| A non-canonical repressor function of JUN restrains YAP activity and liver cancer growth | | Publication | 2024 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Pollen-Food Allergy Syndrome: From Food Avoidance to Deciphering the Potential Cross-Reactivity between Pru p 3 and Ole e 7 | | Publication | 2024 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| An NADH-controlled gatekeeper of ATP synthase | | Publication | 2024 | | | 60 SPD | Bruker timsTOF Ultra, Thermo Orbitrap Fusion Lumos | Read publication here
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| vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics | | Publication | 2024 | | | 60 SPD | Bruker timsTOF HT, Thermo Orbitrap Astral | Read publication here
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| Central role of SUMOylation in the regulation of chromatin interactions and transcriptional outputs of the androgen receptor in prostate cancer cells | | Publication | 2024 | | | 60 SPD | timsTOF Pro | Read publication here
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| A non-autonomous protein quality control mechanism targeting tau aggregate propagation | | Publication | 2024 | | | 60 SPD | Thermo Orbitrap Fusion Lumos | Read publication here
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| A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway | | Publication | 2024 | | | 100 SPD, 60 SPD | | Read publication here
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| Plasma proteome profiling for AKI biomarker candidates associated with first-line ART in people living with HIV in South Africa | | Publication | 2024 | | | 60 SPD | | Read publication here
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| Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics | | Publication | 2024 | | | 30 SPD, 60 SPD | timsTOF Pro 2 | Read publication here
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| Facing death: a multidisciplinary analysis of a Romano-Egyptian mummy mask at the Ny Carlsberg Glyptotek, Copenhagen | | Publication | 2024 | | | 60 SPD | Thermo Q Exactive HF | Read publication here
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| Proteomic analysis identifies dysregulated proteins in albuminuria: a South African pilot study | | Publication | 2024 | | | 60 SPD | | Read publication here
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| Population scale proteomics enables adaptive digital twin modelling in sepsis | | Publication | 2024 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| VfENko-Kae01 is a flagellum-specific jumbo phage infecting Klebsiella aerogenes | | Publication | 2024 | | | 60 SPD | timsTOF Pro | Read publication here
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| Early Holocene preservation differences between cortical and trabecular bone proteomes | | Publication | 2024 | | | 60 SPD | Bruker timsTOF fleX, Thermo Orbitrap Exploris 480 | Read publication here
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| Rhythmic variation in proteomics: challenges and opportuninites for statistical power and biomarker identification | | Publication | 2024 | | | 60 SPD | | Read publication here
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| Evolocumab as an immunomodulator in glioma: A window of opportunity trial evaluating PCSK9 inhibition to enhance surface MHC-I on tumor | | Publication | 2024 | | | 100 SPD, 60 SPD | Thermo Orbitrap Astral | Read publication here
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| Single cell proteomics by mass spectrometry reveals deep epigenetic insight into the actions of an orphan histone deacetylase inhibitor | | Publication | 2024 | | | 100 SPD, 200 SPD, 30 SPD, 500 SPD, 60 SPD | Bruker timsTOF SCP | Read publication here
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| Highly Repeatable Tissue Proteomics for Kidney Transplant Pathology: Technical and Biological Validation of Protein Analysis using LC-MS/MS | | Publication | 2024 | | | 60 SPD | Bruker timsTOF HT | Read publication here
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| An automated workflow based on data independent acquisition for practical and high-throughput personalized assay development and minimal residual disease monitoring in multiple myeloma patients | | Publication | 2024 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| A co-culture system of macrophages with breast cancer tumoroids to study cell interactions and therapeutic responses | | Publication | 2024 | | | 60 SPD | Bruker timsTOF fleX | Read publication here
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| Rapid Novor: Evosep One delivers high throughput and performance consistency in a clinical proteomics lab | | Case study | 2024 | | | 60 SPD | | Read case study here
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| Circulating pre- and postprandial extracellular vesicle proteomic profiles | | Publication | 2024 | | | 60 SPD | timsTOF Pro | Read publication here
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| AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics | | Publication | 2024 | | | 60 SPD, Whisper 40 SPD | timsTOF Pro 2 | Read publication here
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| A novel hybrid high speed mass spectrometer allows rapid translation from biomarker candidates to targeted clinical tests using 15N labeled proteins | | Publication | 2024 | | | 30 SPD, 60 SPD | Thermo Orbitrap Astral, Thermo Orbitrap Exploris 480 | Read publication here
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| Longitudinal plasma proteomic analysis of 1117 hospitalized patients with COVID-19 identifies features associated with severity and outcomes | | Publication | 2024 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics | | Publication | 2024 | | | 100 SPD, 60 SPD | Thermo Orbitrap Astral, Thermo Orbitrap Exploris 480 | Read publication here
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| The balance between antiviral and antibacterial responses during M. Tuberculosis infection is regulated by the ubiquitin ligase CBL | | Publication | 2024 | | | 30 SPD, 60 SPD | Bruker timsTOF HT, timsTOF Pro 2 | Read publication here
