A5017261756- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Isotope Analysis in Ecology
- Algorithms and Data Compression
- Analytical Chemistry and Chromatography
- S100 Proteins and Annexins
- Time Series Analysis and Forecasting
- Cancer Research and Treatments
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Click Chemistry and Applications
- Parallel Computing and Optimization Techniques
- Music and Audio Processing
- Machine Learning and Algorithms
- Photosynthetic Processes and Mechanisms
- Protein Structure and Dynamics
- Plant Stress Responses and Tolerance
- Innovative Microfluidic and Catalytic Techniques Innovation
- vaccines and immunoinformatics approaches
- Data Analysis with R
- Genomics and Phylogenetic Studies
- Seismology and Earthquake Studies
- Advanced Electrical Measurement Techniques
- Ion-surface interactions and analysis
University Medical Center
2025
University Medical Center of the Johannes Gutenberg University Mainz
2019-2024
Johannes Gutenberg University Mainz
2019-2024
University of Warsaw
2015-2017
Abstract Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, patient individuality. Here, we develop a highly sensitive method identifying using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, train timsTOF-specific peak intensity MS 2 PIP model tryptic...
In this work, we studied the changes in high-light tolerance and photosynthetic activity leaves of Arabidopsis (
Abstract Data-independent acquisition (DIA) approaches provide comprehensive records of all detectable pre-cursor and fragment ions. Here we introduce midiaPASEF, a novel DIA scan mode using mobility-specific micro-encoding overlapping quadrupole windows to optimally cover the ion population in mobility-mass charge plane. Using mobility-encoded windows, midiaPASEF maximizes information content acquisitions which enables determination precursor m/z each with precision less than 2 Th. The...
Including ion mobility separation (IMS) into mass spectrometry proteomics experiments is useful to improve coverage and throughput. Many IMS devices enable linking experimentally derived of an its collisional cross-section (CCS), a highly reproducible physicochemical property dependent on the ion's mass, charge conformation in gas phase. Thus, known peptide mobilities can be used tailor acquisition methods or refine database search results. The large space potential sequences, driven also by...
As high-resolution mass spectrometry (HRMS) becomes increasingly available, the need of software tools capable handling more complex data is surging. The complexity HRMS stems partly from presence isotopes that give rise to peaks interpret compared lower resolution instruments. However, a new generation fine isotope calculators on rise. They calculate smallest possible sets isotopologues. none these lets user specify joint probability revealed envelope in advance. Instead, must provide limit...
The Bruker timsTOF Pro is an instrument that couples trapped ion mobility spectrometry (TIMS) to high-resolution time-of-flight (TOF) mass (MS). For proteomics, lipidomics, and metabolomics applications, the typically interfaced with a liquid chromatography (LC) system. resulting LC-TIMS-MS data sets are, in general, several gigabytes size are stored proprietary Tims format (TDF). raw can be accessed using binaries C, C++, Python on Windows Linux operating systems. Here we introduce suite of...
Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions-primarily different forms charge reduction-occur under ETD conditions, as evidenced by distorted isotope patterns usually observed. In this work, we analyze these compare stability nondissociative (ETnoD) products, specifically noncovalent c/z fragment complexes,...
The introduction of more sensitive mass spectrometers allows researchers to adapt front-end liquid chromatography (LC) individual needs for the analysis complex proteomes. Where absolute sensitivity is not paramount, it advantageous switch from a highly nanoflow-LC setup, de facto standard platform in mass-spectrometry (MS)-based discovery proteomics, robust, high-throughput-compatible microflow or conventional-flow setup. To enhance microflow-LC-MS electrospray process proteomic samples, we...
Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform a prominent commercial tool this purpose, particularly in bottom-up acquisition scenarios. additional ion mobility dimension requires more complex data processing, yet most current software solutions raw are proprietary or closed-source, limiting integration into custom workflows. We introduce rustims, framework implementing flexible toolbox designed processing data, currently focusing on...
High-resolution mass spectrometry becomes increasingly available with its ability to resolve the fine isotopic structure of measured analytes. It allows for high-sensitivity spectral deconvolution, leading less false-positive identifications. Analytes can be identified by comparing their theoretical signal observed peaks. Necessary calculations are, however, computationally demanding and lead long processing times. For wheat (trictum oestivum) alone, Uniprot holds more than 142 000 candidate...
In this paper we present extensions to the original adaptive Parallel Tempering algorithm. Two different approaches are presented. first one introduce state-dependent strategies using current information perform a swap step. It encompasses wide family of potential moves including standard and Equi-Energy type move, without any loss in tractability. second one, online trimming number temperatures. Numerical experiments demonstrate effectiveness proposed method.
Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe proteome. They rely on fragmentation of intact protein ions inside spectrometer. Among existing methods, electron transfer dissociation is known for its precision and wide coverage different cleavage sites. However, several side reactions can occur under (ETD) conditions, including nondissociative proton reaction. Evaluating their extent provide insight into reaction kinetics as well...
The analysis of the secretome provides important information on proteins defining intercellular communication and recruitment behavior cells in specific tissues. Especially context tumors, data can support decisions for diagnosis therapy. mass spectrometry-based cell-conditioned media is widely used unbiased characterization cancer secretomes vitro. Metabolic labeling using azide-containing amino acid analogs combination with click chemistry facilitates this type presence serum, preventing...
Electron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists several concurrent reactions triggered by an electron from its anion source to sample cations. Transferring causes peptide backbone cleavage while leaving labile post-translational modifications intact. The obtained fragmentation spectra provide valuable information sequence and structure analyses. In this study, we propose formal...
In this paper we present extensions to the original adaptive parallel tempering algorithm. Two different approaches are presented. first one introduce state-dependent strategies using current information perform a swap step. It encompasses wide family of potential moves including standard and Equi Energy type move, without any loss in tractability. second one, online adjustment number temperatures. Numerical experiments demonstrate effectiveness proposed method.
This paper presents a brand new methodology to deal with isotopic fine structure calculations. By using the Poisson approximation in an entirely novel way, we introduce mathematical elegance into discussion on trade-off between resolution and tractability. Our considerations unify concepts of fine-structure, equatransneutronic configurations, aggregate natural simple way. We show how boost theoretical seemingly costless way by several orders magnitude respect already very efficient...
Abstract The analysis of the secretome provides important information on proteins defining intercellular communication and recruitment behavior cells in specific tissues. Especially context tumors, data can support decisions for diagnosis therapy. mass spectrometry-based cell-conditioned media is widely used unbiased characterization cancer secretomes vitro . Metabolic labeling using azide-containing amino acid analogs combination with click chemistry facilitates this type presence serum,...
Among many techniques of modern mass spectrometry, the top down methods are becoming continuously more popular in overall strive to describe proteome. These based on fragmentation ions inside spectrometers instead being proteolytically digested. In some these techniques, is induced by electron transfer. It can trigger several concurring reactions: transfer dissociation, without and proton reaction. The evaluation extent reactions important for proper understanding functioning instrument and,...