The 60 samples per day method

STANDARD METHOD

More than 4000 proteins in 21 minutes

The 60 SPD method is one of our most popular standard methods as it provides an excellent balance between throughput and depth.

The method is ideal for deep fractionated proteomes as well as single-shot analyses, where more than 4000 proteins are routinely identified with DIA.

ENHANCED PROTEOME COVERAGE WITH THE PERFORMANCE COLUMN

The performance column is for exceptional restult and available for the 60 samples per day method. It is packed with 1.5 μM C18 beads, which puts some demands on usage such as requiring elevated column temperature control to manage system backpressure.

The smaller beads reduces peaks capacity of 60%. Consequently, the proteome coverage is enhanced, and the column provides a robust and competetive commercial option – on the same level as the home-pulled and packed options, but with better reproducibility and life-time.

The boost in sensitivity is particularly noticeable for lower loads, where peptide and protein coverage is improved with 100%.

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QUANTITATIVE RAT ORGAN PROTEIN ATLAS BY TMT AND dia-lfq

In this publication, the Olsen Group from the Novo Nordisk Foundation Center for Protein Research, Denmark, perform a comprehensive rat tissue specific protein atlas. They compare tandem mass tags (TMT11-plex) with DIA-based label-free quantification of 12 tissues covering the major mammalian organs from three individual male rats.

The spectral library generated, represents 213,000 unique peptides covering 12,909 protein-coding genes and should represent a resource for the proteomics community.

Unsupervised hierarchical clustering of relative protein abundances across tissues reveal very similar protein expression patterns between DIA-FAIMS and TMT experiments, suggesting that both quantification strategies provides very similar biological insights.

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UNLEASHING THE TRUE POWER OF DIA ACQUISITION WITH SHORT GRADIENTS

In this case study, Ben C. Collins from Queen’s University, Belfast and Ting Huang, Northeastern University, Boston discuss the importance of fast and standardized workflows

Analysis speed can be increased by one order of magnitude with the Evosep One, reducing analysis time from roughly 10 days to a little more than 1 day without significant loss of information at the protein complex level. This enables novel applications for profiling proteome organization dynamics.

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Data courtesy: Moritz Heusel and Isabell Bludau, ETH Zürich

FAST AND REPRODUCIBLE PHOSPHOPROTEOMICS

This application note describes an automated workflow for protein digestion as well as enrichment of phosphopeptides using MagReSyn magnetic beads for the entire workflow.

By employing a streamlined and automated workflow for phosphopeptide enrichment in  combination with fast and robust chromatographic performance delivered by the Evosep One, we offer a workflow for routine use in large clinical studies, which can also be easily extended to tissue samples.

The use of automation in the entire workflow eliminates the hands-on challenges and ensures excellent reproducibility when handling a large number of samples.

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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 device how fast you want to go. 

Standard method

The highest peak capacity per minute with our fastest method for ultra-high throughput analysis.

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Standard method

Excellent sequencing speed with most peptides per minute among our standard methods.

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Standard method

A great “in-between” method with run-to-run reproducibility of just one second.

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Standard method

The most popular method with an excellent balance of throughput and depth.

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Standard method

The longest method with a 44-minute gradient providing the best overall proteome coverage.

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application note
Towards a Standardized Omics Platform with the 60 samples per day method
APPLICATION NOte 
THE PROTEOMICS DILEMMA – HIGH THROUGHPUT ANALYSIS VERSUS PROTEOME DEPTH
CASE STUDY
Unleashing the true power of DIA/SWATH data acquisition with short gradients
application note
Fast and reproducible phosphoproteomics using MagReSyn® Amine and Ti-IMAC HP magnetic beads and the Evosep One
application note
Improve and enhance your proteome coverage with the Performance column

Explore more

Do you want to know how our users are already taking advantage of the 300 Samples per day method? Find all publications from users and collaboration partners here. Visit our Literature Room for a full overview.

TitleSubjectMaterialYearSummaryInstituteEvosep methodMS instrumentationLearn More
Towards a Standardized Omics Platform with the 60 samples per day method2020This method has a 21-minute gradient and a cycle time of 24 minutes. The method is designed for our EV-1064 column and we highly recommend to use this column with our range of emitters and spray adapters for optimal performance.

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Improve and enhance your proteome coverage with the Performance column2019We have developed an additional Performance column for the 60 and 100 samples per day methods (SPD) to address applications with high demands.,

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The proteomics dilemma – High throughput analysis versus proteome depth2019With 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., , , ,

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Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids, , 2021The Van Eyk group presents a standardized workflow for precise high-throughput proteomics of blood biofluids using the 60 SPD method. They established optimal conditions for sample preparation and DIA analysis in plasma, then automated and adapted this for depleted plasma and whole blood.

