The 30 samples per day method
STANDARD METHOD
The longest standard method
The 30 SPD method is the longest of our standard methods with a 44-minute gradient.
It is a popular choice for routine applications such as measuring proteome and post-translational modified peptides.
HIGHEST PROTEOME COVERAGE
This method provides the highest proteome coverage among our standard methods with close to 25,000 unique peptides identified in data-dependent acquisition mode.
The five standard methods
With the five standard methods, the Evosep One covers a range of use cases from comprehensive proteome analysis with fractionation strategies to ultra high-throughput single-shot analysis. You decide how fast you want to go.
Standard method
The highest peak capacity per minute with our fastest method for ultra-high throughput analysis.
Standard method
Excellent sequencing speed with most peptides per minute among our standard methods.
Standard method
A great “in-between” method with run-to-run reproducibility of just one second.
Standard method
The most popular method with an excellent balance of throughput and depth.
Standard method
The longest method with a 44-minute gradient providing the best overall proteome coverage.
Explore more
Do you want to know how our users are already taking advantage of the 30 Samples per day method? Find all publications from users and collaboration partners here. Visit our Literature Room for a full overview.
| Title | Subject | Material | Year | Summary | Institute | Evosep method | MS instrumentation | Learn More |
|---|---|---|---|---|---|---|---|---|
| The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies | FAIMS, FFPE | Publication | 2022 | 30 SPD | Thermo Orbitrap Fusion Lumos | |||
| Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6 | DIA | Publication | 2022 | 30 SPD | Thermo Orbitrap Fusion Lumos | |||
| High throughput and high confidence sequence variant analysis in therapeutic antibodies using Evosep One liquid chromatography tandem mass spectrometry with synthetic heavy peptides | Antibodies, Peptidomics | Publication | 2022 | 30 SPD | Thermo Orbitrap Fusion Lumos | |||
| Osteocytes Serve as a Reservoir for Intracellular Persisting Staphylococcus aureus Due to the Lack of Defense Mechanisms | Inflammation | Publication | 2022 | 30 SPD | Thermo Orbitrap Exploris 480 | |||
| Neddylation tunes peripheral blood mononuclear cells immune response in COVID-19 patients | Covid-19, Plasma | Publication | 2022 | 30 SPD | Bruker timsTOF Pro | |||
| High-throughput quantitative proteomics using Zeno SWATH data-independent analysis (DIA) and the Evosep One system | DIA, Peptidomics, Protein interaction | Application note | 2022 | 100 SPD, 200 SPD, 30 SPD, 60 SPD | SCIEX ZenoTOF 7600 | |||
| Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF | DDA, DIA, Phosphoproteomics | Publication | 2022 | 100 SPD, 30 SPD, 60 SPD | Bruker timsTOF Pro | |||
| Brain proteome profling implicates the complement and coagulation cascade in multiple system atrophy brain pathology | Brain, DIA, Inflammation | Publication | 2022 | 30 SPD | Thermo Q Exactive HF-X | |||
| Proteomic phenotype of cerebral organoids derived from autism spectrum disorder patients reveal disrupted energy metabolism, cellular components, and biological processes | TMT | Publication | 2022 | 30 SPD | Thermo Orbitrap Fusion | |||
| Inflammation-induced downregulation of succinate dehydrogenase regulates adrenocortical function | Inflammation | Publication | 2022 | 30 SPD | Bruker timsTOF Pro | |||
| Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies distinct proteotypes associated with patient outcomes | Cancer, Lung | Publication | 2022 | 30 SPD | Thermo Orbitrap Fusion Lumos | |||
| DebaryOmics: an integrative –omics study to understand the halophilic behaviour of Debaryomyces hansenii | DIA, Phosphoproteomics, Yeast | Publication | 2022 | 30 SPD | Thermo Orbitrap Exploris 480 | |||
| Comprehensive proteomics with 8.000 proteins identified with DIA-PASEF using the 30 samples per day method | Application note | 2022 | 30 SPD | |||||
| Improve and enhance your proteome coverage with the performance column for our long methods | DDA | Application note | 2022 | 30 SPD, Extended method | Bruker timsTOF Pro | |||
| Toxoplasma gondii ROP1 subverts murine and human innate immune restriction | Plasma | Publication | 2022 | 30 SPD | Thermo Orbitrap Fusion Lumos | |||
| Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase | Phosphorylation | Publication | 2021 | This publication by the Costa group describes the mechanism whereby the Dbf4 dependent kinase selectively targets fully loaded MCM double hexamers on the path to helicase activation, and uncover the mechanism whereby the checkpoint kinase Rad53 blocks this function. | 30 SPD | Thermo Orbitrap Lumos | ||
| Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19 | Covid-19, DDA, Plasma | Publication | 2022 | This publication by the Zinkernagel group, assess the influence of COVID-19 plasma hypercytokinemia on the functional responses of myeloid immune cells upon bacterial challenges from acute-phase COVID-19 patients and their corresponding recovery-phase. We show that a severe hypercytokinemia status in COVID-19 patients correlates with the development of bacterial superinfections. | 30 SPD | Bruker timsTOF Pro | ||
| Data independent acquisition enables deep and fast label-free dynamic organellar mapping | DIA, Spatial proteomics | 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 | ||
| Plasma extracellular vesicles in people living with HIV and type 2 diabetes are related to microbial translocation and cardiovascular risk | DDA, Extracellular vesicles, HIV, Plasma | Publication | 2021 | This publication, led by the Trøseid group at Oslo University Hospital investigates the potential role of plasma extracellular vesicles (EVs) in relation to gut microbiota alterations and low-grade endotoxemia in HIV and type 2 diabetes. | 30 SPD | Thermo Q Exactive HF | ||
| DebaryOmics: an integrative –omics study to understand the halophilic behaviour of Debaryomyces hansenii | DIA, Phosphorylation, PTM, Yeast | Publication | 2021 | This publication by the Martinez group at the Technical University of Denmark, presents the first global phosphoproteomics analysis in Debaryomyces hansenii, a non-conventional yeast considered to be a well-suited option for a number of different industrial bioprocesses. | 30 SPD | Thermo Orbitrap Exploris 480 | ||
| Evaluation of Disposable Trap Column nanoLC–FAIMS–MS/MS for the Proteomic Analysis of FFPE Tissue | Clinical proteomics, DDA, FFPE | 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 | ||
| High-Throughput Drug Discovery with the Evosep One | Drug discovery | Webinar | 2021 | In this webinar we will look into how the Evosep One with high-throughput and sensitivity is a good fit when developing new drug applications or biologics license applications. | 30 SPD | Thermo Orbitrap Exploris 480 | ||
| Plasma Proteomics with the Evosep One | DIA, Liver, Plasma | Webinar | 2021 | In this webinar you will learn how the Evosep One, with high reproducibility and robustness, is ideally suited for analysis of large sample cohorts of blood plasma. | 30 SPD | Bruker timsTOF Pro, Thermo Orbitrap Exploris 480 | ||
| A deeper look at carrier proteome effects for single-cell proteomics | DDA, Single cell, TMT | Publication | 2021 | This publication by the Olsen group at University of Copenhagen describes the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. Using the 30 SPD method, they show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. | 30 SPD | Thermo Orbitrap Exploris 480 | ||
| Time evolution of PEG-shedding and serum protein coronation determines the cell uptake kinetics and delivery of lipid nanoparticle formulated mRNA | DDA, Drug discovery, Protein interaction | Publication | 2021 | This publication, led by the Esbjörner group at the Chalmers University of Technology in Gothenburg, Sweden investigates the uptake and delivery of mRNA formulated into MC3 lipid nanoparticles focusing on the role of serum proteins in driving the temporal evolution of PEG-shedding reactions and protein coronation events. | 30 SPD | Thermo Q Exactive HF | ||
| PD-L1 Overexpression, SWI/SNF Complex Deregulation, and Profound Transcriptomic Changes Characterize Cancer-Dependent Exhaustion of Persistently Activated CD4+ T Cells | Breast cancer, DDA, Secretome | Publication | 2021 | This publication from the Sarnowska group at Maria Sklodowska-Curie National Research Institute of Oncology in Poland investigates the mechanisms of immune response during continuous stimulation of tumor-infiltrating lymphocytes by tumors. They use the Evosep One to measure the secreted proteins from restimulated CD4+ T cells grown with cancer cells. | 30 SPD | Thermo Orbitrap Exploris 480 | ||
| 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 | ||
