Automated workflows

Automation is becoming more and more important for modern proteomics laboratories, where large number of samples are prepared daily.

Explore how Evosep One users have standardized their sample prep workflows and learn the advantages of combining automated sample prep workflows with the Evosep One.

Automation elimintates variations and increase lab efficiency

Automated sample prep workflows have gained in popularity in proteomics laboratories. With an increased sample throughput on the Evosep One, it is possible to prioritize a high number of technical and biological replicates in a dataset providing excellent strength in the downstream bioinformatic analysis.

Automated workflows as part of the sample preparation process offers some great potential. Automation can remove human variation and increase lab efficiency, bottlenecks that most labs are constantly working to remove.

There are already many effective solutions available when it comes to setting up an automated sample preparation workflow. Based on the work of our users we have collected some examples for you to get inspired by.

Novo Nordisk center for protein research

Fully automated End-to-end workflow using the KingFisher™ Flex

At the University of Copenhagen the Olsen group has developed streamlined fully automated workflows for sample preparation in collaboration with Resyn Biosciences.

Protein digestion and phospho-enrichment is fully automated for up to 96 samples in parallel with the Kingfisher Flex robot from Thermo Scientific. It takes advantage of the fast scanning speed on the Orbitrap Exploris 480 MS – the ideal combination with short gradients on the Evosep One.

Read more about their work here


University of oxford

Automated Workflow for Immunoprecipitation using the Agilent Bravo AssayMAP liquid handling robot

This publication from University of Oxford led by Adan Pinto-Fernandez, describes a new methodology named ABPP-HT (high-throughput-compatible activity-based protein profiling).

It implements a semi-automated proteomic sample preparation workflow on the Agilent Bravo AssayMAP robot that increases the throughput capabilities of the classical ABPP workflow approximately ten times while preserving its enzyme profiling characteristics.

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Novozymes produces recombinant enzymes and microbial solutions for a plethora of bio-based industries.

To meet regulatory demands, they have developed a highly efficient and streamlined HCP workflow, which translate raw samples to data in less than 24 hours, with less than 2 hours of hands-on time.
With a focus on throughput, they have standardized on the Evosep One 200 samples per day method, combined with the Bruker timsTOF Pro and automated data processing by GeneData.

This platform allows them to robustly identify 700-1200 intra-cellular microbial proteins in a sample with average CVs of less than 5% based on five replicate injections.
Source: Anders Giessing, Senior Scientist at Novozymes



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Automated sample prep workflows

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In this webinar, we will focus on automated samples prep workflows. Users will share how they have standardized their sample prep workflows and discuss the advantages of combining automated sample prep workflows with the Evosep One.

More research using an automated sample prep workflow

Here you can see publications available using an automated sample preparation workflow featuring Evosep One. For a full overview of publications published using the Evosep One Technology visit our Literature room here

TitleSubjectMaterialYearSummaryInstituteEvosep methodMS instrumentationLearn More
Scalability for high-throughput proteomics – Evotip Pure integration with the Biomek i5 liquid handler, 2024With the development of faster and more sensitive mass spectrometers, proteomics has become an essential tool across diverse applications in both academia and industry. As proteomics studies become larger and analyses become more routine, the demand for standardized and scalable solutions is increas- ing. To address this need, we present four fully automated workflows developed …,

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Cost-efficient and scalable end-to-end workflow on the Opentrons OT-2 for neat plasma utilizing Evotip Pure, 2024Plasma proteomics stands at the forefront of biomedical research as it offers invaluable insights into disease progression and holds immense potential for minimally invasive diagnostics. With recent advancements toward faster LC-MS analysis, the demand for robust, high-throughput, and cost-efficient sample preparation has increased. To address this, we present a fully automated plasma sample preparation workflow …, ,

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Efficient proteomics with an automated sample preparation strategy leveraged by Evotip Pure and the AssayMAP Bravo2024Proteomics is undergoing a significant shift and rapidly evolving towards more efficient and user-friendly technologies that can handle higher quantities of samples. The Evosep One, combinedwith improvements in high-end mass spectrometry, has played a vital role in transforming this field, making it possible to analyze hundreds of proteomes daily. Consequently, the bottleneck in high-throughput proteomics …, , ,

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Unlocking the plasma proteome with Evotip Pure based, standardized and scalable workflows, 2024Plasma stands out as one of the most readily accessible biofluids, with an estimated pres- ence of over 10,000 distinct proteins. A significant portion of these are released from organs and tissues. The ability to measure such proteins in a robust manner holds tremendous potential for advancing next-generation multiplexed biomarker discovery. However, methods must be …

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Evotip Pure brings innovative sample storage and introduction to high-sensitivity and scalable LC-MS workflows2024The Evotip Pure technology has emerged as a key component of proteomics workflows enabling seamless integration of upstream sample prepa- ration with LC-MS analysis by reducing sample handling steps and thereby efficiently minimizing sample losses to plasticware, which significantly improves recovery and reproducibility. These properties are even more critical in single-cell proteomics (SCP), a rapidly …

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MassSpecPreppy—An end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications2023

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Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel, , , 2023

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End-to-end, fully automated digestion protocol and Evotip Pure workflow on the Opentrons OT-22023The Evosep One provides a standardized and user-friendly platform that enables routine analysis of hundreds of proteomes per instru- ment per day, which has shifted the bottleneck for realizing high-throughput proteomics towards sample preparation. To address this, we have developed a fully automated Evotip loading protocol, based on a unique layered sandwich approach, which is …,

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Fully automated, rapid, robust sample loading on Evotip Pure with the Agilent AssayMAP Bravo2023Automation and robotics have revolutionized the field of proteomics, offering solutions to the growing need for streamlined workflows and efficient sample processing. In this context, automated loading of Evotips has emerged as a pivotal advancement in sample preparation workflows. The Evotip can now be loaded using an innovative and fully automated strategy with the Agilent …, ,

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A complete and automated sample preparation strategy for high-throughput and standardized proteomics, applied to a clinical cohort of patient plasma samples2022,

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Automated sample prep workflows2021In this webinar, we will focus on automated samples prep workflows. Users will share how they have standardized their sample prep workflows and discuss the advantages of combining automated sample prep workflows with the Evosep One.

Watch webinar

Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures, , , , , 2021In 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.,

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Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids, , , 2021In 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.

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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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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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