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| The comprehensive SARS-CoV-2 ‘hijackome’ knowledge base— reveals signicant changes in host cell protein expression and activation by multiple SARS-CoV-2 variants | | Publication | 2024 | | | 60 SPD | timsTOF Pro | Read publication here
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| Reduced ATP turnover during hibernation in relaxed skeletal muscle | | Publication | 2024 | | | 60 SPD | timsTOF Pro | Read publication here
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| O-linked glycosylations in human milk casein and major whey proteins during lactation | | Publication | 2024 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage | | Publication | 2024 | | | 60 SPD | Bruker timsTOF HT | Read publication here
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| Matrimeres are systemic nanoscale mediators of tissue integrity and function | | Publication | 2024 | | | 60 SPD | Thermo Q Exactive HF | Read publication here
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| DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes | | Publication | 2024 | | | 60 SPD | Thermo Q-Exactive Plus Hybrid Quadrupole-Orbitrap | Read publication here
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| NFATC2IP is a mediator of SUMO- dependent genome integrity | | Publication | 2024 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| Deciphering molecular mechanisms of synergistic growth reduction in kinase inhibitor combinations | | Publication | 2024 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Human Dermal Decellularized ECM Hydrogels as Scaffolds for 3D In Vitro Skin aging Models | | Publication | 2024 | | | 60 SPD | Bruker timsTOF fleX | Read publication here
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| Neat plasma proteomics: getting the best out of the worst | | Publication | 2024 | | | 100 SPD, 60 SPD, Whisper 40 SPD | timsTOF Pro | Read publication here
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| Structure and interactions of the endogenous human Commander complex | | Publication | 2024 | | | 60 SPD | timsTOF Pro | Read publication here
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| Phosphoproteomic investigation of targets of protein phosphatases in EGFR signaling | | Publication | 2024 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Proteomics of colorectal tumors identifies the role of CAVIN1 in tumor formation and progression | | Publication | 2024 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery | | Publication | 2024 | | | 100 SPD, 30 SPD, 60 SPD | Bruker timsTOF HT, timsTOF Pro 2 | Read publication here
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| Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis | | Publication | 2024 | | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Multi-omics profiling with untargeted proteomics for blood-based early detection of lung cancer | | Publication | 2024 | | | 60 SPD | Bruker timsTOF HT | Read publication here
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| Single cell proteomics by mass spectrometry reveals deep epigenetic insight and new targets of a class specific histone deacetylase inhibitor | | Publication | 2024 | | | 100 SPD, 200 SPD, 30 SPD, 300 SPD, 500 SPD, 60 SPD | Bruker timsTOF SCP | Read publication here
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| Modeling the simultaneous dynamics of proteins in blood plasma and the cerebrospinal fluid in human in vivo | | Publication | 2023 | | | 60 SPD | Bruker timsTOF HT | Read publication here
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| Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimen | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480, Thermo Orbitrap Fusion Lumos, Thermo Q Exactive HF, Thermo Q Exactive HF-X, timsTOF Pro | Read publication here
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| In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response | | Publication | 2023 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| Cryopreservation of highly extended pig spermatozoa remodels its proteome and counteracts polyspermic fertilization in vitro | | Publication | 2023 | | | 60 SPD | Bruker timsTOF fleX | Read publication here
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| Fully automated workflow for integrated sample digestion and Evotip loading enabling high-throughput clinical proteomics | | Publication | 2023 | | | 100 SPD, 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| IMBAS-MS discovers organ-specific HLA peptide patterns in plasma | | Publication | 2023 | | | 15 SPD, 30 SPD, 60 SPD, Whisper 40 SPD | Bruker timsTOF Ultra | Read publication here
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| INPP5D regulates inflammasome activation in human microglia | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Eclipse Tribid | Read publication here
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| Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens | | Publication | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| The social and structural architecture of the yeast protein interactome | DDA, Interactomes, Proteomics, Yeast | Publication | 2023 | | | 60 SPD | timsTOF Pro | Read publication here
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| Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component | | Publication | 2023 | | | 30 SPD, 60 SPD | timsTOF Pro 2 | Read publication here
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| Synaptic involvement of the human amygdala in Parkinson’s disease | Clinical proteomics, DIA, Parkinson's disease | Publication | 2023 | | | 60 SPD | timsTOF Pro | Read publication here
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| Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification | DIA, Proteomics | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Ventricular CSF proteomic profiles and predictors of surgical treatment outcome in chronic hydrocephalus | Clinical proteomics, CSF, DIA | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| A chemoproteomic platform for selective deubiquitinase inhibitor discovery | DIA, Proteomics | Publication | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Fusion Lumos | Read publication here
