues | | | KTH Uhlen Lab - CZI |
| N-terminal amino acid identification using targeted mass spectrometry | | | Macquarie U Jaschke Lab - N-terminal amino acid identification |
| Target Expression Profiling Identifies FLT3 as a BiTE® Target for Acute Myeloid Leukemia | | | Amgen - FLT3 MS1 Areas in Cerebellum |
| Utilisation of a dextran ladder to standardise PGC-LC-MS-based glycomics | | | Macquarie U - Dextran ladder to standardise PGC-LC-MS-based glycomics |
| Homeostatic and Interferon-induced gene expression represent different states of promoter-associated transcription factor ISGF3 | | | Decker Lab - STAT1, STAT2, IRF9 BioIDs |
| Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability | | | PNNL - Kinase-substrate pair study in breast cancer |
| IFI16 pyrin oligomerization mediates antiviral actions | | | Cristea - IFI16 Oligomerization |
| Versatile polyketide biosynthesis platform for controlled production of aromatic compounds in yeast | | | JBEI - Tadas |
| Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor | | | JBEI - D. D. Luu et al. RaxX |
| Endo-Lysosomal Proteins and Ubiquitin CSF Concentrations in Alzheimer’s and Parkinson’s Disease | | | U of Gothenburg - PRM-MS EndoLys ADPD |
| In vitro kinase assay of human FLNc domain 18-21 with Akt and PKC alpha | | | Warscheid Lab - In vitro kinase assay of hFLNc domain 18-21 |
| International Ring Trial of a Broad-Spectrum Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis [System Suitability Files] | | | Duke - p400HR Ring Trial System Suitability |
| Validation of N-terminal Labeling Mass Spectrometry for Characterization of Partially Hydrolyzed Gluten Proteins | | | Nebraska U FARRP - Validation of N-terminal Labeling MS for Gluten |
| Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages | | | MFPL - Ammerer Lab - Novel interconnections of HOG signaling |
| Rebuilding core abscisic acid signaling pathways of Arabidopsis in yeast | | | Kuster Lab - Ruschhaupt et al. 2019 |
| Milk glycopeptide across lactation | | | Utrecht U Biomass - Milk glycopeptides |
| Matched Matrix Calibration Curves | | | matched matrix cal curves |
| Light-dependent N-terminal phosphorylation of LHCSR3 and LHCB4 are interlinked in Chlamydomonas reinhardtii | | | IBBP Münster Hippler Lab - Chlamy HL |
| PrEST resource | | | KTH Uhlen Lab - PrEST resource |
| Developing a robust assay to monitor and quantify key players of metabolic pathways during adipogenesis by targeted proteomics | | | Ahrends Lab - Metabolic pathways targeted proteomics |
| An automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbes | | | JBEI - Automated Proteomic Sample Preparation |
| Cell cycle validation | | | Cristea Lab - Heart Proteome |
| Targeted MRM assay Complement System in health and infectious disease | | | Radboud University - Targeted LC tandem MS MRM of complement system in health and infectious disease |
| A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships | | | Wollscheid - Listeria monocytogenes |
| ARIH2 is a novel Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection | | | UCSF Krogan Lab - CRL5_HIV_interactome |
| A targeted strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancer | | | UCSF Krogan Lab - Ovarian cancer biomarker |
| Analysis of endogenous peptides released from osteoarthritic cartilage unravels novel pathogenic markers | | | INIBIC - Neopeptides OA cartilage |
| Light-dependent dynamics of phosphorylation of the thylakoid structural protein CURT1B | | | U. Turku Plant Biology - CURT1B |
| Unique-region phosphorylation targets LynA for rapid degradation, tuning its expression and signaling in myeloid cells | | | Freedman Lab - LynA |
| Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells | | | PNNL - Sporadic ERK pulses drive non-genetic resistance |
| Matched Matrix Calibration Curves | | | MacCoss - matched matrix cal curves |
| Prion MRM assay development and clinical study | | | Carr - CSF_Prion_TSQQuantiva_directMRM |
| Absolute Quantification | | | UFOP - EsoCAT_LN1 |
| Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow Cytometry | | | TNN PRM Manuscript |
| Peptide signature for the fast detection of bacterial species in Urinary Tract infections using LC-MS | | | CRCHUL Droit Lab - Bacterial species identification in urine |
| Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow Cytometry | | | Gundry Lab - TNN PRM Manuscript |
| HDL proteome remodeling post-stroke | | | OHSU Pamir Lab - High-density lipoprotein proteome post-stroke |
| Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase | | | JBEI - Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase |
| Urinary PRM analysis of early type 1 diabetes | | | U of Toronto Diamandis Lab - Urinary peptidomics in type 1 diabetes |
| Multiplexed MRM concentration measurements of >200 endogenous proteins in dried blood spots for biomarker discovery and validation | | | U Victoria - MRM assay development in DBS |
| Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics | | | Skyline for Small Molecules, A Unifying Software Package for Quantitative Metabolomics |
| Personalized human milk proteome | | | Utrecht U Biomass - Personalized milk proteome |
| Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics | | | Duke Proteomics Core - Skyline for Small Molecules |
| Chemical and phosphoproteomics illuminate the cellular mode of action of AKT inhibitors | | | TUM Kuster Lab - Wiechmann et al. 2019 |
| Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes | | | Gundry Lab - CM Glyco Diff Manuscript |
| FeS levels in Arabidopsis plants expression a mutated NEET protein | | | Gehrke Proteomics Center - Mittler Fe-S proteins |
| Antibody-free multiplex measurement of 23 human cytokines in primary cell culture secretome using targeted multiple reaction monitoring mass spectrometry | | | QIMRBerghofer - Cytokines in primary cell culture secretome |
| Comprehensive Detection of Isopeptides between Human Tissue Transglutaminase and Gluten Peptides | | | Leibniz Institute - Isopeptide analysis |
| Min protein in vitro protein expression kinetics | | | TUDelft Danelon Lab - Min project |
| Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision QPrEST-Based SRM Assay | | | KTH Uhlen Lab - APO-project (Effect1) |
| PRM of Nth1 phospho-peptides | | | U of Geneva Loewith Lab - 20191004_AGC_kinases |
| Targeted assay for differentiation and monitoring the concentration of GDF 8 (Myostatin) and GDF11 in mouse serum | | | ISAS - Quantification of GDF8 and GDF11 in serum |
| Characterization and relative quantitation of wheat, rye and barley gluten protein types by LC-MS/MS | | | Leibniz Institute - Characterization of gluten protein types |
| Identification of an intronic enhancer in the tilapia glutamine synthetase gene. | | | Kim and Kültz (2020) Sci. Rep. |
