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Oktoberfest: Open ‐source spectral library generation and rescoring pipeline based on Prosit
AbstractMachine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting th...
Source: Proteomics - September 7, 2023 Category: Biochemistry Authors: Mario Picciani, Wassim Gabriel, Victor ‐George Giurcoiu, Omar Shouman, Firas Hamood, Ludwig Lautenbacher, Cecilia Bang Jensen, Julian Müller, Mostafa Kalhor, Armin Soleymaniniya, Bernhard Kuster, Matthew The, Mathias Wilhelm Tags: TECHNICAL BRIEF Source Type: research

Four ‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF
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Source: Proteomics - February 9, 2023 Category: Biochemistry Authors: Dong ‐Gi Mun, Rohit Budhraja, Firdous A. Bhat, Roman M. Zenka, Kenneth L. Johnson, Abhay Moghekar, Akhilesh Pandey Tags: RESEARCH ARTICLE Source Type: research

Targeting Bcl-2 Family Proteins: What, Where, When?
AbstractProteins of the Bcl-2 family are known as regulators of apoptosis, one of the most studied forms of programmed cell death. The Bcl-2 protein family is represented by both pro- and antiapoptotic members. Antiapoptotic proteins are often exploited by tumor cells to avoid their death, thus playing an important role in carcinogenesis and in acquisition of resistance to various therapeutic agents. Therefore, antiapoptotic proteins represent attractive targets for cancer therapy. A detailed investigation of interactions between Bcl-2 family proteins resulted in the development of highly selective inhibitors of individual...
Source: Biochemistry (Moscow) - October 1, 2020 Category: Biochemistry Source Type: research

The Age of Data ‐Driven Proteomics: How Machine Learning Enables Novel Workflows
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Source: Proteomics - April 7, 2020 Category: Biochemistry Authors: Robbin Bouwmeester, Ralf Gabriels, Tim Van Den Bossche, Lennart Martens, Sven Degroeve Tags: Viewpoint Source Type: research

Successful adaption of a forensic toxicological screening workflow employing nontargeted liquid chromatography‐tandem mass spectrometry to water analysis
Forensic toxicology and environmental water analysis share the common interest and responsibility in ensuring comprehensive and reliable confirmation of drugs and pharmaceutical compounds in samples analyzed. Dealing with similar analytes, detection and identification techniques should be exchangeable between scientific disciplines. Herein, we demonstrate the successful adaption of a forensic toxicological screening workflow employing nontargeted LC/MS/MS under data‐dependent acquisition control and subsequent database search to water analysis. The main modification involved processing of an increased sample volume with ...
Source: Electrophoresis - March 1, 2016 Category: Biochemistry Authors: Julia Steger, Kathrin Arnhard, Sandra Haslacher, Klemens Geiger, Klaus Singer, Michael Schlapp, Florian Pitterl, Herbert Oberacher Tags: Research Article Source Type: research

Successful adaption of a forensic toxicological screening workflow employing non‐targeted liquid chromatography‐tandem mass spectrometry to water analysis
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Source: Electrophoresis - January 21, 2016 Category: Biochemistry Authors: Julia Steger, Kathrin Arnhard, Sandra Haslacher, Klemens Geiger, Klaus Singer, Michael Schlapp, Florian Pitterl, Herbert Oberacher Tags: Research Paper Source Type: research

Proteogenomic strategies for identification of aberrant cancer peptides using large‐scale next‐generation sequencing data
Cancer is driven by the acquisition of somatic DNA lesions. Distinguishing the early driver mutations from subsequent passenger mutations is key to molecular subtyping of cancers, understanding cancer progression, and the discovery of novel biomarkers. The advances of genomics technologies (whole‐genome exome, and transcript sequencing, collectively referred to as NGS (next‐generation sequencing)) have fueled recent studies on somatic mutation discovery. However, the vision is challenged by the complexity, redundancy, and errors in genomic data, and the difficulty of investigating the proteome translated portion of abe...
Source: Proteomics - November 17, 2014 Category: Biochemistry Authors: Sunghee Woo, Seong Won Cha, Seungjin Na, Clark Guest, Tao Liu, Richard D. Smith, Karin D. Rodland, Samuel Payne, Vineet Bafna Tags: Research Article Source Type: research

Proteogenomic strategies for identification of aberrant cancer peptides using large‐scale next generation sequencing data
This article is protected by copyright. All rights reserved
Source: Proteomics - September 29, 2014 Category: Biochemistry Authors: Sunghee Woo, Seong Won Cha, Seungjin Na, Clark Guest, Tao Liu, Richard D Smith, Karin D Rodland, Samuel Payne, Vineet Bafna Tags: Research Article Source Type: research