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| Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow | DIA, Plasma, Proteomics | Publication | 2023 | | | 60 SPD | timsTOF Pro | Read publication here
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| Müller glial cells located in the peripheral retina are more susceptible to high pressure: implications for glaucoma | Vitro | Publication | 2023 | | | 60 SPD | timsTOF Pro | Read publication here
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| Postpartum defects in inflammatory response after gestational diabetes precede progression to type 2 diabetes: a nested case-control study within the SWIFT study | Clinical proteomics, Plasma | Publication | 2023 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Sex differences in brain protein expression and disease | Brain, Clinical proteomics, DDA, TMT | Journal article | 2023 | | | 60 SPD | Thermo Orbitrap Eclipse Tribid | Read publication here
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| Emergence of the Dickeya genus involved duplication of the OmpF porin and the adaptation of the EnvZ-OmpR signaling network | | Journal article | 2023 | | | 60 SPD | SCIEX ZenoTOF 7600 | Read publication here
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| Deep and fast label-free Dynamic Organellar Mapping | DIA, Proteomics, Spatial proteomics | Journal article | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Cell-type-specific regulation of APOE and CLU levels in human neurons by the Alzheimer’s disease risk gene SORL1 | Alzheimer Disease, DDA, TMT | Journal article | 2023 | | | 60 SPD | Thermo Orbitrap Eclipse Tribid | Read publication here
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| Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae | DIA, Proteomics, PTM | Journal article | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Cofilin-Driven Nuclear Deformation Drives Dendritic Cell Migration through the Extracellular Matrix | DIA, Phosphoproteomics, Proteomics, PTM | Publication | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| A seven-transmembrane methyltransferase catalysing N-terminal histidine methylation of lytic polysaccharide monooxygenases | Methylation, Proteomics, PTM, TMT | Journal article | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling | DDA, DIA, Phosphorylation, Proteomics, PTM, TMT | Publication | 2023 | | | 30 SPD, 60 SPD, Whisper 20 SPD, Whisper 40 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Rapid and robust PTM peptide mapping for biologics with the Evosep One and the ZenoTOF 7600 | | Poster | 2023 | | | 100 SPD, 200 SPD, 300 SPD, 60 SPD | SCIEX ZenoTOF 7600 | Read app note here
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| Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer | | Publication | 2023 | | | 100 SPD, 15 SPD, 200 SPD, 30 SPD, 60 SPD | Bruker timsTOF | Read publication here
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| Evotip Pure simplifies workflows with excellent reproducibility, storage and recovery | | Application note | 2023 | The Evotip plays a vital role in the workflow of the Evosep One. It seamlessly integrates front-end sample preparation with liquid chromatography, facilitating efficient mass spectrometry analysis. Evotip Pure can be utilized for sensitive targeted assays, here illustrated in combination with the Agilent 6495C | | 100 SPD, 60 SPD, Whisper 40 SPD | | Download app note
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| Towards a Standardized Omics Platform with the 60 samples per day method | Technology | Application note | 2023 | This application note describes the 60 samples per day standard method. Get an overview of the method, the chromatographic performance and the results expected from Hela standard injections. | | 60 SPD | Thermo Orbitrap Exploris 480 | Download application note
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| Evosep One solves the proteomics dilemma – covering high throughput analysis and proteome depth | Fractionation, Technology | Application note | 2023 | The Evosep One offers a diverse range of applications, utilizing its six standard methods. It caters to various use cases, spanning from comprehensive proteome analysis with fractionation strategies to ultra high-throughput single-shot analysis. | | 100 SPD, 200 SPD, 30 SPD, 300 SPD, 60 SPD | | Download application note
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| Resolving the Temporal Splenic Proteome during Fungal Infection for Discovery of Putative Dual Perspective Biomarker Signatures | | Journal article | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| In situ digestion of alcohol-fixed cells for quantitative proteomics | | Publication | 2022 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Astaxanthin supplementation counters exercise-induced decreases in immune-related plasma proteins | | Journal article | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Reduced binding of apoE4 to complement factor H promotes amyloid-β oligomerization and neuroinflammation | | Publication | 2023 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| A Longitudinal Study of Individual Radiation Responses in Pediatric Patients Treated with Proton and Photon Radiotherapy, and Interventional Cardiology: Rationale and Research Protocol of the HARMONIC Project | | Publication | 2023 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| Flexibility, speed, and throughput for high proteome coverage using Zeno SWATH data-independent acquisition (DIA) coupled with the Evosep One system | | Application note | 2023 | | | 100 SPD, 200 SPD, 30 SPD, 300 SPD, 500 SPD, 60 SPD | SCIEX ZenoTOF 7600, timsTOF Pro 2 | Read publication here
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| Myosin inhibitor reverses hypertrophic cardiomyopathy in pediatric iPSC-cardiomyocytes to mirror variant correction | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Fusion Lumos | Read publication here