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High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe, 2021The 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., ,

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A robust mass spectrometer for precision medicine – the Orbitrap Exploris 240 mass spectrometer for large-scale plasma protein profiling, 2021This 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.

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Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers, , , 2021In 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.,

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Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease, , 2021In 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 …

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SPIN – Species by Proteome Investigation, 2021This 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., ,

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High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion, 2021This 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.

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R1441G but not G201S Mutation Enhances LRRK2 Mediated Rab10 phosporylation in human Peripheral blood neutrophils, , 2021This publication from University of Dundee led by Esther Sammler, describes that in vivo LRRK2 dependent

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Spatial-proteomics reveal in-vivo phospho-signaling dynamics at subcellular resolution, , , 2021This 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.

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Deciphering the LRRK code: LRRK1 and LRRK2 phosphorylate distinct Rab proteins and are regulated by diverse mechanisms, 2020This 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.

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Development of a multiplexed targeted mass spectrometry assay for LRRK2-phosphorylated Rabs and Ser910/Ser935 biomarker sites, , 2020This 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.,

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diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition, 2020A 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., ,

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High throughput proteome and phosphorpoteome sample processing coupled to fast gradient DIA, , , , , , , 2020High throughput workflows for proteomics, ,

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Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides in vitro, , , 2019Urinary peptidomics in early type 1 diabetes

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New Orbitrap Exploris 480 Mass Spectrometer Coupled with Evosep One, , , 2020Brochure of Exploris 480 with Evosep data from piece no 1, ,

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Development of a robust and reprodusible method for detection of citrullination in complex samples, , , 2018Detection of citrullination in complex samples

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How to get Speed and Depth in yout Host Cell Protein, , 2018

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A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-Robust Proteomics, , , 2018Description of Evosep

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Robust and Reprodusible Protein Quantification in Plasma Using the Evosep One and the Agilent 6495 Triple Quadrupole LC/MS, , 2020Agilent feasibility study

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Development of a Novel LC Concept for Clinical Proteomics, , 2018Description of Evosep One

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Increasing proteome coverage using cysteine-specific DIA Mass spectrometry – Cys-DIA, 2020DIA on cysteine-specific peptides

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Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags While Significantly Reducing Instrument Time, , , 2019Comparison study with TMT, same coverage in shorter time,

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A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism, 2020

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Improving proteome coverage and peptide identification rates in short LC gradients, , , , , 2020, ,

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High-throughput proteomics with Evosep One, , , , , 2020, ,

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Rapid proteome analyses using the Evosep One, , , 2018

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Sensitive, Rapid, Robust and Reproducible Workflow for Host Cell Protein Profiling in Biopharmaceutical Process Development, , 2020HCP analysis in Biopharma,

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Using Artificial Intelligence on Ultrafast LC-MSMS-DIA runs for Bacterial Identification in Urine, , 2019View 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.  , ,

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High-throughput 4D-Proteomics – Application of dia-PASEF® and the Evosep One for short gradients, 2020diaPASEF app note  , , ,

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Fast and reproducible phosphoproteomics using MagReSyn® Amine and Tim-IMAC HP magnetic beads and the Evosep One, , 2020Read 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.

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Consistency, consistency – Automated Sample Prep for Translational Proteomics, 2020In 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.

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An Ultra High-Throughput Plasma Protein Profiling (uHTPPP) Workflow Using a Modified Quadrupole-Orbitrap Mass Spectrometer, , , , , 2020In 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.,

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Scalable and Automated Plasma Workflow Based on the Thermo Scientific Q Exactive HF-X MS Platform, , , , 2019In 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., ,

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Advancing Interactomics Workflows with 4D-Proteomics on the timsTOF Pro, 2020In 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.

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Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites, , , , 2019In 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.

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timsTOF Pro with PASEF and Evosep One: Maximizing throughput, robustness and analytical depth for shotgun proteomics, 2018Read 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., ,

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Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV, , , 2020This 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.,

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Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags While Significantly Reducing Instrument Time, , 2019Comparison study with TMT, same coverage in shorter time,

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Increasing Throughput: From Pre-Clinical Models To Protein Complexes, 2019Comparison study with >400 samples, same coverage in shorter time

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Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles, , 2020In 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.

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A Compact Quadrupole-Orbitrap Mass Spectrometer With Faims Interface Improves Proteome Coverage In Short Lc Gradients, , , , , , , , , 2020Test of Orbitrap Exploris with DIA and TMT, proteome and phospho., ,

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Advanced Host Cell Protein (Hcp) Analysis With Tims Qtof Ms Powers Biopharmaceutical Development , , 2019Descriptive piece of HCP analysis on the timsTOF

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High-Throughput Proteomics Quantification Enabled by Fast LC Separation and Advanced PRM Acquisition, , 2018High throughput LC-PRM to monitor the main protein components of AKT/mTOR signaling pathway., ,

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