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Bruker Expands dia-PASEF® on the timsTOF 4D Proteomics and Epiproteomics Platform to Identify up to 13,000 Protein Groups with 1% FDR
Innovative TIMScore™ algorithm, combined with TIMS DIA- NN deep learning, now integrated into ‘Run & Done’ Bruker PaSER™2022 proteomics system Identifies and
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[{"type":"text","content":"\n\nInnovative TIMScore™ algorithm, combined with TIMS DIA- NN deep learning, now integrated into ‘Run & Done’ Bruker PaSER™2022 proteomics system\n\n\nIdentifies and quantifies more than 8000 protein groups (PG) in 35 minute-gradient single dia-PASEF runs from ultra-deep libraries containing over 13,000 PGs in cell-line assays with 1% FDR (false discovery rate) specificity\n\n\nOver 25% more phosphopeptides identified using TIMScore\n\n\n LEIPZIG, Germany--(BUSINESS WIRE)--\nAt the Proteomic Forum | EuPA 2022, Bruker Corporation (Nasdaq: BRKR) announced expanded capabilities for deeper proteomic and epiproteomic coverage, including enhanced phosphopeptide analysis using the innovative TIMScore algorithm, which is now a part of the new PaSER 2022 GPU-based platform. The novel TIMScore algorithm takes advantage of machine learning (ML) to predict CCS values of tryptic and phosphorylated peptides. Experimentally measured CCS values are referenced against the predicted CCS value to call the most probable assignment, thereby increasing peptide confidence and coverage in high sensitivity applications. The TIMScore algorithm is especially adept in identifying phosphopeptides even at the strictest false localization rate (1% FLR) using LuciPHOr1, where it typically identifies 10%-25% more phosphopeptides.\n\nThe human kinome comprises over 500 kinases and is essential for catalyzing protein phosphorylation, which during dysregulation is a known contributor to oncogenesis.2 In a previous human cancer cell line study by Mann et. al., at least three-fourths of the detected proteome (7832 out of 10,801 proteins) were found to be phosphorylated3. In a recent study performed in the Tenzer Lab at the University Medical Center of the Johannes Gutenberg University Mainz, some 27,768 phosphopeptides contained 4,672 isobaric phosphopeptide pairs of which 51% were chromatographically coeluting. TIMScore could separate 19% of the coeluting isomer pairs, refining the view of the phosphoproteome of a human osteosarcoma cell line.\n\nDr. Stefan Tenzer is Professor of Quantitative Proteomics and the Head of the Mass Spectrometry Core Facility at the University Medical Center of the Johannes Gutenberg University Mainz. Dr. Tenzer commented: “In our lab we use four timsTOF systems to understand posttranslational modifications and signaling pathways. TIMS...