publications

Here, you can find the latest material presented by Evosep and our collaboration partners and also discover older publications.

Featured PUBLICATIONS

FAST AND ROBUST PROTEOME SCREENING PLATFORM IDENTIFIES NEUTROPHIL EXTRACELLULAR TRAP FORMATION IN THE LUNG IN RESPONSE TO COBALT FERRITE NANOPARTICLES

This study demonstrate a proteomics-based toxicity screening with high sample throughput easily transferrable to other nanoparticle types.

Authors: Anja M. Billing, Kristina B. Knudsen, Andrew J. Chetwynd, Laura-Jayne A. Ellis, Selina V. Y. Tang, Trine Berthing, Håkan Wallin, Iseult Lynch, Ulla Vogel,Frank Kjeldsen

A COMPACT QUADRUPOLE-ORBITRAP MASS SPECTROMETER WITH FAIMS INTERFACE IMPROVES PROTEOME COVERAGE IN SHORT LC GRADIENTS

In collaboration with Thermo Fisher Scientific, the Olsen Group and Novo Nordisk Foundation Center for Protein Research have described the new Thermo Scientific™ Orbitrap Exploris™ 480 mass spectrometer for high-throughput analyses with short gradients using the Evosep One.

Advanced Host Cell Protein (HCP) Analysis with TIMS QTOF MS Powers Biopharmaceutical Development 

This recent study from Bruker Daltonics looks into the ever increasing requirement for analytical methods with rigorous impurity testing, to monitor contaminants during manufacture and prior to product release.

TECH NOTE: EVOSEP ONE: A GRADIENT OFF-SET FOCUSING UHPLC INSTRUMENT FOR ROBUST AND HIGH THROUGHPUT PROTEOMICS

Evosep One has been designed specifically to address and eliminate the prevalent challenges associated with throughput and robustness of nano-flow LC-MS workflows while maintaining sufficient sensitivity and resolving power for clinical omics applications.

Authors: Nicolai Bache, Ole Hoerning, Lasse Falkenby and Ole Vorm

Publications

Here you can find tbe latest publications from our users and collaboration partners

Sampling the human population – ultra-highthroughput plasma protein profiling (uHTPPP) sample preparation for translational proteomics

This application note by Thermo Fisher Scientific presents a robust, precise, and reproducible highthroughput sample preparation workflow for mass spectrometry-based large population cohort studies.

Authors: Sarah Trusiak, Sergei Snovida, Bhavin Patel, Ryan Bomgarden, Emily I. Chen

Increasing proteome coverage using cysteine-specific DIA Mass spectrometry – Cys-DIA

A group at University of Southern Denmark demonstrate a new DIA mass spectrometric method for quantitative proteomics using only systeine containing peptides which increased the coverage of the identifiable and quantifiable proteome in DIA/SWATH analyses by >35% compared to the conventional DIA/SWATH methods.

Authors: Muhammad Tahir, Arkadiusz Nawrocki, Henrik J. Ditzel, View ORCID ProfileMartin R. Larsen 

Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles

This study demonstrate a proteomics-based toxicity screening with high sample throughput easily transferrable to other nanoparticle types.

Authors: Anja M. Billing, Kristina B. Knudsen, Andrew J. Chetwynd, Laura-Jayne A. Ellis, Selina V. Y. Tang, Trine Berthing, Håkan Wallin, Iseult Lynch, Ulla Vogel,Frank Kjeldsen*

MaxQuant software for ion mobility enhanced shotgun proteomics

Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. For the plasma proteome samples, the Evosep One (Evosep) was used to achieve low overhead times and a high sample throughput by using the 100 sample/day method.

Authors: Nikita Prianichnikov, Heiner Koch, Scarlet Koch, Markus Lubeck, Raphael Heilig, Sven Brehmer, Roman Fischer and Jürgen Cox 

Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

In a collaboration with Robert Rissman of UC San Diego, the Yates group at the Scripps Research Institute in La Jolla developed a method to quantitatively measure protein misfolding across a proteome.

