Bruker at US HUPO 2022

Bruker at US HUPO

Bruker at US HUPO 2022

If we missed you during US HUPO in Charleston, South Carolina, this past February, please be sure to visit our Poster Hall and download the latest information around the entire timsTOF family including our timsTOF Pro 2, timsTOF SCP and timsTOF fleX mass spectrometers. The timsTOF family is best-in-class for proteomics, single cell, spatialOMx, imaging and multi-Omic applications.


Please watch our pre-presentation on 4D-Proteomics™ with PaSER™.

Also watch on-demand our presentation from Dr. Ben Orsburn, one of our guest speakers during our lunch seminar held Monday, February 28th.

Bruker Lunch Seminar: Monday,  February 28, 1-2 pm

Lunch Seminar Title: Precision Medicine, Single Cell Proteomics and Real-time Bioinformatics

Location: Crystal D room at the Charleston Marriott, 170 Lockwood Blvd, Charleston, SC 29403.

Talk title: Next steps in personalized medicine

Jenny Van Eyk, Ph.D.

Erika Glazer Chair in Women's Heart Health, the Director of Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, the Director of Basic Science Research in the Women's Heart Center, Professor in Medicine and in Biomedical Sciences at Cedars-Sinai, Los Angeles, CA

Jennifer Van Eyk, Ph.D., is an international leader in the area of clinical proteomics and her lab has focused on developing technical pipelines for de novo discovery and larger scale quantitative mass spectrometry methods. This includes multiple reaction monitoring (MRM, also known as SRM) and most recently data independent acquisition. Dr. Van Eyk's laboratory is well known for the extreme technical quality of the data generated, rigorous quality control with tight %CV while applying these to key clinical questions. The aim is to maximize throughput and reproducibility in order to move targeted and robust discovery methods into large population healthy continuous assessment and clinical grade assays focusing on brain and cardiovascular diseases.

Talk title: Introduction and short presentation on 4D-Proteomics™ with PaSER™

Chris Adams, Ph.D., Global Business Development Director Bioinformatics, Life Science Mass Spectrometry, Bruker Daltonics, Billerica, MA, USA

Talk title: Accurate highly multiplexed protein quantification with sub-nanogram sensitivity

Ben Orsburn, Ph.D.

Research Faculty at The Johns Hopkins University School of Medicine, Baltimore, MD

Ben Orsburn received his Ph.D. from Virginia Tech for using mass spectrometry to study the cell walls of bacterial pathogens. He performed two postdoctoral fellowships, at the Johns Hopkins University and the National Cancer Institute, respectively where he expanded his skills toward the transcriptomics and proteomics of cancer.

After extensive trainings in mass spectrometry and proteomics, he spent 8 years traveling the globe as a senior field applications scientist in proteomics for Thermo Fisher Scientific. To date, he has helped to develop advanced applications in proteomics and metabolomics in over 160 labs around the world.

He is the founder of News in Proteomics Research, the highest frequently visited mass spectrometry and proteomics blog on the internet, dedicated to breaking down today’s most relevant advances in the field in the most approachable format possible. He is a contributing author of over 40 scientific articles and editorials, as well as three books on mass spectrometry. In 2018 he founded, a site dedicated to improving proteomics and mass spectrometry through the release of instrument methods curated by subject matter experts. For this work he was awarded a position on the Workflow Interest Network of the Association of Biomedical Research Facilities. His research has been featured in Science Daily, GenomeWeb and other media outlets. In March of 2020 his work on accelerating the development of COVID diagnostic assays received mainstream media attention.

Today, he has returned to Johns Hopkins as a faculty member in the Department of Pharmacology and Molecular Sciences. His research is focused on the application of proteomics and single-cell proteomics toward more comprehensive understanding of drug activity and toxicity.