| Exploitation of the Secretory Pathway by SARS-CoV-2 Envelope | Covid-19, DDA, Protein interaction | Publication | 2021 | This publication by the Carlton group investigates the mechanism, by which Coronaviral Eenvelope proteins achieves its steady state localization to the Endoplasmic Reticulum Golgi Intermediate Compartment. They use proximity biotinylation to define the vicinal proteome of wild type and ER-restricted versions of Envelope. | 30 SPD | Thermo Orbitrap Fusion Lumos | ||
| Mass Spectrometry Provides a Highly Sensitive Noninvasive Means of Sequencing and Tracking M-Protein in the Blood of Multiple Myeloma Patients | Antibodies, DDA, Myeloma, Targeted workflow | Publication | 2021 | The amino acid sequence of the M-protein for multiple myeloma is unique compared to the polyclonal antibodies in patients’ blood. This publication from Rapid Novor describes a targeted MS/MS assay to detect and quantify the unique M-protein sequence in serum samples from multiple myeloma patients. | 30 SPD | Thermo Q Exactive | ||
| An ultrasensitive method for analysis of viral spike N-glycoforms | DDA, Glycosylation, PTM | Publication | 2021 | This publication from the Yates group describes a new ultrasensitive “single-pot” method applicable for analysis of site-specific glycosylation of any glycoprotein and characterizing glycosylation of viral spike proteins and potential vaccines. | 30 SPD, Extended method | Bruker timsTOF Pro | ||
| 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 | ||
| Towards a Standardized Omics Platform with the 30 samples per day method | Technology | Application note | 2020 | This application note describes the 30 samples per day standard method. Get an overview of the method, the chromatographic performance and the results expected from Hela standard injections. | 30 SPD | Thermo Orbitrap Exploris 480 | ||
| The proteomics dilemma – High throughput analysis versus proteome depth | Technology | Application note | 2019 | With the five standard methods, the Evosep One covers a range of use cases from comprehensive proteome analysis with fractionation strategies to ultra high-throughput single-shot analysis. | 100 SPD, 200 SPD, 30 SPD, 300 SPD, 60 SPD | |||
| Co-translational assembly and localized translation of nucleoporins in nuclear pore complex biogenesis | DDA, Protein interaction | Publication | 2021 | In this study, the Palancade group provides the complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC) in yeast. Their data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits. | 30 SPD | |||
| Hemorrhage and saline resuscitation are associated with epigenetic and proteomic reprogramming in the rat lung | DDA, Lung, Tissue | Publication | 2021 | In this study, the Sillesen group investigates the alteration of the proteome in the context of hemorrhage and saline resuscitation in trauma patients. They used rat lungs as a model and pooled 10 rats in one combined TMT experiment subjected to high pH offline fractionation. | 30 SPD | Thermo Orbitrap Fusion | ||
| Malaria Parasite Schizont Egress Antigen-1 Plays an Essential Role in Nuclear Segregation during Schizogony | DDA, Malaria, Protein interaction | Publication | 2021 | This publication by the Blackman group describes the role of SEA1, a suggested malaria vaccine antigen candidate. They conclude that SEA1 does not play a direct mechanistic role in egress to invade new erythrocytes but instead is an essential blood-stage protein that plays an important role in orchestrating the correct partitioning of DNA into merozoites. | 30 SPD | Thermo Orbitrap Fusion Lumos | ||
| The COVIDome Explorer Researcher Portal | Clinical research, Covid-19, DDA, Plasma | Publication | 2021 | Researchers from University of Colorado led by Joaquin M. Espinosa, have created a user-friendly researcher portal enabling easy access and real-time analysis of matched multi-omics datasets for COVID-19, termed the COVIDome Explorer. They illustrate the use through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19. | 30 SPD | Bruker timsTOF Pro | ||
| The Host Interactome of Spike Expands the Tropism of SARS-CoV-2 | Clinical research, Covid-19, Protein interaction | Publication | 2021 | This publication from the Yates lab, investigates the host interactome determining whether a SARS-CoV-2 infection is productive. They find an “S2 only” dependent, alternative infection of additional cell types with SARS-CoV-2 may impact vaccination strategies and provide a molecular explanation for a severe or prolonged progression of disease in select COVID-19 patients. | 30 SPD | Bruker timsTOF Pro | ||