A COMPACT QUADRUPOLE-ORBITRAP MASS SPECTROMETER WITH FAIMS INTERFACE IMPROVES PROTEOME COVERAGE IN SHORT LC GRADIENTS

In collaboration with Thermo Fisher Scientific, the Olsen Group, Novo Nordisk Foundation Center for Protein Research has described the new Orbitrap Exploris 480 mass spectrometer for high-throughput analyses with short gradients using the Evosep One.

NEW THERMO SCIENTIFIC™ ORBITRAP EXPLORIS™ 480 MASS SPECTOMETER COUPLED WITH EVOSEP ONE

In this brochure, Thermo Fisher Scientific introduce the new Thermo Scientific™ Orbitrap Exploris™ 480 mass spectrometer which, combined with the Evosep One, increased proteome coverage by up to two times with short gradients enabling high-throughput applications.

COVALENT PROTEIN PAINTING REVEALS STRUCTURAL CHANGES IN THE PROTEOME IN ALZHEIMER DISEASE

This paper by the Scripps Research Institute introduces a mass spectrometry-based structural proteomics approach which reveals structural changes in the proteome in Alzheimer disease. Evosep One coupled with Thermo Fisher™ Orbitrap Exploris™ 480 mass spectrometer was used during this research for brain samples analysis.

Authors: C. Bamberger, S. Pankow, S. Martinez-Bartolome, M. Ma, J. Diedrich, R. A. Rissman, J. R. Yates III

Advanced Host Cell Protein (HCP) Analysis with TIMS QTOF MS Powers Biopharmaceutical Development 

This recent study from Bruker Daltonics looks into the ever increasing requirement for analytical methods with rigorous impurity testing, to monitor contaminants during manufacture and prior to product release.

Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides in vitro 

Using unbiased and targeted mass spectrometry-based techniques this paper aimed to predict peptide bioactivity and to identify the potential proteases responsible for generating the peptides.

Authors: Julie A. D. Van, Sergi Clotet-Freixas, Joyce Zhou, Ihor Batruch, Chunxiang Sun, Michael Glogauer, Luca Rampoldi,  Yesmino Elia, Farid H. Mahmud, Etienne Sochett,  Eleftherios P. Diamandis, James W. Scholey, Ana Konvalinka

Accurate Detection of the Four Most Prevalent Carbapenemases in E. coli and K. pneumoniae by High-Resolution Mass Spectrometry

A team at Erasmus MC have developed a new method to accurately and rapidly detect specific resistance mechanisms simultaneously by combining high-resolution mass spectrometry with liquid chromatography.

Authors: Dimard E. Foudraine, Lennard J. M. Dekker, Nikolaos Strepis, Michiel L. Bexkens, Corné H. W. Klaassen, Theo M. Luider, Wil H. F. Goessens

Rapid Host Cell Protein (HCP) Detection with Advanced Trapped Ion Mobility Spectrometry (TIMS) Technology

The robust and reproducible 21 min gradient on the Evosep One instrument provides rapid analysis of downstream processes, with fast runs and high throughput, enabling batch-to-batch fingerprinting. Quantitation is often necessary and the faster analysis with Bruker’s timsTOF Pro is advantageous for more routine applications with coverage of 50+ HCPs at 1% false discovery rate (FDR). 

Authors: Guillaume Tremintin, Stuart Pengelley, Michael Greig

Scalable and Automated Plasma Workflow Based on the Q Exactive HF -X MS Platform

Read about our recent developments with the Thermo Fisher Scientific Precision Medicine Science Center and see the results of our joint work to develop standardized workflows for large cohort plasma profiling. 

Authors: Jing Wang, Sarah Trusiak, Ryan D. Bomgarden, Sergei Snovida, Emily I. Chen, Thermo Fisher Scientific Precision Medicine Science Center

Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites

The need for scalable methods for functional annotation of phosphotyrosine sites has led the Olsen group, Novo Nordisk Foundation Center for Protein Research in Copenhagen, to develop a new mass spectrometry-based workflow for high-throughput analyses.  