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| Rapid Profiling of Protein Complex Reorganization in Perturbed Systems | | Journal article | 2023 | | | 60 SPD | SCIEX TripleTOF 6600 MS system | Read journal article here
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| A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics | | Publication | 2023 | | | 60 SPD | timsTOF Pro 2 | Read publication here
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| A Streamlined High-Throughput Plasma Proteomics Platform for Clinical Proteomics with Improved Proteome Coverage, Reproducibility, and Robustness | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 240 | Read publication here
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| Cell-type-specific regulation of APOE levels in human neurons by the Alzheimer’s disease risk gene SORL1 | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Eclipse Tribid | Read publication here
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| INPP5D/SHIP1 regulates inflammasome activation in human microglia | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Eclipse Tribid | Read publication here
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| DIP-MS: A novel ultra-deep interaction proteomics for the deconvolution of protein complexes | | Publication | 2023 | | | 60 SPD | Thermo Q Exactive 970 TM Plus Hybrid Quadrupole-Orbitrap | Read publication here
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| First trimester serum apolipoproteins in the prediction of late-onset preeclampsia | | Publication | 2023 | | | 60 SPD | Thermo Altis triple quadrupole | Read publication here
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| Proteomic characteristics and diagnostic potential of exhaled breath particles in patients with COVID-19 | Covid-19 | Journal article | 2023 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Vacuum Insulated Probe Heated ElectroSpray Ionization source (VIP-HESI) enhances micro flow rate chromatography signals in the Bruker timsTOF mass spectrometer | | Publication | 2023 | | | 100 SPD, 200 SPD, 30 SPD, 60 SPD, Extended method | Bruker timsTOF Pro | Read publication here
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| Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry | | Journal article | 2023 | | | 60 SPD | SCIEX TripleTOF 6600 MS system | Read publication here
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| A chemoproteomic platform for reactive fragment profiling against the deubiquitinases | | Publication | 2023 | | | 30 SPD, 60 SPD | Thermo Orbitrap Fusion Lumos | Read publication here
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| PRMT5-mediated regulatory arginine methylation of RIPK3 | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Identification of Highly Sensitive Pleural Effusion Protein Biomarkers for Malignant Pleural Mesothelioma by Affinity-Based Quantitative Proteomics | | Publication | 2023 | | | 60 SPD | Thermo Altis triple quadrupole | Read publication here
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| Differential proteomic profile of lumbar and ventricular cerebrospinal fluid | | Publication | 2023 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Chromatographic separation of peptides and proteins for characterization of proteomes | | Journal article | 2022 | | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| A targeted multiplex mass spectrometry method for quantitation of abundant matrix and cellular proteins in formalin-fixed paraffin embedded arterial tissue | | Journal article | 2022 | | | 60 SPD | Thermo Altis triple quadrupole | Read publication here
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| Rapid and robust PTM peptide mapping for biologics with the Evosep One and the SCIEX ZenoTOF 7600 | | Application note | 2022 | | | 100 SPD, 300 SPD, 60 SPD | SCIEX ZenoTOF 7600 | Read application note here
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| Plasma proteomic profling in postural orthostatic tachycardia syndrome (POTS) reveals new disease pathways | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Synchro-PASEF allows precursor-specific fragment ion extraction and interference removal in data-independent acquisition | | Publication | 2022 | | | 100 SPD, 60 SPD | Bruker timsTOF Pro | Read publication here
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| Common variable immunodeficiency in two kindreds with heterogeneous phenotypes caused by novel heterozygous NFKB1 mutations | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| SARS-CoV-2 Production, Purification Methods and UV Inactivation for Proteomics and Structural Studies Inactivation for Proteomics and Structural Studies | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Optimizing data points per protein increases protein identifications while maintaining quantitative precision in short gradient data-independent acquisition proteomics | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Rapid profiling of protein complex re-organization in perturbed systems | | Publication | 2022 | | | 60 SPD | AB Sciex TripleTOF 6600 | Read publication here
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| Structural studies reveal that endosomal cations promote formation of 2 infectious CVA9 A particles, facilitating RNA and VP4 release. | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| High-throughput quantitative proteomics using Zeno SWATH data-independent analysis (DIA) and the Evosep One system | | Application note | 2022 | | | 100 SPD, 200 SPD, 30 SPD, 60 SPD | SCIEX ZenoTOF 7600 | Read publication here
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| Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF | | Publication | 2022 | | | 100 SPD, 30 SPD, 60 SPD | Bruker timsTOF Pro | Read publication here
