Single Cell proteomics

Single cell proteomics is a field in rapid development, enabled by significant technological improvements over the last years and it presents a key contribution to answer fundamental biological questions about heterogeneity within complex systems.

Explore how our customers have used the ultra sensitive Evosep One Whisper methods to achieve these technological advantages for single-cell proteomics.


Single cell proteomics is an emerging technology with a lot of promise but there are still several challenges, mainly about how to efficiently deliver minute sample amounts to the mass spectrometer and secondly how to scale the workflow to cohorts of several thousand cells.

A great deal of effort has been made in how to re-think sample preparation workflows to be automated and involve as few steps as possible to minimize sample losses. Evotips support handling and preservation of single cell digests and is a key component for loading very small sample amounts for ultra-sensitive chromatography with the Whisper methods.


One of the greatest goals of single-cell proteomics is to reach the needed sensitivity and maintain the performance throughout the lifetime of a project.

Andreas-David Brunner from the Mann group at the Max Planck Institute of Biochemistry has developed a robust workflow combining miniaturized sample preparation, the Whisper 40SPD beta method and diaPASEF on the timsTOF SCP mass spectrometer.

This workflow allowed the accurate quantification of proteomes and their changes during the cell cycle up to a depth of 1,300 proteins when loading single, FACS-isolated cells.

Read more here


US HUPO 2021 seminar

LEVERAGING THE POWER OF WHISPER for high-throughput single-cell proteomics

The Schoof group at the Technical University of Denmark has developed a multiplexed single-cell proteomics strategy to identify protein landscapes of individual cells within cellular hierarchies.

By using the latest state-of-the-art instrumentation and labelling kits with intelligent data acquisition, the Evosep Whisper methods provide a careful balance between unprecedented throughput and proteome depth of single cells.

Listen to the presentation from US-HUPO 2021 on YouTube.


“Single cell proteomics is becoming a practical reality and we are now able to routinely measure large cohorts of single cell proteomes to reveal new biological information. The Evosep One has been pivotal to scale this robustly to thousands of real single cell measurements, making an ideal and standardized platform for future biomarker discovery work”,

Professor Matthias Mann, Max-Planck Institute of Biochemistry,
Proteomics and Signal Transduction


MEET OUR USERS and learn how they have implemented the Whisper methods in their work with Single cell proteomics

Whisper is here

Available on demand

Whisper is the latest Evosep One innovation that allow plug-and-play, split-free 100 nl/min performance. The new methods make use of Evosep’s unique low pressure gradient formation and very accurate flow control on the same standard system without technical modifications. 

More research with single cell proteomics

Here you can see publications available single cell proteomics featuring Evosep One. For a full overview of publications published using the Evosep One Technology visit our Literature room here

TitleSubjectMaterialYearSummaryInstituteEvosep methodMS instrumentationLearn More
Ultra sensitive and high throughput proteomics on the standardized Evosep One platform, 2021The recently introduced Whisper™ Flow Technology uses preformed gradients and disposable Evotip trap columns with the sample preloaded and immobilized to robustly and reproducibly handle very small sample amounts, down to actual single cells, at sub-100 nl/min flowrates.,

Watch webinar here

High sensitivity limited material proteomics empowered by data- independent acquisition on linear ion traps2022,

Read publication here

Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation, 2022

Read publication here

Ultra-high sensitivity proteomics on the timsTOF SCP2021This application note by Bruker describes the timsTOF SCP instrument and demonstrates robust proteome coverage down to 250 pg of peptide using the Whisper 40SPD method.

Read application note here

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation, , 2020In this publication, the Mann group in Münich describes their innovative workflow for single-cell proteomics. They apply a nearly loss-less miniaturized sample preparation workflow to our robust Whisper 40SPD method and combine it with diaPASEF on a modified timsTOF mass spectrometer for a total of 420 FACS sorted single cells.,

Download publication or learn more on our website

Proteomics at the single cell level with Evosep Whisper and the timsTOF SCP2022In this app note from Bruker you can learn about our joint work to bring more sensitivity to proteomics at the single cell level. The timsTOF SCP and the Evosep One has proven to be a great match to unlock the potential of single cell proteomics.

Read publication here

A deeper look at carrier proteome effects for single-cell proteomics, , 2021This 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.

Read publication here

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