| Identification of an intronic enhancer in the tilapia glutamine synthetase gene. | | | KueltzLab UCDavis - Kim01 |
| ACE over expression in myeloid cells 1 increases oxidative metabolism and cellular ATP | | | Cedars-Sinai Parker Lab - ACE10 Bernstein Study |
| Differences in amino acid sequences of high-molecular weight glutenin subunits in spelt and emmer compared to common wheat by mass spectrometry of in-gel digests | | | Leibniz Institute - HMW-GS in Ancient Wheats |
| Characterization of signaling pathways associated with pancreatic β-cell adaptive flexibility in compensation of obesity-linked diabetes in db/db mice | | | U of So Denmark Martin Lab - MCP PRM Skyline dbdb |
| PRM method for detection of both casein and whey milk allergens from baked food matrix | | | Nebraska U FARRP - PRM Method for Detection of Casein and Whey Allergens |
| Targeted metabolomics profiling of acute myocardial infarction risk human sera | | | Korea U - Targeted metabolomics of acute myocardial risk Sera |
| Assessment of Serological Early Biomarker Candidates for Lung Adenocarcinoma by using Multiple Reaction Monitoring-Mass Spectrometry | | | NCKU - 2019_MRM_35pep |
| CRK2-mediated control of ROS production by phosphorylation of the RBOHD C-terminus in Arabidopsis | | | MPIPZ - MW_SaKi |
| Identification of Putative Early Atherosclerosis Biomarkers by Unsupervised Deconvolution of Heterogeneous Vascular Proteomes - DIA-MS confirmation of FP-lesion markers | | | Cedars-Sinai Parker Lab - CAM_DIA_FPplex |
| Arbacia sperm chemosensation protein components | | | Ruhr University - Arbacia sperm chemosensation |
| Quantitative proteomics analysis of Angiostrongylus vasorum-induced alterations in dog serum | | | Functional Genomics Center Zurich - p2242 |
| Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass Spectrometry | | | Waters - Quantitative Analysis XL Peptides |
| MS-GUIDE | | | Wollscheid - MSGUIDE |
| Detection of head and neck cancer based on longitudinal changes in serum protein abundance | | | PNNL - Detection of head and neck cancer based on longitudinal changes in serum protein abundance |
| Identification of cGAS post-translational modifications | | | Cristea Lab - cGAS PTM |
| pUL37 and pUL13 interaction validation | | | Princeton University Cristea Lab - Inter-ViSTA |
| Targeted Mass Spectrometry of a Clinically Relevant PSA Variant from Post-DRE Urines for Quantitation and Genotype Determination | | | Eastern Virginia Med School - Otto et al Proteomics Clinical Applications |
| Data independent acquisition-based proteomics reveals a multi-scale picture of gene expression in Escherichia coli | | | BayBioMS - Ludwig_Ecoli_PQP_Absolute_AQUA_RiboSeq |
| A mouse brain-based multi-omics integrative approach reveals potential blood biomarkers for ischemic stroke | | | Vall d'Hebrón Institute - A mouse brain-based multi-omics integrative approach reveals potential blood biomarkers for ischemic stroke |
| Parallel reaction monitoring assay development for multiple sclerosis biomarkers in cerebrospinal fluid. | | | University of Bergen Berven Lab - PRM assay project CSF |
| Identification of Isopeptides Between Human Tissue Transglutaminase and Wheat, Rye, and Barley Gluten Peptides | | | Leibniz Institute - Isopeptides of gluten protein types |
| PINE: An Automation Tool to Extract & Visualize Functionally Enriched Networks from Mass Spectrometry-Based Proteomics Datasets | | | Cedars-Sinai Van Eyk Lab - PINE |
| LipidCreator: A workbench to probe the lipidomic landscape | | | Ahrends Lab - LipidCreator_HumanPlatelet_application |
| Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds | | | P100 |
| Global Chromatin Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds | | | GCP |
| Mapping of the multiple myeloma cell surface N-glycoproteome and targeted validation
in patient samples uncovers immunotherapy targets | | | Med College Wisconsin - Medin MM vs BCell |
| Interspecies assertiveness of Lactobacillus curvatus and Lactobacillus sakei in sausage fermentations | | | BayBioMS - Bacteriocin peptides Lactobacillus curvatus |
| Global Chromatin Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds | | | LINCS PCCSE GCP 2020 |
| Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds | | | LINCS PCCSE P100 2020 V.1 |
| Proteomics of osmoregulatory versus general stress responses in threespine stickleback gills | | | Li and Kültz (2020) Integ. Comp. Biol. |
| Proteomics of osmoregulatory versus general stress responses in threespine stickleback gills | | | KueltzLab UCDavis - JoLi02 |
| Clinical application of multiple reaction monitoring-mass spectrometry to HER2 measurements as a potential diagnostic tool for breast cancer therapy | | | Seoul National University - Clinical application of multiple reaction monitoring-mass spectrometry to HER2 measurements as a potential diagnostic tool for breast cancer therapy |
| Acarbose improves late-life physical function in mice of both sexes, but rejuvenates cardiac structure and lipid profile in males only | | | MacCoss - Acarbose Paper |
| Targeted FLNc S2233 S2236 phosphorylation assay | | | Warscheid Lab - Targeted FLNc S2233 S2236 phosphorylation assay |
| MitoPlex: A Targeted Multiple Reaction Monitoring Assay for Quantification of a Curated Set of Mitochondrial Proteins | | | Cedars-Sinai Parker Lab - Mitoplex-Mouse |
| Accurate MS-based Rab10 phosphorylation stoichiometry determination as a readout for LRRK2 activity in Parkinson’s disease | | | MPI - MS-based clinical assay for LRRK2 phosphorylated Rab10 occupancy calculation |
| Malignant pleural mesothelioma targeted proteomics signature from blood | | | OSU - Meso20 |
| Antibody-free targeted proteomics assay for absolute measurement of α-tubulin acetylation | | | QIMRBerghofer - Alpha-tubulin acetylation estimation |
| Highly Multiplex Targeted Proteomics Enabled by Real-Time Retention Time Alignment | | | MacCoss - Real-Time Chromatogram Alignment |
| PCSK9 55 test | | | OHSU Proteomics Shared Resource - Fazio Lab |
| Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer | | | Protypia - Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer |
| Tissue-based Proteomic Classifier for Early Prediction of Prostate Cancer Progression | | | PNNL - Prostate_Biomarker_PNNL_2019 |
| Translation Error Clusters Induced by Aminoglycoside Antibiotics | | | Rodnina - Translation Error Clusters Induced by Aminoglycoside Antibiotics |
| Antibody RING-Mediated Destruction (ARMeD) of endogenous proteins | | | U of Dundee Hay Lab - NEDP1_ARMeD_knockdown |
| Marked increased production of acute phase reactants by skeletal muscle during cancer cachexia | | | U of Liege - InterCachectomics project |