Authors: Alicia Lundby, Giulia Franciosa, Kristina B. Emdal, Jan C. Refsgaard, Sebastian P. Gnosa, Dorte B. Bekker-Jensen, Anna Secher, Svetlana R. Maurya, Indranil Paul, Blanca L. Mendez, Christian D. Kelstrup, Chiara Francavilla, Marie Kveiborg, Guillermo Montoya, Lars J. Jensen, Jesper V. Olsen 

Standardized and scalable plasma protein quantitative profiling workflow using human blood based on the Thermo Scientific™ Q Exactive™ platform

Together, Thermo Scientific™ Q Exactive™ platform and Evosep are on a joint mission to develop standardized and scalable plasma protein quantitative profiling workflows. Our recent developments have been featured in this application note by the Precision Medicine Science Centre led by Dr. Emily Chen.

Authors: Jing Wang, Sarah Trusiak, Ryan D. Bomgarden, Sergei Snovida, Michelle Dubuke, Emily I. Chen

Study: Increased De Novo Protein Sequencing Coverage with Optimal Protease Cocktail

This study from Rapid Novor Inc presents how they de novo sequence 166 mAb using Evosep One coupled to Thermo Scientific™ Orbitrap Fusion™ Tibrid™ mass spectrometer.  

Authors: Le Bihan, T., Taylor, P., McDonald, Z., Liu, Q., Shen, J., Gorospe, K., Xu, X., Hosfield, C., Ma, B.

A NOVEL LC SYSTEM EMBEDS ANALYTES IN PRE-FORMED GRADIENTS FOR RAPID, ULTRA-ROBUST PROTEOMICS

This paper presents a novel concept that opens entirely new possibilities in proteomics in general and in clinical proteomics. With a simplified design it enables a robust operation over thousands of sample injections and analyzes samples in an extremely robust and high throughput manner, without sacrificing in depth proteomics coverage.

Authors: Nicolai Bache, Philipp E. Geyer, Dorte B. Bekker-Jensen, Ole Hoerning, Lasse Falkenby, Peter V. Treit, Sophia Doll, Igor Paron, Johannes B. Muller, Florian Meier, Jesper V. Olsen, Ole Vorm, and Matthias Mann

Plasma proteomics goes high throughput – timsTOF Pro with PASEF and 4D feature alignment to quantify 500 plasma proteins in 11.5 min

The timsTOF Pro with PASEF and the Evosep One for biomarker discovery in large  sample cohorts of human blood plasma.

Authors: Thomas Kosinski, Raphael Heilig, Dalila Bensaddek, Nicolai Bache, Ole Bjeld Hørning, Roman Fischer, Heiner Koch

Evosep One Enables Robust Quantitative Deep Proteome Coverage using Tandem Mass Tags while Significantly Reducing Instrument Time

This paper by Jonathan Krieger, PhD and collagues shows how Evosep One coupled to a Thermo Scientific™ Orbitrap Fusion™ Lumos™ Tribrid™ mass spectrometer enables robust quantitative deep proteome coverage using tandem mass tags while significantly reducing instrument time.

Authors: Jonathan R. Krieger, Leanne E. Wybenga Groot, Jiefei Tong,  Nicolai  Bache, Ming S. Tsao, Michael F. Moran

Online parallel accumulation − serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

In bottom−up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, while mass spectra are acquired in about 100 microseconds with time−of−fight (TOF) instruments.

Authors: Florian Meier, Andreas-David Brunner, Scarlet Koch, Heiner Koch, Markus Lubeck, Michael Krause, Niels Goedecke, Jens Decker, Thomas Kosinski, Melvin A Park, Nicolai Bache, Ole Hoerning, Jürgen Cox, Oliver Räther and Matthias Mann

High-Throughput Proteomics Quantification Enabled by Fast LC Separation and Advanced PRM Acquisition

To support proteomics studies the Evosep One combined with Thermo Scientific™ Q Exactive™ HF-X Hybrid Quadrupole-Orbitrap™ mass spectrometer are used to develop High-throughput LC-PRM set-ups based on fast LC separations and advanced PRM acquisition schemes. A novel IS-PRM method variant was also developed to further increase the analytical throughput and open the way to fast broad-coverage/multi-pathway monitoring studies.