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| Noninvasive proteomic biomarkers for alcohol-related liver disease | | Publication | 2022 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Advances in data‐independent acquisition massspectrometry towards comprehensive digital proteomelandscape | | Publication | 2022 | | | 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Proteomics based markers of clinical pain severity in juvenile idiopathic arthritis | | Publication | 2022 | | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| The social architecture of an in-depth cellular protein interactome | | Publication | 2021 | This publication by the Mann group describes a comprehensive and scalable strategy to define the network architecture of the cellular interactome. They applied this to more than 4000 pull-downs not generate a highly structured network of 3,909 proteins connected by 29,710 connections using the 60 SPD method and a timsTOF Pro mass spectrometer. | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Data independent acquisition enables deep and fast label-free dynamic organellar mapping | | Publication | 2021 | This publication by the Borner group, describes a DIA workflow to establish organellar maps, which combines cell fractionation and shotgun proteomics into a profiling analysis of subcellular localization. They apply this to HeLa cells and investigate changes in response to starvation/disruption of lysosomal pH. | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Evaluation of Disposable Trap Column nanoLC–FAIMS–MS/MS for the Proteomic Analysis of FFPE Tissue | Clinical proteomics, DDA, FFPE, Fractionation | Publication | 2021 | This publication by the Kuster group presents a robust workflow to support the analysis of large cohorts of patient samples using formalin-fixed paraffin-embedded FFPE tissue. They make use of online fractionation by FAIMS requiring 50% less sample than conventional high pH fractionation. | | 30 SPD, 60 SPD, Extended method | Thermo Orbitrap Exploris 480 | Read publication here
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| AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization | DDA, DIA, Technology | Publication | 2021 | This publication by the Mann group, introduces the open-source AlphaTims package with a stand-alone graphical user interface or as part of their AlphaPept ecosystem. With this package, unprocessed data are indexed, accessed, and visualized by a combination of tools. | | 200 SPD, 60 SPD | Bruker timsTOF Pro | Read publication here
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| A universal peptide matrix interactomics approach to disclose motif dependent protein binding | DDA, Protein interaction | Publication | 2021 | This publication by the Mertins group describes an optimized method to study protein-protein interactions mediated by intrinsically disordered regions. They demonstrate the feasibility of an optimized method for a PRotein Interaction Screen on a peptide MAtrix (PRISMA) with the 60 samples per day method. | | 60 SPD | Thermo Q Exactive HF-X | Read publication here
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| A personalized mass spectrometry-based assay to monitor M-protein in multiple myeloma patients (EasyM) | Antibodies, DDA, Myeloma, Targeted workflow | Publication | 2021 | This publication by the Trudel group describes the development of a non-invasive MS-based assay, called EasyM, which is used to assess minimal residual disease, a measure of depth of response to treatment, which has become an important parameter in assessing the disease burden in multiple myeloma. | | 30 SPD, 60 SPD | Thermo Orbitrap Fusion, Thermo Q Exactive | Read publication here
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| Synthetic Antigen Presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses | DDA | Publication | 2021 | In this publication, the Dustin group investigates the synaptic particle biogenesis and composition in different T-cell subsets. They use proteomics to reveal the diversity and functional specialization of extracellular vesicles composing the fourth signal of T cell immunological synapses. | | 60 SPD | Bruker timsTOF Pro | Read publication here
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| Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures | Automation, DDA, DIA, Phosphorylation, PTM, T-ALL | Publication | 2021 | In this publication, the Olsen group highlights the potential of proteomics to dissect alterations in cellular signaling and identify druggable pathways in cancer. They identify protein kinase C delta (PKCδ) inhibition as a strategy to overcome resistance to Notch1 inhibition in T-cell acute lymphoblastic leukemia. | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Read publication here
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| Unleashing the power of DIA combined with short gradients using Evosep One | DIA, Technology | Webinar | 2021 | This webinar is part of our Evosep webinar series and hosted by Nicolai Bache, Evosep. Florian Meier and Vadim Demichev discuss their use of the Evosep One, using novel DIA methodologies. | | 100 SPD, 200 SPD, 60 SPD | Bruker timsTOF Pro | Watch webinar
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| Improve and enhance your proteome coverage with the Performance column | Technology | Application note | 2019 | We have developed an additional Performance column for the 60 and 100 samples per day methods (SPD) to address applications with high demands. | | 100 SPD, 60 SPD | | Download application note
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| Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids | Automation, Clinical research, DIA, Plasma | Webinar | 2021 | In this seminar from the Canadian National Proteomics Network (CNPN) meeting 2021, Angela McArdle presents a standardized workflow for precise high-throughput proteomics of blood biofluids. They established optimal conditions for sample preparation and DIA analysis in plasma, then automated and adapted this for depleted plasma and whole blood. | | 60 SPD | Thermo Orbitrap Exploris 480 | Download publication
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| High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe | diaPASEF, Technology development | Publication | 2021 | The Ralser and Nesvizhskii groups introduce the latest addition to the DIA-NN software with a neural network-based ion mobility module. DIA-NN was originally conceived to maximize the performance of fast proteomics experiments and here they demonstrate the identification of more than 5000 proteins from the 200 SPD method. | | 100 SPD, 200 SPD, 60 SPD | Bruker timsTOF Pro | Download publication or learn more on our website