| Discovery of biomarkers associated with the risk of short- and long-term relapse after infliximab withdrawal in Crohn’s patients: a proteomics-based study | | | U of Liege - STORI study |
| Phosphoproteomic Effects of Acute Depletion of PP2A Regulatory Subunit Cdc55 | | | U of Geneva Loewith Lab - Cdc55-AID |
| Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis | | | U Victoria - Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis |
| Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing | | | BayBioMS - Merits of proteomics for SARS-CoV2 research and testing |
| Phage Phix174 - Wildtype and engineered proteome | | | Macquarie U Jaschke Lab - Decompressed PhiX174 Proteomics |
| Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma. | | | BRFAA - Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma |
| PRM Quantification of TET2, GATA3 and ER | | | CRUK Proteomics Core - TET2_Project |
| Seasonally relevant changes in UV-A alter neurohormone levels and behavior via cOpsin1 | | | Max Perutz Labs - Tessmar-Raible - c-opsin1 |
| Identification of candidate circulating glucocorticoid response biomarkers in humans using a proteomic approach | | | QIMRBerghofer - Identification of candidate circulating glucocorticoid response biomarkers in humans using a proteomic approach |
| S-Adenosylmethionine Depletion Activates La Ribonucleoprotein Domain
Family Member 1 to Induce Protein Translation | | | Cedars-Sinai Van Eyk Lab - LARP1_Paper |
| ADAM17 cytoplasmic domain modulates Thioredoxin-1 | | | LNBio Mas Lab - ADAM17 Trx-1 |
| OSCC saliva peptidomics | | | LNBio Mas Lab - PaesLeme_SalivaPeptidomics |
| Development of a potential salivary biomarker panel for Oral Squamous Cell Carcinoma using a proteomics-based approach. | | | PGIMER Arnab Lab - Targeted MS-OSCC saliva |
| Validation of MiXCR/HIGH-VQUEST pipeline for the selection of clonotypic peptides in MM cell lines | | | Radboud University Medical Center - COMMPASS_database_study_validation |
| Targeted proteomics measurements for Genetically controlled membrane synthesis in liposomes | | | TUDelft Danelon Lab - pGEMM project |
| Rat sciatic nerve injury, axoplasm | | | UCSF-MSF - Axonal injury |
| Detection of flg22 peptide upon treatment with different Arabidopsis root-derived bacterial supernatant | | | MPIPZ - PSL_KaMa |
| An Optimised Proteomics Workflow for the Detection of Small Proteins. | | | U Greifswald - SPP2002_SmallProteins - BSubtilis_NC000964_3 |
| Combining label-free and label-based accurate quantifications with SWATH-MS: comparison with SRM and PRM for the evaluation of bovine muscle type effects. | | | U of Strasbourg LSMBO - SWATH-MS_PRM_SRM_BovineMuscles |
| Comparative quantitative LC-MS/MS analysis of 13 amylase/trypsin inhibitors in ancient and modern Triticum species | | | Leibniz Institute Biopolymers - Quantitation of 13 ATIs in ancient and modern wheat species |
| Temporal quantitative proteomics of mGluR-induced protein translation and phosphorylation in neurons | | | Utrecht U Targeted Proteomics - vanGelder_et_al._2020 |
| Longitudinal Protein Profiling using Targeted Proteomics and Recombinant Standards | | | KTH Uhlen Lab - Wellness PRM - Pooled samples and dilution series |
| Impaired processivity of translation elongation is a bottleneck for PURE system self-replication | | | TUDelft Danelon Lab - pTFM1 project |
| Quantitative MRM Assays for the Large-scale Measurement of Proteins from 20 Mouse Tissues | | | U Victoria - Quantitative MRM Assays for the Large-scale Measurement of Proteins from 20 Mouse Tissues |
| Characterization and statistical modeling of glycosylation changes in sickle cell disease and trait | | | U of Nebraska Medical Center Gundry Lab - Sickle Cell Manuscript |
| Dynamic glycoproteomics identifies a role of N-glycosylation and Galectin-1 on myogenesis and muscle development | | | Macquarie U Glyco Lab - Dynamic glycoproteomics identifies a role of N-glycosylation and Galectin-1 on myogenesis and muscle development |
| IP-MS Analysis of ESX-5 and ESX-1 Substrates Enables Mycobacterial Species Identification | | | Tulane U Biochem Hu Lab - PRM for EsxN and CFP10 |
| Data used to demonstrate Peptide Correlation Analysis (PeCorA) | | | Meyer Lab MCW - PeCorA |
| A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus | | | Kueltz Lab UCDavis - LMR0015_Oreni-Kidney |
| High throughput targeted proteomics assays for quantifying large-scale pathway proteins in Pseudomonas putida KT2440 | | | AgileBioFoundry - High throughput LC-SRM analysis of large-scale pathway proteins in P. Putida KT2440 |
| Supplemental data files Thor et al 2020 | | | Sainsbury Lab TSL Proteomics - Thor et al 2020 |
| Development of mass spectrometry-based targeted assay for the diagnosis of novel SARS-CoV-2 coronavirus from clinical specimens | | | Mayo Clinic Pandey Lab - PRM diagnosis of COVID-19 |
| PRM_60min | | | Group Fleury - Fleury_SARS-CoV-2 |
| BAC-DROP: Rapid digestion of proteome fractionated via dissolvable polyacrylamide gel electrophoresis and its application to bottom-up proteomics workflow | | | Ehime HBFP - BACDROP |
| Genome-scale metabolic rewiring to improve titers, rates and yields of the non-native non-ribosomal peptide product indigoidine at scale | | | JBEI - Genome-scale rewiring indigoidine |
| Proteomic characterization of human neural stem cells during in vitro differentiation | | | Institute of Animal Physiology and Genetics LAPA - SWATH NSC Skyline |
| Quantification of HER2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) and Frozen Breast Cancer Tissues | | | Paulovich - HER2_cellularity_breast_cancer_tissue_frozen_FFPE_immunoMRM |
| Targeted mass spectrometry-based assays for multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling | | | Paulovich - Ras_assay_development |
| The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistance | | | PNNL - PTRC |
| ‘The long tail of Covid 19’ - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients | | | University College London BMSC - Covid19 post infection |
| Assessment of streptavidin peptides shed from beads | | | U of Nebraska Medical Center Gundry Lab - AVIDITY |
| Targeted MRM assay Complement System for Complement deficiencies | | | Radboud University Medical Center Translational Metabolic Lab - Targeted MRM assay Complement System for Complement deficiencies |
| Microwave oven-assisted derivatization of histone proteoforms using trimethylacetic anhydride | | | CEITEC MU Core Facility - TMA alkylation PRM |
| A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling | | | TUM SIeber Lab - Phosphoaspartate probe for P. aeruginosa interkingdom signaling study |
| COVID_Plasma_MRM | | | IIT Bombay Proteomics - COVID_PLASMA |
| Targeted mass spectrometry quantification of total soy protein residues from commercially processed ingredients for food allergen management | | | Nebraska U FARRP - Soy Quantitative Method |
| Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients | | | U of Ghent Pharma Biotech Lab - Supplementary Data |
| Improving SILAC quantification with data independent acquisition to investigate bortezomib-induced protein degradation | | | U of Pennsylvania Garcia Lab - SILAC-DIA |
| Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics | | | PNNL - EGFR pathway peptide standards at different DDM concentrations |
| The reproductive toxicant acrylamide modulates the mouse epididymal proteome to drive alterations to the sperm epigenome and dysregulate embryo development. | | | U of Newcastle Nixon Lab - Natalie - Nature Comms - Acrylamide PRM |
| IgG M-protein quantification by PRM in blood of multiple myeloma patient | | | Rapid Novor - MM P1 Tech |
| Validation of detected viral peptides from COVID-19 nasopharyngeal swabs samples | | | IIT Bombay Proteomics - COVID_Swab_MRM |
| Targeted quantification of phosphorylation sites in S. macrospora wildtype and STRIPAK-mutants | | | ISAS Protein Dynamics - Stein et al. KIN3 2020 |
| Tissue plasminogen activator effects on fibrin volume and the ocular proteome in a juvenile rabbit model of lensectomy | | | Medical College of Wisconsin Kassem Lab - Ocular Proteome - tPA |
| Lysosomal targetomics in ghrKO mice reveals a role for chaperone-mediated autophagy in shaping the nucleocytosolic acetyl-coA production pathway | | | MacCoss - Lysosome and Liver DIA Quant |
| Factor H and related proteins in AMD | | | U of Manchester Unwin Lab - FH Skyline |
| N-terminal Labeling of Bench-Scale Brewing Samples | | | Nebraska U FARRP - Tracking Gluten throughout Brewing Using N-Terminal Labeling Mass Spectrometry |
| Bear Serum Proteomics | | | MacCoss - Grizzly Bear Serum DIA Proteomics |
| Smoothened Transduces Hedgehog Signals via Activity-Dependent Sequestration of PKA Catalytic Subunits | | | UCSF Krogan Lab - Smo_phospho |
| Shadow ORFs illuminated: long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection | | | BayBioMS - Kreitmeier_OLG_PSE |
| Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring in vivo Arginine Isotope Incorporation in Alzheimer’s Disease Mouse Models | | | CE-MS for Measuring in vivo Arginine Isotope Incorporation in Alzheimer’s Disease Mouse Models |
| Capillary Electrophoresis-High Resolution Mass Spectrometry for Measuring in vivo Arginine Isotope Incorporation in Alzheimer’s Disease Mouse Models | | | Duke Proteomics Core - CE-MS for Measuring in vivo Arginine Isotope Incorporation in Alzheimer’s Disease Mouse Models |
| Endogenous THBS1 is C-mannosylated by human induced pluripotent stem cells. | | | U of Heidelberg Mass Spec Core - Cirksena et. al. Implications of ADAMTS16 C-Mannosylation on Optic Fissure Fusion |
| Identification of proteins deregulated by platinum-based chemotherapy as novel biomarkers and therapeutic targets in non-small cell lung cancer | | | QUT CARP - NSCLC_Cisplatin |
| Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium | | | U of Pennsylvania Garcia Lab - dictyostelium_histone_ptms |
| Mouse Heart SS31 Targeted Proteomics | | | MacCoss - SS31-PTM |
| PRMT6 substrate specificity analysis | | | U of New South Wales Wilkins Lab - PRMT6 substrate specificity analysis |
| Post-translational control of ACONITASE 3 by reversible phosphorylation affects mitochondrial dysfunction responses in Arabidopsis | | | University of Turku Plant Biology - ACONITASE 3 |
| Utilizing Skyline to Analyze Lipidomics Data Containing Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry Dimensions | | | NCSU Baker Lab - Lipid Libraries |
| Regulation of electrogenic Na+/HCO3- cotransporter 1 (NBCe1) in mouse cortical astrocytes and its dependence on m-TOR mediated phosphorylation of Ser245. | | | BayBioMS - Giannaki_NBCe1_pospho_proteomics |
| Targeted plasma proteome analysis using vacuum-dried protein standards | | | KTH Uhlen Lab - SIS-PrESTs Stability |
| Comparison of temperature-induced liver proteome changes in threespine stickleback (Gasterosteus aculeatus) by data-independent acquisition mass spectrometry | | | Kueltz Lab UCDavis - BL0002_Gasac-Liver |
| Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus | | | Kueltz Lab UCDavis - LMR0015_Oreni-Gill |
| Cross species kinase profiling | | | Pfizer Biomarkers Mass Spec - Cross species kinase profiling in spleen |
| Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping | | | UC Davis Parker Lab - Targeted GVP |
| Comparison of acute temperature-induced liver proteome Changes in threespine stickleback (Gasterosteus aculeatus) by data-independent acquisition mass spectrometry | | | Kueltz Lab UCDavis - BL0003_Gasac-Liver |
| MRM for validation of Brain tumor biomarkers | | | IIT Bombay Proteomics - Brain_Tumor_marker_MRM |
| Mood disorder (MDD and BD) Plasma proteomic Study | | | Seoul National University - Quantitative proteomic approach for discriminating major depressive disorder and bipolar disorder by multiple reaction monitoring-mass spectrometry |
| Quantitative Proteomics Reveals that the OGT Interactome is
Remodeled in Response to Oxidative Stress | | | JHU Zachara Lab - The oxidative-stress induced OGT interactome |
| Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds | | | P100_GctMaker |
| Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological Backgrounds | | | LINCS PCCSE P100 2020 |
| Common modular workflow for precise mid- and high-throughput proteomics of blood biofluids | | | Cedars-Sinai Van Eyk Lab - Modular Workflow |
| Quantification of Raloxifene Specific 471 Da Adducts in CYP3A4 and P450-Reductase | | | MacCoss - CYP3A4 Raloxifene |
| A microbial supply chain for production of anti-cancer drug vinblastine | | | JBEI - J. Zhang et al. - vinblastine paper |
| Targeted Phosphoinositides Analysis Using High Performance Ion Chromatography-Coupled Selected Reaction Monitoring Mass Spectrometry | | | ISAS Protein Dynamics - 2021_Targeted_Lipidomics_PIPsIC-MS_Cheung |
| Towards zero variance in proteomics - positive pressure FASP in 96-well format (PF96) enables highly reproducible and time-efficient analysis of sample cohorts | | | ISAS Protein Dynamics - Loroch_et_al_PF96_Mouse_Heart_Targeted_Short_Gradient |
| Biomarker Discovery in FFPE tissues by SRM | | | Roche pRED proteomics - Triple-negative breast cancer FFPE tissues |
| A Workflow Towards The Reproducible Identification and Quantitation of Protein Carbonylation Sites in Human Plasma | | | U of Leipzig AG Bioanalytics - A Workflow Towards The Reproducible Identification and Quantitation of Protein Carbonylation Sites in Human Plasma |
| Quantitation of frataxin-related proteins in I151F mice | | | University of Lleida Biochemistry of Oxidative Stress - I151F characterization |
| Alzheimer's Disease Isomerization | | | MacCoss - AD Isomer Paper |
