Publications

Publications

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 Fisher Scientific Orbitrap Fusion Series instrument.  

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 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™ 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 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

HIGH-THROUGHPUT PROTEOMICS QUANTIFICATION ENABLED BY FAST LC SEPARATION AND ADVANCED PRM ACQUISITION

Depth of coverage in shotgun proteomics workflows is usually achieved by high resolution nano-LC peptide separation, coupled to ESI-MS/MS. While good analytical depth is currently achievable, reaching the throughput required to analyze hundreds or even thousands of samples needed to obtain sufficient statistical power for biomarker validation studies, is unachievable with traditional nano-ESI LC-MS/MS systems.

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

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

Thermo and Evosep’s data from the joint use of the Evosep One system and Thermo’s QExactive mass spectrometers. The samples were measured using an Evosep One coupled to an 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