publications
Here, you can find the latest material presented by Evosep and our collaboration partners and also discover older publications.
Publications
Here you can find the latest publications from our users and collaboration partners.
An Ultra High-throughput Plasma Protein Profiling (uHTPPP) Workflow Using a Modified Quadrupole-Orbitrap Mass Spectrometer
An automated plasma protein profiling workflow on the new Thermo Scientificâ„¢ Orbitrap Explorisâ„¢ 240 mass spectrometer can deliver the consistency, sensitivity, and versatility required for translational research.
Authors: Michelle L. Dubuke, Sarah Trusiak, Sitara Chauhan, Ryan D. Bomgarden, Sergei Snovida, Bhavin Patel, Emily I. Chen
High dynamic range proteome analysis with BoxCarDIA and super-resolution Orbitrap mass spectrometry
Two-fold scan speed allows rapid proteome analysis and efficient implementation of BoxCar DIA.
Authors: Florian Meier, Kyle Fort, Arne Kreutzmann, Daniel Mourad, Konstantin Aizikov, Dmitry Grinfeld, Johannes B Mueller, André C Michaelis, Alexander A. Makarov, Matthias Mann
In-depth characterization of Staurosporine induced proteome thermal stability changes
This study presents deep comprehensive profiling of Staurosporine induced proteome thermal stability alteration utilizing different experiment layouts.
Authors: , , , , ,Â
Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV
To understand how SARS-CoV-2 and related coronaviruses manipulate the host this study characterized interactome, proteome and signaling processes in a systems-wide manner. DIA measurments were done with Evosep One coupled to a Q Exactiveâ„¢ HF-X Hybrid Quadrupole-Orbitrapâ„¢.
Authors: Alexey Stukalov, Virginie Girault, Vincent Grass, Valter Bergant, Ozge Karayel, Christian Urban, Darya A. Haas, Yiqi Huang, Lila Oubraham, Anqi Wang, Sabri M. Hamad, Antonio Piras, Maria Tanzer, Fynn M. Hansen, Thomas Enghleitner, Maria Reinecke, Teresa M. Lavacca, Rosina Ehmann, Roman Wölfel, Jörg Jores, Bernhard Kuster, Ulrike Protzer, Roland Rad, John Ziebuhr, Volker Thiel, Pietro Scaturro, Matthias Mann and Andreas Pichlmair
Robust and Reproducible Protein Quantification in Plasma using the Evosep One and the Agilent 6495 Triple Quadrupole LC/MS
This application note showcases the reproducibility, robustness, and analytical sensitivity of MRM-based LC/MS analysis of human plasma proteins using the Agilent 6495 triple quadrupole LC/MS with the Evosep One LC system.
Authors: Linfeng Wu, Nicolai Bache, Dorte B. Bekker-Jensen
Serum proteomics in COVID-19 patients: Altered coagulation and complement status as a function of IL-6 level
The present study provides the first proteomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to markers of inflammation and renal function.
Authors: , , , , , , , , ,Â
High throughput 4D-Proteomics – Application of dia-PASEF® and the Evosep One for short gradients
About 5200 proteins were quantified in only 21-minute run time using the dia-PASEF® technology on the timsTOF platform coupled to Evosep One. timsTOF Pro using dia-PASEF® and 4D-Proteomics in combination with the Evosep One system proved to be ideally suited for very high-throughput proteomics akin to clinical settings.
Authors:Â Stephanie Kaspar-Schoenefeld, Thomas Kosinski, Markus Lubeck, Oliver Rather, Gary Kruppa, Nicolai Bache, Dorte B. Bekker-Jensen
A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism
Authors of this study suggest that an oxygen-sensitive RBP cluster controls anaerobic metabolism to confer hypoxia tolerance.
Authors: J. J. David Ho, Nathan C. Balukoff, Phaedra R. Theodoridis, Miling Wang, Jonathan R. Krieger, Jonathan H. Schatz, Stephen Lee
NEW THERMO SCIENTIFICâ„¢ ORBITRAP EXPLORISâ„¢ 240 MASS SPECTOMETER
Thermo Fisher Scientific designed their fourth-generation quadrupole-Orbitrap mass spectrometer. Spectrometer delivers high-confident characterization and therefore, offers a reliable and flexible solution for highperformance biopharmaceutical characterization.
A Sensitive, Rapid, Robust and Reproducible Workflow for Host Cell Protein Profiling in Biopharmaceutical Process Development
In this study, a sensitive, robust, and reproducible workflow was developed for HCP detection and quantification in the significantly shorter turnaround time than previously reported using an Evosep One LC system coupled to an Orbitrap Fusionâ„¢ Lumosâ„¢ mass spectrometer.
Authors: Jiao Ma, Greg W. Kilby
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:Â Muhammad Tahir, Arkadiusz Nawrocki, Henrik J. Ditzel, View ORCID ProfileMartin R. LarsenÂ
Fast and Robust Proteome Screening Platform Identifies Neutrophil Extracellular Trap Formation in the Lung in Response to Cobalt Ferrite Nanoparticles
This study demonstrates 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, HÃ¥kan 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 CoxÂ
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 SCIENTIFICâ„¢ ORBITRAP EXPLORISâ„¢ 480 MASS SPECTOMETER COUPLED WITH EVOSEP ONE
In this brochure, Thermo Fisher Scientific introduce the new Thermo Scientificâ„¢ Orbitrap Explorisâ„¢ 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 Fisherâ„¢ Orbitrap Explorisâ„¢ 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 DevelopmentÂ
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 vitroÂ
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).Â
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.Â
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. Â
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. OlsenÂ
Standardized and scalable plasma protein quantitative profiling workflow using human blood based on the Thermo Scientificâ„¢ Q Exactiveâ„¢ platform
Together, Thermo Scientificâ„¢ Q Exactiveâ„¢ 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 Scientificâ„¢ Orbitrap Fusionâ„¢ Tibridâ„¢ mass spectrometer. Â
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 Scientificâ„¢ Q Exactiveâ„¢ HF-X Hybrid Quadrupole-Orbitrapâ„¢ 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:Â > 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 Scientificâ„¢ Orbitrap Fusionâ„¢ Lumos â„¢ Tribridâ„¢ 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 Scientificâ„¢ Q Exactiveâ„¢ HF-X Hybrid Quadrupole-Orbitrapâ„¢ 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