| Proteomic analysis of spermatozoa reveals caseins play a pivotal role in preventing short-term periods of subfertility in stallions | | | U of Newcastle Gibb Lab - Casein and short term stallion fertility fluctuations |
| Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring | | | MacCoss - Q-OT vs Q-LIT submission |
| C.auto_3gas_absquant: Anchor protein absolute quantification | | | U of Tartu GasFermTEC - Anchors |
| C.auto_3gas_absquant: Label-free proteome-wide absolute quantification | | | U of Tartu GasFermTEC - Label-free |
| C.auto_3gas_absquant: Spike-in SIL-protein stock absolute quantification | | | U of Tartu GasFermTEC - PRM |
| Mapping interactome networks of FOSL1 and FOSL2 in human Th17 cells | | | Turku Bioscience Lahesmaa Group - FOSL |
| Cell cycle phosphorylation dynamics in vivo reveals switch-like control of intrinsic disorder | | | Utrecht Univeristy Biomolecular MS and Proteomics - Single embryo phosphoproteomics - PRM |
| Analytical Comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cells | | | ISAS Protein Dynamics - 2021_Insulin signaling pathway in fat cells_TingtingLi |
| GFAP and MBP peptides in Traumatic Brain Injury | | | Gryphon Bio - GFAPMBP_TBI_PEPTIDES |
| Targeted validation of interaction between ErbB4 JM-a isoform and β1 integrin | | | University of Turku Elenius Lab - B1_integrin |
| The global Proteome and Ubiquitinome of bacterial and viral co-infected Bronchial Epithelial Cells | | | U Greifswald Inst. Microbiology MS Lab - Co-infection_16HBE |
| Multiple reaction monitoring (MRM) based data for targeted validation of proteins in Labeo rohita | | | IIT Bombay Proteomics - MRM_Rohu_Peptide_Atlas_Validation |
| Validation of proteins showing significant dysregulation from shotgun proteomics experiments in longitudinal plasma samples of COVID-19 patients | | | IIT Bombay Proteomics - Longitudinal plasma MRM |
| Targeted validation of significantly altered semen proteins in COVID-19 patients | | | IIT Bombay Proteomics - COVID-19_Semen_Proteomics_Host |
| Targeted Detection of SARS-CoV-2 Protein Variants by Mass Spectrometry | | | Mayo Clinic Pandey Lab - Targeted Detection of SARS-CoV-2 Protein Variants |
| Targeted Proteomics Using Stable Isotope Labeled Protein Fragments Enables Precise and Robust Determination of Total Apolipoprotein(a) in Human Plasma | | | KTH Uhlen Lab - LPA |
| Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantification | | | Ehime HBFP - ALACAT |
| Optimized liquid and gas phase fractionations increase HLA-peptidome coverage for primary cell and tissue samples | | | Carr - HLA_Melanoma_TSQQuantiva |
| Evaluation of a targeted LC-MS/MS method for the quantification of egg, milk, and peanut in food | | | US FDA SMSB - Xiong et al. Anal Bioanal Chem 2021 |
| Loss of DNAJC3 impairs cholesterol metabolism and mitochondrial function | | | ISAS Protein Dynamics - 2021_DNAJC3_loss_impairs_cholesterol_metabolism_and_mitochondrial_function_ChiNguyen |
| DDR2 pharmacodynamic profiling | | | Paulovich - DDR2_cell_treatment_dataset |
| The metabolome as a biomarker of aging in Drosophila melanogaster | | | MacCoss - SRM_Data-The metabolome as a biomarker of aging in Drosophila melanogaster |
| Age-Related Disruption of the Proteome and Acetylome in Mouse Hearts Correlates with Differential Loss of Function that is Attenuated by SS-31 and NMN | | | MacCoss - Age-Related Disruption of the Proteome and Acetylome in Mouse Hearts Correlates with Differential Loss of Function that is Attenuated by SS-31 and NMN |
| Quantification of the ratio between the two PsbO protein isoforms in the thylakoids lumen of Arabidopsis thaliana | | | University of Turku Plant Biology - PsbO |
| Profiling Tryptophan Catabolites of Human Gut Microbiota and Acute-Phase Protein Levels in Neonatal Dried Blood Specimens | | | U of Masaryk RECETOX - Aust Benesova et al. |
| Targeted mass spectrometry enables multiplexed quantification of immunomodulatory proteins in clinical biospecimens | | | Paulovich - IO1 immunoMRM panel |
| Targeted MRM assay Compleemntsystemfor AMD cohort | | | Radboud University Medical Center - Targeted MRM assay Complement System for AMD cohort |
| Uncovering functional protein modifications by site-resolved protein turnover (SPOT) profiling | | | TUM Kuster Lab - Zecha et al. 2020 |
| PPROM | | | Seoul National University Proteomics Core - PPROM |
| Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS) | | | NCSU Baker Lab - Pine Needle PFAS |
| WB peptide assay stability | | | MRM Proteomics - WB peptide assay stability |
| Targeted MS based multi-omic analysis of blood plasma from COVID-19 patients to predict survival | | | MRM Proteomics - COVID 270 panel |
| Multisite proteome provides insights into the biology and prognostic markers for head and neck cancer | | | LNBio Mas Lab - Projeto1_BuffyCoat-SalivaPellet_2019 |
| A comparative study of synthetic winged peptides for absolute protein quantification | | | U of Masaryk RECETOX - Benesova et al. Sci Rep 2021 Supplementary |
| Simultaneous quantitative profiling of clinically relevant immune markers in neonatal stool swabs to reveal inflammation | | | U of Masaryk RECETOX - Vidova et al. Sci Rep 2021 Supplementary |
| A hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzae | | | Sainsbury Lab TSL Proteomics - Osés-Ruiz et al |
| Plasma Protein Biomarker Model for Screening Alzheimer Disease Using Multiple Reaction Monitoring-Mass Spectrometry | | | Seoul National University - Plasma Protein Biomarker Model for Screening Alzheimer Disease Using Multiple Reaction Monitoring-Mass Spectrometry |
| 2020_BAK125_RT | | | MRM Proteomics - 2020_BAK125_RT |
| Mitochondrial inorganic polyphosphate (polyP) is a contributor towards maintaining cellular bioenergetics in SH-SY5Y cells: a proteomics and metabolomics approach | | | MacCoss - MitoPPX Paper |
| Triage of >1300 candidate biomarkers in plasma using internal standard-triggered parallel reaction monitoring mass spectrometry | | | Paulovich - ISPRM_breast_cancer_human_plasma_protein_biomarkers_early_detection |
| Ocular proteomic and transcriptomic changes with aging in response to lensectomy in a rabbit model of lensectomy with intraocular lens insertion | | | MCW Kassem Lab - Ocular proteins in an aging rabbit model of lensectomy |
| Organ wise targeted mass spectrometric analysis of proteins in Labeo rohita using SRM/MRM approach | | | IIT Bombay Proteomics - Organwise_SRM_ROHU |
| HDL proteomics on CPROBE samples | | | UW Shao Lab - CPROBE_CKD_HDL |
| SARS-CoV2 Immunocomplex by LC-MS/MS on vaccinated cohort | | | University College London BMSC - Immunocovidome assay |
| Next-generation Serology by Mass Spectrometry:Readout of the SARS-CoV-2 Antibody Repertoire | | | Northwestern Proteomics Core - Glycan_2021 |
