Protein-protein interactions

Proteins are the fundamental building blocks and control all biological systems in a cell. The physical interaction between proteins define specific biological functions and signaling networks.

Explore how our customers have used Evosep One to scale the study of complex protein environments and understand cell biology.


Proteins are the functional molecules in our body and contribute to all processes of life. Like humans, proteins act in social networks and the understanding of the cellular machinery and disease mechanisms can be found in the dynamic networks of protein complexes. Insights into the physical rewiring of protein-protein interactions in response to i.e., mutations and pathological conditions can lead to the identification of potential druggable targets.

By using quantitative mass spectrometry-based proteomics, unbiased disease-mediated changes in protein-protein interactions can be studied on a global scale. The Evosep One nicely facilitates large-scale studies in a high-throughput manner.


It is important to leave the proteins in their native conformation for pull-down assays. Thus, non-ionic detergents are often used in the lysis buffer to solubilize proteins.

However, even minute levels of detergent severely decreases chromatographic resolution in LC-MS as it accumulates in the analytical column and the backpressure increases with each sample.

This can be circumvented by using the Evosep One as the Evotip is a disposable trap column, which is discarded after each sample. Our patented partial elution concept leaves all contaminants on the tip ensuring the feasibility of large-scale interactome studies.


Researchers from the Olsen Group at University of Copenhagen have mapped the EGF-dependent in vivo phosphotyrosine signaling in lung tissue quantifying more than 1000 phosphotyrosine sites.

To assign function to all EGF-regulated sites, they determined their recruited protein signaling complexes in lung tissue by interaction proteomics. This provides insights to how mutations near tyrosine residues introduce molecular switches that rewire cancer signaling networks and revealed oncogenic properties of such a lung cancer EGFR mutant.

They demonstrated the scalability of their approach by performing more than 1000 phosphopeptide pulldowns and analyzed them with the 60 samples per day method using DIA on a Q Exactive HF-X mass spectrometer.

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The collaboration between the Mann group at the Max-Planck Institute for Biochemistry and the Chan Zuckerberg Biohub integrates genome engineering, confocal imaging, mass spectrometry and data science to systematically map protein localization in live cells and protein interactions under endogenous expression conditions.

They generated 1311 CRISPR-edited cell lines and applied a machine learning framework to encode the interaction and localization profiles of each protein. This resulted in almost 4000 pull-downs, which were analyzed with the 60 samples per day method, in just over two months of measurement time on a timsTOF Pro.

Their approach provides a data-driven description of the molecular and spatial networks that organize the human proteome.

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MEET OUR USERS and their research with protein-protein interaction analysis 


Available on demand 

During this webinar Leonard Foster (University of British Colombia, Vancouver) and Lisa Jones (University of Maryland, Baltimore) will provide their insight into the use of Evosep One in the study of complex protein environments.

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Find all publications, product brochures and presentations with Evosep One

More research on Protein-protein interactions

Here you can see publications available on protein-protein interaction analysis featuring Evosep One. For a full overview of publications published using the Evosep One Technology visit our Literature room here

TitleSubjectMaterialYearSummaryInstituteEvosep methodMS instrumentationLearn More
Time evolution of PEG-shedding and serum protein coronation determines the cell uptake kinetics and delivery of lipid nanoparticle formulated mRNA, , 2021This 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.

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A universal peptide matrix interactomics approach to disclose motif dependent protein binding, 2021This 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.

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Exploitation of the Secretory Pathway by SARS-CoV-2 Envelope, , 2021This 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.

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Co-translational assembly and localized translation of nucleoporins in nuclear pore complex biogenesis, 2021In 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.

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Malaria Parasite Schizont Egress Antigen-1 Plays an Essential Role in Nuclear Segregation during Schizogony, , 2021This 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.

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The Host Interactome of Spike Expands the Tropism of SARS-CoV-2, , 2021This 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.

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Interactions of Viral Proteins from Pathogenic and Low or Non-Pathogenic Orthohantaviruses with Human Type I Interferon Signaling, 2021A 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.

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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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application note
Evosep One solves the proteomics dilemma – covering high throughput analysis and proteome depth
application note
end-to-end, fully automated digestion protocol and evotip pure workflow on the opentrons ot-2
application note
fully automated, rapid, robust sample loading on evotip pure with the agilent assaymap bravo
EVOSEP ONE: A Standardized Separation
Tool for Clinical Omics