Authors: Sebastien Gallien, Aaron Gajadhar, Bhavin Patel, Tabiwang Arrey, Dave Sarracino, Yue Xuan, Emily Chen

MAXIMIZED THROUGHPUT AND ANALYTICAL DEPTH FOR SHOTGUN PROTEOMICS USING PASEF ON A TIMS EQUIPPED QTOF

While good analytical depth is currently achievable in (MS)-based proteomics, the throughput required in screening or clinical applications is not achievable with traditional nanoESI LC-MS/MS systems. Combining the Evosep One with low overhead times and the timsTOF Pro with the fast PASEF acquisition method (Meier et al., JPR 2015). We show highly reproducible identification and quantification with low sample amounts over ~100 runs, demonstrating the potential for high throughput applications.

Authors: Thomas Kosinski; Scarlet Koch; Markus Lubeck; Nicolai Bache; Ole Bjeld Horning; Lasse Falkenby; Heiner Koch

HIGH THROUGHPUT HCP SCREENING IS HERE: > 50 HCPS IDENTIFIED IN 21 MINUTES

Here, the high speed of PASEF, (parallel accumulation and serial fragmentation) as implemented on the timsTOF Pro, coupled with the Evosep One LC system were used to detect HCPs using a 21 minute gradient.

Authors: Stuart Pengelley, Heiner Koch, Thomas Kosinski, Eckhard Belau; Bruker Daltonik, Bremen

Clinical proteomics

As the protein concentration in plasma is so high (50 μg/μl), a simple fingerprick delivering just 1μl of plasma is enough to analyze the human plasma proteome.

Authors: Philipp E. Geyer, Lesca M. Holdt, Daniel Teupser and Matthias Mann

DEVELOPMENT OF A ROBUST AND REPRODUCIBLE METHOD FOR DETECTION OF CITRULLINATION IN COMPLEX SAMPLES

An initial separation by traditional LC using HFBA as ion-pairing reagent followed by short LC-MSMS separation on an Evosep system coupled to Thermo Scientific™ Orbitrap Fusion™ Lumos ™ Tribrid™ mass spectrometer is compared to a traditional LC-MS/MS setup, with the aim of developing a system, where specific ion pairing reagents are used to separate arginine, containing peptides from equivalent citrullinated ones.

Authors: Daniel Nyberg Larsen, Christian Engelbrecht Mikkelsen, Jan Potempa, Jakub Z. Kaczmarek, Peter Højrup

DEVELOPMENT OF A NOVEL LC CONCEPT FOR CLINICAL PROTEOMICS

Mass spectrometry based proteomics and metabolomics are fast growing and powerful technologies, with the potential to revolutionize health care and precision medicine. Here we describe a conceptually novel low-flow chromatography system, that delivers the robustness and throughput required for clinical applications while maintaining the sensitivity of current nano-flow LC instrumentation.

Authors: Nicolai Bache, Philipp E. Geyer, Ole Hoerning, Lasse Falkenby, Peter Treit, Igor Paron, Florian Meier, Ole Vorm and Matthias Mann

OPTIMIZING DATA PROCESSING PARAMETERS FOR SAMPLES ACQUIRED ON INSTRUMENTS USING ADVANCED PEAK DETERMINATION

Thermo Fisher Scientific’s and Evosep’s data from the joint use of the Evosep One system and Thermo Fisher Scientific’s  mass spectrometers. The samples were measured using an Evosep One coupled to the Thermo Scientific™ Q Exactive™ HF-X Hybrid Quadrupole-Orbitrap™ mass spectrometer, and the Evotip technology improves overall system throughput and robustness by reducing column clogging and carryover.

Authors: Bernard Delanghe; Tabiwang N. Array; Aaron Gajahar; David Horn; Pedro Navarro; Eugen N. Damoc; Andreas Huhmer

TIMSTOF PRO WITH PASEF AND EVOSEP ONE: MAXIMIZING THROUGHPUT, ROBUSTNESS AND ANALYTICAL DEPTH FOR SHOTGUN PROTEOMICS

The recent release of Evosep one, has changed the game, ceasing the need for concatenation and cutting MS analysis time in half. The results presented here demonstrate combining the timsTOF Pro and the Evosep One, for the first time enables high-throughput measurements while maintaining analytical depth.

Authors: Thomas Kosinski; Scarlet Koch; Markus Lubeck; Pierre-Olivier Schmit; Nicolai Bache; Ole Bjeld Horning; Lasse Falkenby; Heiner Koch