| SigPath pSTY enrichment from cells and tissues | | | Carr - SigPath_pSTY_TSQQuantiva |
| Diagnosing pleural effusions using mass spectrometry-based multiplexed targeted proteomics quantitating mid- to high-abundance markers of cancer, infection/inflammation and tuberculosis | | | Polish Acad Sciences IBB MS Lab - 34 marker panel |
| Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach | | | Radboud University Medical Center - Neurodegenerative Disorders |
| Spatiotemporal analysis of organelle membrane contact site proteins during human virus infections | | | Princeton University Cristea Lab - Organelle Contacts & Human Viruses PRM |
| MRM quantification of circulating CFP10 | | | Tulane U Biochem Hu Lab - Quantitative MS of antigens |
| Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment Analysis | | | KTH Uhlen Lab - SARS-CoV-2 SISCAPA |
| Monitoring of histidine methylated Rpl3p | | | U of New South Wales Wilkins Lab - Hpm1 histidine methylation of Rpl3 |
| Selected reaction monitoring based analysis of proteins in liver tissue of Labeo rohita | | | IIT Bombay Proteomics - SRM_ROHU_Liver_Proteomics |
| Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity | | | NCSU Baker Lab - Smoke Inhalation and SRM 1950 |
| RGI-GOLVEN signalling promotes FLS2 abundance to regulate plant immunity | | | BayBioMS - Stegmann_GLV2_phytocytokine_peptide_Arabidopsis |
| Quantification of Soy-Derived Ingredients in Model Bread and Frankfurter Matrices with an Optimized LC-MS/MS External Standard Calibration Workflow | | | Nebraska U FARRP - Soy Quantification Method- Matrix Extension |
| Gill proteome networks explain salinity tolerance of Oreochromis mossambicus | | | Kueltz Lab UCDavis - LR0011_Oremo-Gill |
| Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline | | | 2015-Selevsek |
| Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline | | | 2015-Bruderer |
| Targeted proteomic validation of dysregulated proteins in liver tissue of Labeo rohita after of Aeromonas hydrophila infection | | | IIT Bombay Proteomics - SRM_Rohu_LiverAH |
| Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline | | | MacCoss - 2015-Bruderer |
| Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline | | | MacCoss - 2015-Selevsek |
| A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics | | | U of Ghent - LFQBenchmark across Instrument Platforms |
| Absolute quantification of influenza virus proteins | | | U of Magdeburg Benndorf Lab - Absolute quantification of influenza virus proteins-JK |
| Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning | | | NCSU Baker Lab - PFAS Library |
| Hb variants identification | | | Group Fleury - HbDIA |
| CFP10 result in Italy cohort | | | Tulane U Biochem Hu Lab - patients from Italy cohort CFP10 results |
| Relative quantification of acetylated histone peptides in HAP1 cells after treatment with MS-275 | | | Max Perutz Labs MS Facility - Seiser - Histone acetylation in HAP cells |
| Check of selected NTR peptide spectra by comparison with synthetic peptides | | | UGent VIB09 - Annelies_Bogaert |
| Preserving the phosphoproteome of clinical biopsies using a quick freeze collection device | | | Paulovich - PO4_preservation_in_PDX_tumors_MRM |
| Proteomic Analysis of Oil-Roasted Cashew Using a Customized Allergen-Focused Protein Database | | | Nebraska U FARRP - Cashew Proteome and Method Development |
| Proteomic Blueprint of the Pituitary anterior and posterior lobes for better understanding of the physiology of pituitary gland. | | | IIT Bombay Proteomics - Anterior vs Posterior Pituitary PRM |
| Improving peptide fragment ion detection using travelling wave ion mobility spectrometry with signal enhancement MSE (seMSE) | | | U of Leipzig AG Bioanalytics - seMSE |
| OE240 PFAS Method Validation | | | NCSU METRIC - 20211103 - OE240 PFAS Method Validation |
| FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standards | | | MPICBG Shevchenko Lab - FastCAT_csf_patients |
| One-Pot Isotope Dilution PRM for Quantitative Protein Heterogeneity in Red Blood Cells | | | U Victoria - One-pot Isotope Dilution PRM for Quantitative Protein Heterogeneity in Red Blood Cells |
| The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5 | | | UCSF Krogan Lab - Isl1_Maven_etal |
| Imetelstat Is a Potent Inducer of Ferroptosis That Effectively Diminishes Acute Myeloid Leukemia Burden and Delays Relapse Following Pro-Oxidant Therapy | | | QIMRBerghofer - Targeted Lipidomics - Imetelstat Is a Potent Inducer of Ferroptosis |
| Biosynthesis of polycyclopropanated high energy biofuels | | | Pablo Cruz-Morales et al Biosynthesis of polycyclopropanated high energy biofuels |
| Profiling the diversity of agonist selective effects on the proximal proteome environment of G protein-coupled receptors | | | UCSF Krogan Lab - MOR-APEX |
| Cov²MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein | | | U of Ghent Pharma Biotech Lab - Cov²MS |
| Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum. | | | UC Riverside Metabolomics Core - Karine Le Roch LAB |
| A scalable, targeted mass spectrometry-based assay for monitoring the progression of herpesvirus infections | | | Princeton University Cristea Lab - HSV-1, HCMV, KSHV herpesvirus PRM assay |
| Regional variability, genotypic effects, and pharmacodynamic impact on prion protein concentration in the central nervous system | | | Carr - CSF_Brain_Prion_TSQ_directMRM |
| Skin cancer-associated S. aureus downregulates DNA repair mechanisms, and promotes oxidative stress and DNA damage in human keratinocytes | | | QIMRBerghofer - Staphylococcal PSM (phenol-soluble modulin) peptides |
| Absolute Protein Quantitation of the Mouse Macrophage Toll-Like Receptor and Chemotaxis Pathways | | | NIH_NitaLazar - Manes_BMDM_TLR-Chemotaxis_2021 |
| PRM assay of HSV-1 proteins in WT and IFI16-KO HFF-1 cells | | | Princeton University Cristea Lab - IFI16-KO HSV-1 PRM |
| HDL Proteomics in CACTI | | | UW Shao Lab - CACTIHDL |
| Prediction and experimental validation of a new salinity-responsive cis-regulatory element (CRE) in tilapia | | | Kueltz Lab UCDavis - XW0003-Oremo-OmBcells |
| High-Field Asymmetric Waveform Ion Mobility Spectrometry and Parallel Reaction Monitoring Increases Sensitivity for Clinical Biomarker Quantitation from Formalin-Fixed, Paraffin-Embedded Tumor Biop... | | | AstraZeneca Clinical Proteomics - FAIMS PRM |
| Mouse apolipoproteome study | | | OUH SDU Overgaard Lab - Mouse apolipoproteome study |
| Elevation of fatty acid desaturase-2 in esophageal adenocarcinoma increases polyunsaturated lipids and may exacerbate bile acid-induced genotoxicity | | | QIMRBerghofer - Targeted Lipidomics - FADS2 inhibition in FLO-1 cells |
| An interactive atlas of histone posttranslational modifications in T-cell acute lymphoblastic leukemia. | | | U of Ghent Pharma Biotech Lab - hPTM T-ALL atlas |