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| A robust mass spectrometer for precision medicine – the Orbitrap Exploris 240 mass spectrometer for large-scale plasma protein profiling | DDA, Plasma | Application note | 2021 | This application note from Thermo Fisher Scientific Precision Medicine Science Center demonstrates the reliability and robustness of the Evosep One coupled with the Orbitrap Exploris 240 MS for large-scale, untargeted plasma protein profiling. They observed excellent reproducibility of protein and peptide identifications over 100 injections of human serum performed five weeks apart. | | 60 SPD | Thermo Orbitrap Exploris 240 | Download application note
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| Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers | Clinical research, DIA, Fibrosis, Plasma | Publication | 2021 | In this study, the Theis and Schiller groups at the Helmholtz Zentrum München, investigated the correspondence of cell state changes in diseased organs to peripheral protein signatures in pulmonary fibrosis patient cohorts. From plasma proteome profiling of more than 122 patients, they propose CRTAC1 protein levels in plasma as a novel biomarker. | | 100 SPD, 60 SPD | Thermo Q Exactive HF | Download publication
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| Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease | Brain, Clinical research, DDA | Publication | 2021 | In this study, the Cader group from University of Oxford, presents a global proteomic analysis of the extracellular matrix (ECM) in mouse and human brains. They report the identification of 147 core ECM proteins of the human brain vascular matrisome, including collagens, laminins, fibronectin and nidogens. Network analysis revealed the connection between the ECM proteins … | | 60 SPD | Bruker timsTOF Pro | Download publication
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| Rapid, robust and reproducible host-cell protein analysis with Evosep One | DDA, HCP | Webinar | 2021 | This webinar is part of our Evosep webinar series and hosted by Nicolai Bache, Evosep. Jiao Ma and Anders Giessing discuss their use of the Evosep One to perform rapid, robust and reproducible HCP analysis. | | 200 SPD, 60 SPD | Bruker timsTOF Pro, Thermo Orbitrap Fusion Lumos | Watch webinar
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| Covid-19 research with Evosep One | Covid-19, DIA, Technology | Webinar | 2021 | This webinar is part of our Evosep webinar series and hosted by Nicolai Bache, Evosep. Angela McArdle and Mathias Trost discuss their use of the Evosep One technology in their development of rapid Covid-19 assays. | | 60 SPD | Thermo Orbitrap Exploris 480 | Watch webinar
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| A beginner’s guide to Evosep | DDA, Technology | Webinar | 2021 | This webinar is part of our Evosep webinar series and hosted by Nicolai Bache, Evosep. Nicolai Bache introduces the basics of the Evosep technology, while Alexey Chernobrovkin and Raja Nirojogi share their experience with the Evosep One and present their own data. | | 60 SPD | Thermo Orbitrap Exploris 480 | Watch webinar
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| SPIN – Species by Proteome Investigation | Ancient proteomics, DIA | Publication | 2021 | This publication from the Olsen Group, introduces “Species by Proteome INvestigation” (SPIN), a proteomics workflow capable of querying over 150 mammalian species 200 times a day with the Evosep One. Genetic species determination is an indispensable tool in forensics, archaeology, ecology, and food authentication. | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Download publication
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| High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion | Automation, Clinical research, Covid-19 | Publication | 2021 | This publication from OmicEra Diagnostics, describes alterations of the serum proteome during COVID-19 using a scalable plasma proteome profiling workflow. It comprises the most detailed longitudinal protein trajectories during hospitalization, based on one of the largest MS-based body fluid proteomics efforts with a total of 720 plasma serum samples. | | 60 SPD | Bruker timsTOF Pro | Download publication
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| R1441G but not G201S Mutation Enhances LRRK2 Mediated Rab10 phosporylation in human Peripheral blood neutrophils | Clinical research, Parkinson's disease, Targeted workflow | Publication | 2021 | This publication from University of Dundee led by Esther Sammler, describes that in vivo LRRK2 dependent | | 60 SPD | Thermo Q Exactive HF-X | Download publication
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| Spatial-proteomics reveal in-vivo phospho-signaling dynamics at subcellular resolution | DIA, FAIMS, Fractionation, Phosphorylation, Spatial proteomics | Publication | 2021 | This publication from the Olsen group at the Novo Nordisk Foundation Center for Protein Research, describes a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. | | 60 SPD | Thermo Orbitrap Exploris 480 | Download publication or read more on our website
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| Deciphering the LRRK code: LRRK1 and LRRK2 phosphorylate distinct Rab proteins and are regulated by diverse mechanisms | Parkinson's disease, Targeted workflow | Publication | 2020 | This publication from University of Dundee led by Dario R Alessi, describes how LRRK1, a less studied homologue of LRRK2 regulates growth factor receptor trafficking and osteoclast biology reinforcing that the LRRK enzymes have evolved as major regulators of Rab biology in Parkinson’s disease. | | 60 SPD | Thermo Q Exactive HF-X | Download publication
