Automated workflows

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

Learn about the advantages of automated sample prep workflows and explore how Evosep One users have standardized their sample prep workflows with automation.

Automation eliminates variations and increases lab efficiency

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.

Automation can remove human variation and increase lab efficiency, bottlenecks that most labs are constantly working to remove.

There are already several elegant solutions available when it comes to setting up an automated sample preparation workflow and it is now also possible to perform automated sample loading of Evotips, which can be extended to integrate upfront digestion workflows.



As a step towards end-to-end workflows, we have developed a simple and automation friendly protocol for sample loading on Evotips, which makes use of a layered sandwich approach with defined airgaps between the layers.

This sandwich is pushed through the Evotip with the OT-2 pipette for 100 seconds leaving the Evotip ready for injection on the Evosep One. The automated sample loading protocol relies on a defined sample volume of 20 µl and solvent A volumes of 15 µl and 150 µl respectively to keep the sandwich intact through loading.

The protocol has been converted into an easy-to-use HTML form, that generates a complete python script for use in the Opentrons app, allowing the user to load from 8 to 288 Evotips in a single run.

Learn more about the protocol and how to access it here 


The Agilent AssayMAP Bravo supports efficient and reproducible loading of samples onto Evotips with a median peak area CV of 6.3% and 8.5% across a box of Evotips when using a single column and a full head respectively.

This workflow can easily be combined with a range of already existing workflows on the AssayMAP Bravo. Furthermore, the Evosep One combined with the Agilent 6495C represents a stable analytical platform for targeted applications.

Learn more about the protocol and how to access it here 

Novo Nordisk center for protein research


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.

Read full publication



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



MEET OUR USERS and learn how they have implemented automation as part of the sample preparation

Automated sample prep workflows

available on demand

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
High-Field Asymmetric Waveform Ion Mobility Spectrometry and Parallel Reaction Monitoring Increases Sensitivity for Clinical Biomarker Quantitation from FormalinFixed, Paraffin-Embedded Tumor Biopsies, , , 2022

Read publication here

The setup and optimization of a complete global proteomics two-dimensional liquid chromatography system, using Spider Fractionation, 2021

Read publication here

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.,

Read publication here

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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Find all publications, product brochures and presentations with Evosep One


application note
A complete, automated Opentrons OT-2 loading protocol
for simplified sample loading of Evotip Pure
application note
The proteomics dilemma – High throughput analysis versus proteome depth
Evosep application note for AssayMAP bravo protocol for Evotip
Applicaton Note
A semi-automated AssayMAP Bravo protocol for robust Evotip loading and high-throughput analysis on the Evosep One
EVOSEP ONE: A Standardized Separation
Tool for Clinical Omics