| Targeted proteomics (parallel reaction monitoring) to quantify starch-biosynthetic proteins in yeast | | | Functional Genomics Center Zurich - PRM of heterologously expressed proteins in yeast |
| Iron-Regulated Assembly of the Cytosolic Iron-Sulfur Cluster Biogenesis Machinery | | | UCLA_Wohlschlegel_Lab - xfan_CIA_PRM |
| Evaluation of anti-oxidant and anti-inflammatory treatments in Chronic Obstructive Pulmonary Disease | | | IIT Bombay Proteomics - MRM_COPD |
| Overcoming the protease-bias in quantitative proteomics | | | KTH Uhlen Lab - Multiple Proteases |
| SARS-CoV-2 PRM-MS Assay with Clinical Patient Samples | | | U of Newcastle Trost Lab - SARS-CoV-2 PRM |
| Rapid assessment of lipidomics sample purity and quantity using attenuated total reflectance Fourier-transform infrared spectroscopy | | | QIMRBerghofer - Lipid quality score assessment against targeted plasma lipidomics data |
| Multiple phosphorylation combinatorially regulates IFI16 antiviral immune signaling | | | Princeton University Cristea Lab - IFI16 IDR PRM |
| Monitoring M-proteins in SPEP gels | | | Erasmus MC Neurology - MS-MRD gel study |
| Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipids | | | MPI-CBG Shevchenko Lab - CD1d |
| A Peptide-Centric Quantitative Proteomics Dataset for the Phenotypic Assessment of Alzheimer’s Disease | | | MacCoss - Human AD Clean Diagnosis DIA Data |
| Mass spectrometry-driven discovery of neuropeptides mediating nictation behavior of nematodes | | | KU Leuven Temmerman Lab - Mass spectrometry-driven discovery of neuropeptides mediating nictation behavior of nematodes |
| Tandem Mass Tag-Based Quantitative Proteomic Profiling Identifies Novel Serum Biomarkers of Drug-Induced Liver Injury in Humans | | | Pfizer MS Technologies - DILI Biomarkers |
| Longitudinal evaluation of biomarkers in wound fluids of venous leg ulcers treated with a protease-modulating wound dressing: A prospective study | | | adKeller - SureQuant_biomarker_analysis |
| NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency | | | CedarsSinai Van Eyk Lab - NeuroLINCS |
| MRM based validation of target antigen expression in Pituitary Adenoma patients | | | IIT Bombay Proteomics - PitAdenoma_AutoAB |
| Kinase activity profiling in breast cancer samples | | | Utrecht Univeristy - Kinase activity profiling |
| Overcoming the dynamic-range challenge of the human proteome by mass-spectrometry and emerging single-molecule methods | | | MacCoss - Single_Molecule_Counting_Perspective |
| Validation of known and novel AKT, S6K and RSK substrates by targeted MS | | | University of Freiburg Warscheid Lab - AKT S6K RSK substrate validation |
| Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfei | | | UCLA Loo Lab - Swolfei_Acylations_PRM_2022 |
| Absolute and relative quantitation of ATI in modified wheat | | | KIT Food Chemistry - Absolute and relative quantititation of ATIs in modified wheat |
| Multisite proteome provides insights into the biology and prognostic markers for head and neck cancer | | | LNBio Mas Lab - PROJETO1_PRM-FFPE_2019-2022 |
| Reduction of MRM protein target list using correlation analysis | | | Nestle NDC Askeaton - MRM_data |
| Activity-dependent regulation of SLK phosphorylation | | | CMRI Synapse Proteomics - SLK |
| The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effector | | | Sainsbury Lab TSL Proteomics - Yu et al.,2022 |
| Differential isotope labelling by amino acids (DILAC) reveals metabolic cross-feeding and phenotypic heterogeneity in a clonal cell population | | | Francis Crick Institute Ralser Lab - Kamrad_et_al_13Cproteomics_metabolic_heterogeneity |
| Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetes | | | Turku Bioscience Lahesmaa Group - Serum Protein Markers of Rapid Type 1 Diabetes Progression |
| Analysis of ClpC1 directed antibiotics on ClpC1, ClpC2 and ClpC3 protein levels. | | | Max Perutz Labs - Clausen IMP - bacPROTAC ClpC1_2_3 |
| characterizing the origin of blood plasma proteins from organ tissues in rainbow trout (Oncorhynchus mykiss) using a comparative non-targeted proteomics approach | | | Ontario Tech U Aquatic Omics - Tannouri RT 2022 |
| Sirtuin 5 Reduces Malonylation in Non-mitochondrial Metabolic Pathways in Diabetic Kidney Disease | | | U Michigan Pennathur Lab - JBC - Malonylation paper 2022 |
| Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define diagnostic biosignatures for Parkinson's Disease | | | Purdue University Tao Lab - Hadisurya_Parkinson's_Disease |
| Orthogonal validation of Duchenne Muscular Dystrophy biomarkers | | | KTH Uhlen Lab - Duchenne muscular dystrophy project |
| Effects of alpha-crystallin gene knockout on zebrafish lens development | | | OHSU Proteomics Shared Resource - Posner-Effect of alpha-crystallin KO |
| Dynamic monitoring of myeloma minimal residual disease with targeted mass spectrometry | | | Erasmus MC Neurology - MS-MRD longitudinal monitoring |
| Monitoring extended stable isotope-labeled synthetic peptides as a quality control for protease digestion in targeted, multiplexed mass spectrometry-based assays | | | Paulovich - Extended_peptide_MRM_digestion_QC |
| Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment | | | MacCoss - Dynamic DIA Results |
| HIC1 interacts with FOXP3 multi protein complex: a novel mechanism to regulate human regulatory T cell differentiation and function | | | Turku Bioscience Lahesmaa Group - HIC1 Interactome in Treg Cells |
| Relative complement deficiency predicts development of islet autoimmunity and type 1 diabetes | | | PNNL - Relative complement deficiency predicts development of islet autoimmunity and type 1 diabetes |
| Synergistic targeting of DNA-PK and KIT signaling pathways in KIT mutant acute myeloid leukemia | | | U of Newcastle Verrills Lab - DNAPK and KIT 2021 |
| Metrologically traceable quantification of three apolipoprotein E isoforms in cerebrospinal fluid | | | ApoE Assay Paper |
| Elucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modeling | | | Utrecht U Targeted Proteomics - Veth_et_al_2023 |
| Degradation kinetics of lignocellulolytic enzymes in a biogas reactor by quanti-tative mass spectrometry | | | U of Magdeburg Benndorf Lab - Degradation kinetics of lignocellulolytic enzymes |
| PeakDecoder enables machine learning-1 based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements | | | PNNL - ABF_IMS_SyntheticBio |
| 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) an... | | | Paulovich - IO2 immunoMRM panel |
| Metrologically traceable quantification of three apolipoprotein E isoforms in cerebrospinal fluid | | | TPAD2.0 - ApoE Assay Paper |
| A strategy to characterize the global histone PTM landscape within tissues of non-model organisms | | | Kueltz Lab UCDavis - EAM_chap1 |