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| Development of a multiplexed targeted mass spectrometry assay for LRRK2-phosphorylated Rabs and Ser910/Ser935 biomarker sites | Clinical research, Parkinson's disease, Targeted workflow | Publication | 2020 | This publication from University of Dundee led by Dario R Alessi, describes the validation and development of a new, multiplexed targeted assay that enables the relative quantification of the key components of the LRRK2 pathway, defining the impact of LRRK2 inhibitors and Parkinson’s disease causing mutations. | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Download publication
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| diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition | diaPASEF, Technology | Publication | 2020 | A collaboration led by the Mann group at the Max Planck Institute for Biochemistry, Münich describes the development of the latest addition to the PASEF technology. The diaPASEF workflow combines the advantages of DIA such as high degree of reproducibility and data completeness with the effective PASEF technology. | | 100 SPD, 200 SPD, 60 SPD | Bruker timsTOF Pro | Download publication or learn more on our website
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| High throughput proteome and phosphorpoteome sample processing coupled to fast gradient DIA | DDA, DIA, FAIMS, Phosphorylation, PTM, Technology, Tissue, TMT | Publication | 2020 | High throughput workflows for proteomics | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Download publication
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| Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides in vitro | Clinical research, Peptidomics, Targeted workflow, Urine | Publication | 2019 | Urinary peptidomics in early type 1 diabetes | | 60 SPD | Thermo Q Exactive HF-X | Download publication
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| New Orbitrap Exploris 480 Mass Spectrometer Coupled with Evosep One | DDA, DIA, FAIMS, Technology | Brochure | 2020 | Brochure of Exploris 480 with Evosep data from piece no 1 | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Download brochure
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| Development of a robust and reprodusible method for detection of citrullination in complex samples | Bacteria, Citrullination, DDA, PTM | Poster | 2018 | Detection of citrullination in complex samples | | 60 SPD | Thermo Orbitrap Fusion Lumos | Download poster
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| How to get Speed and Depth in yout Host Cell Protein | Biopharma, DDA, HCP | Video | 2018 | | | 60 SPD | Bruker timsTOF Pro | Watch
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| A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-Robust Proteomics | DDA, DIA, Plasma, Technology | Publication | 2018 | Description of Evosep | | 60 SPD | Thermo Q Exactive HF-X | Download publication
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| Robust and Reprodusible Protein Quantification in Plasma Using the Evosep One and the Agilent 6495 Triple Quadrupole LC/MS | Plasma, Targeted workflow, Technology | Application note | 2020 | Agilent feasibility study | | 60 SPD | Agilent 6495 Triple Quadrupole | Download application note
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| Development of a Novel LC Concept for Clinical Proteomics | DDA, Plasma, Technology | Poster | 2018 | Description of Evosep One | | 60 SPD | Thermo | Download poster
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| Increasing proteome coverage using cysteine-specific DIA Mass spectrometry – Cys-DIA | DIA, PTM | Publication | 2020 | DIA on cysteine-specific peptides | | 60 SPD | Thermo Q Exactive HF-X | Download publication
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| A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism | DDA, TMT | Publication | 2020 | | | 60 SPD | Thermo Orbitrap Fusion Lumos | Download publication
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| Improving proteome coverage and peptide identification rates in short LC gradients | DDA, DIA, FAIMS, Phosphorylation, PTM, Technology | Video | 2020 | | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Watch
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| High-throughput proteomics with Evosep One | DDA, DIA, FAIMS, Phosphoproteomics, PTM, Technology | Video | 2020 | | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Watch
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| Rapid proteome analyses using the Evosep One | DDA, DIA, Phosphorylation, PTM | Video | 2018 | | | 60 SPD | Thermo Q Exactive HF | Watch
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| Sensitive, Rapid, Robust and Reproducible Workflow for Host Cell Protein Profiling in Biopharmaceutical Process Development | Biopharma, DDA, HCP | Publication | 2020 | HCP analysis in Biopharma | | 30 SPD, 60 SPD | Thermo Orbitrap Fusion Lumos | Download publication
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| Using Artificial Intelligence on Ultrafast LC-MSMS-DIA runs for Bacterial Identification in Urine | Bacteria, Clinical research, DIA | Video | 2019 | View the recording of our HUPO 2019 lunch seminar, where Florence Roux-Dalvai from Québec Research Center, Canada presents a new strategy for bacterial species identification in urinary tract infection using artificial intelligence on ultrafast LCMS DIA runs. | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Watch
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| High-throughput 4D-Proteomics – Application of dia-PASEF® and the Evosep One for short gradients | DIA, Technology | Application note | 2020 | diaPASEF app note | | 100 SPD, 200 SPD, 300 SPD, 60 SPD | Bruker timsTOF Pro | Download application note
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| Fast and reproducible phosphoproteomics using MagReSyn® Amine and Tim-IMAC HP magnetic beads and the Evosep One | Phosphorylation, PTM, Technology | Application note | 2020 | Read this application note to learn about the automated workflows for sample preparation developed by the Olsen group in collaboration with Resyn Biosciences. Protein digestion and phosphoenrichment is fully automated for up to 96 samples in parallel with the Kingfisher Flex robot from Thermo Scientific. | | 60 SPD | Thermo Orbitrap Exploris 480 | Download application note