US HUPO Posters 2022

Posters are available for download:  

#1143– Application of a library-free dia-PASEF approach for high throughput and high sensitivity


#1206 – Ultra-Sensitive Proteome Quantification on the timsTOF SCP Mass Spectrometer


Comparing dia-PASEF and prm-PASEF approaches for the absolute quantification of 500 human plasma proteins in colon cancer plasma samples


#1268 – Automated workflows for DIA data using DIA-NN on the PaSER platform

Christopher Adams, Robin Park, Sven Brehmer, Tharan Srikumar, Jonathan Krieger
Data independent acquisition has become the go to method for deep and quantitative proteomic analysis given the ability to sample large m/z windows in a reproducible and non-stochastic manner. Using a method termed dia-PASEF on a TIMS enabled Q-TOF lends additional advantages in both duty cycle and selectivity using the ion mobility space. Dia-PASEF allows for deep proteomes in short gradient times (<20 min.) and therefore 100’s of LCMS runs can be generated in short times. Data analysis in a streamlined automated fashion expedites the time from experiments to discovery. DIA-NN is a novel software package that uses neural networks providing best-in-class DIA output. Here we integrate DIA-NN onto the PaSER platform for a streamlined workflow for the analysis of many samples in a short analysis time with no file transfer or data migration.


#1334 – Compared dda-PASEF and prm-PASEF approaches for quantification of 2000 RAS induced Phosphopeptides


#1366 – Deep and quantitative succinylation profiling from dietary treatment in liver

Joanna Bons, Jacob Rose, Christopher Adams, Francesco Pingitore, Birgit Schilling
Protein succinylation is an unexplored PTM and thought to have dramatic consequences on protein structure and thereby function given the large size of the succinyl moiety (100 Da) and amino acid site selectivity (K) changing charge from +1 to -1. In this study, we combine succinylated peptide-level enrichment with timsTOF technology (DDA and DIA) to both identify sites of lysine succinylation and measure changes in succinylation upon dietary treatment in mouse liver tissues.


P08.05 - TIMS Viz for Mobility Offset Mass Aligned interrogation of complex samples

Philipp Strohmidel, Sebastian Wehner, Jens Decker, Ignacio Jauregui, Christopher Adams, Tharan Srikumar, Sven Brehmer
The PASEF® acquisition mode of the timsTOF Pro has the power to isolate co-eluting, quasi-isobaric peptides separately for fragmentation, based on differences in the peptide’s ion mobility. Such an event is called Mobility Offset Mass Aligned (MOMA) and results in non-chimeric spectra, despite a quadrupoles fidelity. This is especially valuable for PTM analysis, for example to resolve positional isomers of phosphopeptides. TIMS Viz was introduced in PaSER to visualize MOMA events in complex samples.
During acquisition, the MS/MS spectra are streamed to a GPU-powered processing computer performing a real-time database search, called PaSER. The database search utilizes all four dimensions – retention time, CCS value, m/z and fragment spectra – to increase confidence in the identification results. TIMS Viz, a novel data visualization tool to display an interactive heatmap in the m/z ion mobility space, maps MOMA features. Herein, we show the number of MOMA groups, which are sets of at least two MOMA features, that could be identified by TIMS Viz in two different data sets with different m/z tolerance settings. Setting tolerances to 500 mDa (typical lower limits of quadrupole isolation) and a retention time window of 10 s resulted in more than 40,000 MOMA groups containing more than 90,000 spectra for both, the cell lysate sample and the phosphopeptide enriched sample. Without the power of ion mobility separation these spectra would likely be chimeric in nature. Lowering the m/z tolerance to 25 mDa (well below the tolerance of any quadrupole) still leads to more than 18,000 MOMA groups (> 40,000 spectra) for the cell lysate and more than 23,000 MOMA groups (> 52,000 spectra) for the phosphopeptide enriched sample. TIMS Viz helps user to explore their data for MOMA features and is a powerful demonstration how the TIMS dimension can improve the spectral quality for co-eluting, quasi-isobaric peptides. 

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For Research Use Only. Not for use in clinical diagnostic procedures.