| Basement membrane stiffness determines metastases formation | DDA, Lung, Tissue, TMT | Publication | 2021 | In this study, the Erler group from the BRIC Institute at University of Copenhagen, Denmark identifies Net4 as a key regulator of basement membrane stiffness, a special type of extracellular matrix, which presents the major barrier cancer cells have to overcome multiple times to form metastases. | 30 SPD | Thermo Orbitrap Exploris 480 | ||
| Interactions of Viral Proteins from Pathogenic and Low or Non-Pathogenic Orthohantaviruses with Human Type I Interferon Signaling | DDA, Protein interaction | Publication | 2021 | A collaboration led by the Ermonval group from Institute Pasteur describes the interactions of structural and non-structural proteins of pathogenic and low or non-pathogenic orthohantaviruses with human type I Interferon signaling. They suggest that the activation of IFN-I is probably not the only antiviral pathway to be counteracted by orthohantaviruses. | 30 SPD | Thermo Orbitrap Fusion | ||
| Seroconversion stages COVID19 into distinct pathophysiological states | Clinical research, Covid-19, Plasma | Publication | 2020 | In this study, researchers from University of Colorado led by Joaquin M. Espinosa, found highly variable seroconversion status among hospitalized Covid-19 patients. Their results support the existence of distinct pathophysiological states, with seroconversion status being potentially useful as a surrogate marker of underlying processes. | 30 SPD | Bruker timsTOF Pro | ||
| 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 | ||
| High dynamic range proteome analysis with BoxCar DIA and super-resolution Orbitrap mass spectrometry | DIA, Plasma, Technology | Poster | 2020 | BoxCar DIA | 100 SPD, 30 SPD | Thermo Orbitrap Exploris 480 | ||
| Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags While Significantly Reducing Instrument Time | DDA, Lung, Tissue, TMT | Video | 2019 | Comparison study with TMT, same coverage in shorter time | 30 SPD, 60 SPD | Thermo Orbitrap Fusion Lumos | ||
| 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 | ||
| Characterization of glutathione proteome in CHO cells and its relationship with productivity and cholesterol synthesis | DDA, TMT | Publication | 2020 | 30 SPD | Thermo Q Exactive HF-X | |||
| 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 | ||
| 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 | ||
| 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 | ||
| A paired liver biopsy and plasma proteomics study reveals circulating biomarkers for alcohol-related liver disease | Clinical research, DIA, Liver, Plasma | Publication | 2020 | This publication from Matthias Mann groups in Copenhagen and Münich describes a paired liver biopsy and plasma proteomics study, which make use of Boxcar DIA scanning for a large clinical cohort of nearly 600 patients. They have developed a machine learning model based on their biomarker panel, which for the first time outperforms existing tests, … | 30 SPD | Thermo Q Exactive HF-X | ||
| Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags While Significantly Reducing Instrument Time | Offline fractionation, Tissue, TMT | Video | 2019 | Comparison study with TMT, same coverage in shorter time | 30 SPD, 60 SPD | Thermo Orbitrap Fusion Lumos |
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| Covalent Protein Painting Reveals Structural Changes In The Proteome In Alzheimer Disease | Alzheimer Disease, Brain, DDA, Tissue | Publication | 2020 | Development of Covalent Protein Painting (CPP), a structural proteomics approach to quantify changes in protein fold or altered protein-protein interaction for any protein in a proteome. CPP directly determines the relative surface accessibility of amino acid side chains by measuring the molar fraction of a chemical functionality that is accessible for chemical modification on the … | 30 SPD | Thermo Orbitrap Fusion Lumos |
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application note
Towards a Standardized Omics Platform with the 30 samples per day method
APPLICATION NOte
THE PROTEOMICS DILEMMA – HIGH THROUGHPUT ANALYSIS VERSUS PROTEOME DEPTH
TECH NOTE
EVOSEP ONE: A GRADIENT OFF-SET FOCUSING UHPLC INSTRUMENT FOR ROBUST AND HIGH THROUGHPUT PROTEOMICS
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