| Salinity-responsive histone PTMs identified in Mozambique tilapia tissues | | | Kueltz Lab UCDavis - EAM_chap2 |
| Development and validation of a matrix independent calibration strategy for targeted mass spectrometry-based quantification of milk protein allergens from complex food matrices | | | Nebraska U FARRP - Milk Quantitative Method |
| PRM quantification of MCS proteins in HCMV virus microenvironment | | | Princeton University Cristea Lab - VME MCS PRM |
| Moffitt_LSCC_Proteogenomics_Cohort_LC-MRM | | | Moffitt Cancer Center Koomen Lab - LSCC_Proteogenomics_Cohort_LC-MRM |
| Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer | | | Paulovich - PTRC_HGSOC_FFPE_direct_MRM_predictor_metabolism_panels |
| Global response of Octopus berrima to ocean warming | | | Kueltz Lab UCDavis - QQ0001_Octopus |
| PRM data for "Functional analysis of a common BAG3 allele associated with protection from heart failure" | | | UCSF Krogan Lab - PEREZBERMEJO_PRM_BAG3 |
| NUCKS1 IP-PRM_KSHV 48hpr | | | Princeton University Cristea Lab - KSHV TPCA_NUCKS1 IP-PRM |
| Evaluation of Linearity, Lower Limit of Measurement Interval and Imprecision | | | Glucagon and Oxyntomodulin |
| MCJ methylation liver | | | CEDARS-SINAI SHELLY LU LAB - MCJ |
| Assessing the role of trypsin in quantitative plasma- and single-cell
proteomics towards clinical application | | | KTH Uhlen Lab - Trypsin Comparison |
| Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent Acquisition | | | MacCoss - AstralBenchmarking |
| Environmental Conditions Elicit a Slow but Enduring Response of Histone Post-Translational Modifications in Mozambique Tilapia | | | Kueltz Lab UCDavis - EAM_chap3 |
| In-vitro differential redox-labeling of NTRC | | | IBBP Münster Hippler Lab - NTRC_ox_red_labelling |
| Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome | | | MacCoss - Mag-Net Method |
| Deep quantitative proteomics of North American Pacific coast star tunicate | | | Kueltz Lab UCDavis - DMK0051_Botryllus |
| 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 | | | Tulane U Biochem Hu Lab - p24 CFP10 immuno-enrichment MS detection |
| Targeted Proteomics Quantitation of NRF2 and Predictive Biomarkers in HNSCC | | | WUSTL Major Lab - NRF2_HNSCC |
| Improving our understanding of how FAIMS improves peptide identifications | | | MacCoss - FAIMS_vs_QuadGPF_Manuscript |
| Gut Microbiome IMS-MS Experiments | | | UNC Baker Lab - James Dodds Gut Microbiome IMS Publication |
| A novel overlapping gene peu-1 affects the translation of zyxin in C. elegans. | | | BayBioMS - Parmar_azyx1_zyx1 |
| Label-free Parallel Reaction Monitoring (PRM) analysis of selected novel potential targets of IFNg stimulation in Hela cells. | | | DKFZ Krijgsveld Lab - QuaNPA |
| Breeding from 1891 to 2010 did not increase the content of amylase/trypsin-inhibitors in wheat (Triticum aestivum L.) | | | KIT Food Chemistry - WheatScan - ATI |
| Quantitative Measurement of Secretory Protein Mistargeting by Proximity Labeling and Parallel Reaction Monitoring | | | UC Riverside Genereux Lab - Mistargeting Assay Data |
| Validation of a proteomic signature of lung cancer risk from bronchial specimens of risk-stratified individuals | | | PNNL - Signature_of_lung_cancer_risk |
| Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis. | | | BayBioMS - Assaad_BIN2_TRAPPII |
| The phosphorylation landscape of infection-related development by the rice blast fungus | | | Sainsbury Lab TSL Proteomics - Cruz-Mireles_et_al_2023 |
| Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses | | | UNC Baker Lab - 2023 NC Fish PFAS |
| Skeletal Muscle TFEB Signaling Promotes Central Nervous System Function and Reduces Neuroinflammation during Aging and Neurodegenerative Disease | | | MacCoss - Skeletal Muscle TFEB Signaling |
| AD-BXD Mouse Hippocampus Proteomics | | | MacCoss - AD-BXD Mouse Hippocampus Proteomics |
| Cognitive Functions, Neurotransmitter Alterations, and Hippocampal Microstructural Changes in Mice Caused by Feeding on Western Diet | | | IfADO Analytical Chemistry - Custodio et al., Cells, 2023 |
| In-Gel digest and filter-aided sample preparation to identify Dermatophagoides - and yeast protein antigens in severe equine asthma. | | | U of Leipzig AG Bioanalytics - Der p in SEA |
| In-Gel Digest to identify Aspergillus fumigatus protein antigens in severe equine asthma (SEA). | | | U of Leipzig AG Bioanalytics - Asp f in SEA |
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| Acoustic Ejection Mass Spectrometry Empowers Ultra-Fast Peptide Biomarker Quantification... A Paradigm shift | | | U of Ghent Pharma Biotech Lab - Echo-MS SISCAPA |
| METLIN-CCS: an ion mobility spectrometry
collision cross-section database | | | MacCoss - CCS Library |
| Metabolic, Neurotoxic and Immunotoxic Effects of PFAAs and their
Mixtures on the Proteome of Plasma and Head Kidney from Rainbow
Trout | | | Ontario Tech U Aquatic Omics - Pollard RT 2023 |
| Assessment of Kinome-wide Rewiring Upon Picornavirus Infection | | | Utrecht U Targeted Proteomics - VethNouwen_2023 |
| youtube short url | Do you mind if I quote a couple of your posts as long as I provide credit and sources back to your website?
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| PRM quantification of interferon-induced proteins upon Type I IFN-beta, Type II IFN-gamma, and LPS stimulation of differentiated THP-1 cells | | | Princeton University Cristea Lab - THP1 IFN ISG PRM |
| Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics | | | TUM Kuster Lab - 2023_Chang_decryptM_KDACi |
| 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) | | | UNC Baker Lab - SPATT PFAS Publication |
| Modeling the simultaneous dynamics of proteins in blood plasma and the cerebrospinal fluid in human in vivo | | | IRMB PPC - SILK_P017 |
| Development of a Mass Spectrometry-Based Method for Quantification of Total Cashew Protein in Roasting Oil | | | Nebraska U FARRP - Cashew Targeted Method |
| Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation | | | U of Heidelberg Mass Spec Core - Sakson_Beedgen_et_al_MRM |
| De novo Parkinson's disease - plasma experiment | | | UCL ICH Translational Mass Spec Group - DNP_Plasma_Targeted_MS |
| Fecal Microbiota Transplant_Bile Acid | | | UNC Baker Lab - FMT Bile Acid |
| Confirmation of N-Glycosylation for SARS Cov2 expressed RBD variants and M-protein with LC-MS. | | | U of Leipzig AG Bioanalytics - RBD_M_Glyco |
| AD-BXD Mouse PreFrontal Cortex Proteomics | | | MacCoss - AD-BXD Mouse PreFrontal Cortex Proteomics |
| Effect of burn wound treatment with fish skin on mouse skin proteome | | | Kueltz Lab UCDavis - NV0001_Mouse-Skin |
| Holistic quality control for bottom-up quantitative proteomics | | | MacCoss - Sample QC and System Suitability |