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Advances in 4D-Proteomics™

HUPO ReCONNECT 2021

November 15 - 19, 2021, virtual

HUPO goes virtual and Bruker likes to invite you to its seminars 

Plasma Proteomics and Targeted Quantitative Biology
November 16, 18:15 - 19:15 CET (17:15- 18:15 UTC)

Single Cell Proteomics and Bruker ProteoScape Real-Time Search
Friday, November 19, 06:45 - 07:45 am CET (05:45 - 06:45 UTC)

Plasma Proteomics and Targeted Quantitative Biology
November 16, 18:15 - 19:15 CET (17:15- 18:15 UTC)

Prof. Gunnar Dittmar, Head of Quantitative Biology, Luxemburg Institute of Health (LIH)

prm-PASEF-based Biomarker Discovery in serum from Colon Cancer Patients

Patient serum is a preferred biofluid for diagnostic purposes as it is readily available. The biomarker detection in serum is usually hindered by the enormous dynamic range of protein abundance, making the reliable measurement of lower abundant proteins challenging. Targeted proteomic analysis of selected proteins offers an alternative to dig deeper and detect low abundant protein in this complex matrix. The development of PRM-PASEF combines the advantages of PRM with the additional selectivity of ion-mobility. Using an extensive collection of isotope-labeled reference peptides, we systematically screened patient serum for biomarkers with a high dynamic range in a very short time using fast liquid chromatography.

Assistant Prof. Danielle Swaney, Cellular and Molecular Pharmacology, University California San Francisco (UCSF)

Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion

Rapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. Here we apply a simple and accessible tip-based workflow for the generation of DIA spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized non-conventional proteases together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3,309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 minutes of MS-acquisition, including the direct detection of diagnostic Mycobacterium tuberculosis (Mtb) proteins.

Single Cell Proteomics and Bruker ProteoScape Real-Time Search
Friday, November 19, 06:45 - 07:45 am CET (05:45 - 06:45 UTC)

Prof. Catherine C.L. Wong, School of Basic Medical Sciences, Peking University Health Science Center, Center for Precision Medicine Multi-Omics Research

Single Cell Proteome (SCP) using Glass-Oil-Air-Droplet (GOAD) nano chip device and its application on embryo development 

Deep single-cell proteome has great biological significance for understanding cellular heterogeneity. To overcome the barriers along the processes of shotgun SCP, we firstly developed a nanoliterscaled glass-oil-air-droplet (GOAD) chip using miniaturized stationary droplet microreaction and manipulation techniques for multi-step sample pretreatment. We identified more than 1300 protein groups from a 200pg standard cell digest using timsTOF mass spectrometer in parallel-accumulation-serial-fragmentation (PASEF) scanning mode. We further demonstrate the application of GOAD chip device for the first time SCP analysis on embryo development. This method has great potential for achieving ultrasensitive proteomic analysis on single-cell level.

Robin Park, Director of Bioinformatics, Bruker Daltonics

Bruker ProteoScape and CCS-aware 4D Informatics

Bruker ProteoScape is a real time GPU-based search engine designed to take advantage of the massive parallelization possible on GPUs to enable real time search.  Real-time database search means that bottom-up shotgun proteomics data can be processed as quickly as it is acquired by the mass spectrometer.  This results in “Run and Done”, meaning that when your sample run is done the database search results are ready and can be used for making real time decisions about the next steps in your sample queue.  Bruker ProteoScape will also implement the use of CCS values obtained with 4D-Proteomics methods for improving the FDR in database searches and in particular to improving de novo peptide identification.  Additional late breaking developments in Bruker ProteoScape portfolio will be discussed.

For further information, please contact:

Anne Kropp
Bruker Daltonics GmbH & Co. KG
Fahrenheitstrasse 4
28359 Bremen
anne.kropp@bruker.com

This presentation was approved by the Program Committee as an independent activity held in conjunction with the HUPO ReCONNECT 2021. This presentation is not sponsored or endorsed by HUPO ReCONNECT 2021.

 

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