Bruker at US HUPO 2022

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.

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.