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| Consistency, consistency – Automated Sample Prep for Translational Proteomics | Clinical research, Plasma | Video | 2020 | In this webinar, Emily Chen, Sr. Director at the Thermo Fisher Precision Medicine Science Center presents an automated, robust and scalable sample preparation pipeline for large-scale clinical research samples. | | 60 SPD | Thermo | Watch webinar
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| An Ultra High-Throughput Plasma Protein Profiling (uHTPPP) Workflow Using a Modified Quadrupole-Orbitrap Mass Spectrometer | Clinical research, DDA, Lung, Plasma, Serum, Tissue | Application note | 2020 | In this application note, the group of Emily Chen at the Thermo Fisher Precision Medicine Science Center describes a high-throughput plasma and serum proteomics analysis workflow for large population cohort studies that utilizes a standardized sample preparation method, high-throughput data acquisition, and easy to implement QC standard. | | 30 SPD, 60 SPD | Thermo Orbitrap Exploris 240 | Download poster or booklet
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| Scalable and Automated Plasma Workflow Based on the Thermo Scientific Q Exactive HF-X MS Platform | Clinical research, DDA, Lung, Plasma, Serum | Application note | 2019 | In this application note, the group of Emily Chen at PMSC describes a high-throughput plasma and serum proteomics analysis workflow for large population cohort studies that utilizes a standardized sample preparation method, high-throughput data acquisition, and easy to implement QC standard. | | 100 SPD, 30 SPD, 60 SPD | Thermo Q Exactive HF-X | Learn more or download application note
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| Advancing Interactomics Workflows with 4D-Proteomics on the timsTOF Pro | DDA, Yeast | Video | 2020 | In this webinar organized by Bruker, André Michaelis from Matthias Mann’s group presents his large-scale yeast interactome study. He describes a robust platform for affinity purification and an LCMS workflow with Evosep One and timsTOF Pro with more than 8000 LCMS runs completed in just 20 weeks. | | 60 SPD | Bruker timsTOF Pro | Watch webinar
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| Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites | DIA, Liver, Lung, Protein interaction, Tissue | Publication | 2019 | In this publication, the Olsen Group have combined DIA with short LC gradients to describe how cancer mutations close to tyrosine phosphorylation sites in the EGF receptor rewire signaling pathways by switching protein interactors. The performed 1200 pulldown experiments in just 20 days of LC-MS instrument time. | | 60 SPD | Thermo Q Exactive HF-X | Learn more or download publication
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| timsTOF Pro with PASEF and Evosep One: Maximizing throughput, robustness and analytical depth for shotgun proteomics | DDA, Technology | Application note | 2018 | Read this application note to learn more about the timsTOF Pro with PASEF and the Evosep One for maximizing throughput, robustness and analytical depth for shotgun proteomics. Increased peak capacity via trapped ion mobility spectrometry allows the analysis of 200 samples/day, at formidable analytical depth, with unparalleled robustness. | | 100 SPD, 200 SPD, 60 SPD | Bruker timsTOF Pro | Download publication or download poster
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| Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV | Clinical research, Covid-19, DIA, PTM | Publication | 2020 | This publication describes the molecular functions of viral proteins and their interactions with the host proteome of SARS-CoV-2. The impact of viral infection on the proteome and phosphoproteome were analyzed in a time-resolved manner by DIA. The analysis revealed key pathways perturbed during the infection identifying potential vulnerable points of SARS-CoV-2. | | 30 SPD, 60 SPD | Thermo Q Exactive HF-X | Download publication
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| Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags While Significantly Reducing Instrument Time | Fractionation, Tissue, TMT | Video | 2019 | Comparison study with TMT, same coverage in shorter time | | 30 SPD, 60 SPD | Thermo Orbitrap Fusion Lumos | Watch
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| Increasing Throughput: From Pre-Clinical Models To Protein Complexes | DIA, Large-scale | Video | 2019 | Comparison study with >400 samples, same coverage in shorter time | | 60 SPD | SCIEX | Watch
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| Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles | DDA, Lung, Tissue | Publication | 2020 | In vivo study of biocompatibility of magnetic nanoparticles. Toxicity of magnetic metal oxide nanoparticles on the respiratory system was examined in vivo by single intratracheal instillation in mice. Bronchoalveolar lavage fluid (BALF) samples were collected for proteome analyses by LC−MS/MS. | | 60 SPD | Thermo Orbitrap Fusion Lumos | Download
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| A Compact Quadrupole-Orbitrap Mass Spectrometer With Faims Interface Improves Proteome Coverage In Short Lc Gradients | Automation, DDA, DIA, FAIMS, Fractionation, Phosphoproteomics, PTM, Technology, Tissue, TMT | Publication | 2020 | Test of Orbitrap Exploris with DIA and TMT, proteome and phospho. | | 100 SPD, 200 SPD, 60 SPD | Thermo Orbitrap Exploris 480 | Download
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| Advanced Host Cell Protein (Hcp) Analysis With Tims Qtof Ms Powers Biopharmaceutical Development | Antibodies, DDA, HCP | Publication | 2019 | Descriptive piece of HCP analysis on the timsTOF | | 60 SPD | Bruker timsTOF Pro | Download
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| High-Throughput Proteomics Quantification Enabled by Fast LC Separation and Advanced PRM Acquisition | Phosphorylation, PTM, Targeted workflow | Poster | 2018 | High throughput LC-PRM to monitor the main protein components of AKT/mTOR signaling pathway. | | 100 SPD, 200 SPD, 60 SPD | Thermo Q Exactive HF-X | Download
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