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.

Unlock the potential of single cell proteomics with Evotip Pure

With single cell proteomics, we can gain valuable biological insights from individual cells, but the limited amount of material in a single cell poses significant challenges. To ensure high-quality, reproducible, and comparable data at a single cell level, standardization is key.

Our Evotip technology is an integral component of the Evosep One system, designed to streamline proteomics workflows. The Evotip enables efficient front-end sample preparation, combining peptide purification with sample loading and elution, facilitating seamless integration with liquid chromatography and mass spectrometry analysis.

Capture low-abundance proteins with
Whisper Flow Technology

To overcome challenges associated with single cell analysis, Whisper methods combined with fully automated sample preparation on the Evotip Pure is the perfect match for ultra-high sensitivity applications, where sample amounts are limited.

The plug’n play approach eliminates the need for extensive instrument modifications or specialized expertise. This streamlines your analytical workflow and reduces the barriers to perform high-sensitivity proteomics. And most importantly, the technology seamlessly integrates into standard Evosep One hardware, allowing researchers to adopt the methods quickly and efficiently.

Process thousands of samples on the same emitter and column without loss of performance. The system remains stable over extended periods, ensuring reproducibility for large sample cohorts.

The Olsen group

One-tip protocol delivers Easy and sensitive, end-to-end label-free single cell proteomics 

To accommodate the demands of single cell proteomics, the Olsen group have introduced the One-Tip protocol, a simplified workflow using Evotip Pure. The Evotip serves as a sample storage and introduction device for the Evosep One. By integrating cell lysis and digestion on the Evotip directly, you get a simple one-pot workflow for proteomics, as no further sample handling is needed. 

Coupled with the Whisper 40 SPD method, they benchmarked the sensitivity and reproducibility of the One-Tip methodology by varying the number of HeLa cells from 20 to 3,000 cells.

 The simplicity of the workflow makes it easy to automate on liquid handling robots and to become a new cornerstone for sensitive and high throughput proteomics.

Cellenion CellenOne

Automated Simple, seamless
sample preparation

Sample collection, preparation, and transfer, are often the primary sources of sample losses in high sensitivity proteomics applications.

To address this, a prototype chip, proteoCHIP™ Evo96, compatible with the Cellenion cellenONE instrument has been developed. The chip enables an automated workflow for direct transfer of peptides into Evotips and removes manual handling steps.

This workflow combines sample preparation with the Cellenion platform, pipetting-free transfer of single cell protein digests into Evotips, and analysis with the Whisper 40 SPD method together with the Bruker timsTOF SCP mass spectrometer.

High sensitivity is required in all steps of a workflow and this solution demonstrates excellent proteome coverage for single cells, with up to 4000 protein groups identified per single cell.

The Mann lab

ultra-high sensitivity workflow from readily available components

In a recent publication from the Mann lab they describe an improved workflow building on recent developments in multiplex-DIA.Their tailored mDIA workflow includes user-friendly dimethyl labelling on the Evotip, automation capabilities, and enhanced quantification options to directly address the needs of many single cell researchers, offering simplicity, reliability, and expanded possibilities for proteomics research.The mDIA workflow, especially when combined with reference channels, offers increased throughput and depth in proteomic analysis. It has the potential to enable the characterization of a significant portion of the expressed proteome in single cells, making it a valuable technology for precision oncology and clinical proteomics.

Their entire ultra-high sensitivity workflow builds entirely upon readily available components. With only three pipetting steps, it is easily automatable on standard liquid handling robots.

“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 developed new innovative workflows in their research with Single cell proteomics

Single Cell proteomics

Available on demand

See how the Evosep One empowers researchers to investigate the proteomic landscapes within single cells, paving the way for new discoveries and innovative therapeutic approaches.

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

Read publication here

Unique DUOX2+ACE2+ small cholangiocytes are pathogenic targets for primary biliary cholangitis, 2023

Read publication 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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Find all publications, product brochures and presentations with Evosep One


application note
A specialized method using Whisper Flow technology with a throughput of 80 samples per day
application note
Evosep One solves the proteomics dilemma – covering high throughput analysis and proteome depth
Application Note
Pushing the boundaries for robust and high-throughput single cell analysis
EVOSEP ONE: A Standardized Separation
Tool for Clinical Omics