A5023657229- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Ubiquitin and proteasome pathways
- vaccines and immunoinformatics approaches
- Peptidase Inhibition and Analysis
- Advanced Biosensing Techniques and Applications
- Sirtuins and Resveratrol in Medicine
- Immunotherapy and Immune Responses
- Chronic Kidney Disease and Diabetes
- Acute Kidney Injury Research
- Gene expression and cancer classification
- Dialysis and Renal Disease Management
- Microbial Metabolic Engineering and Bioproduction
- Image and Signal Denoising Methods
- Fault Detection and Control Systems
- Prostate Cancer Treatment and Research
- Histone Deacetylase Inhibitors Research
- German Literature and Culture Studies
- Systemic Lupus Erythematosus Research
- Historical, Literary, and Cultural Studies
- Monoclonal and Polyclonal Antibodies Research
- Receptor Mechanisms and Signaling
- Advanced Image Processing Techniques
- Cytomegalovirus and herpesvirus research
Biognosys (Switzerland)
2015-2025
The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with reproducibility and precision selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into better protein profiling compared established proteomics.We implemented on widely used Orbitrap platform retention-time-normalized (iRT) spectral libraries for targeted data...
Comprehensive, reproducible and precise analysis of large sample cohorts is one the key objectives quantitative proteomics. Here, we present an implementation data-independent acquisition using its parallel nature that surpasses limitation serial MS2 data-dependent on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot acquisition, identified quantified 6,383 proteins in human cell lines 2-or-more peptides/protein over 7100 when including 717 were basis peptide...
Quantitative phosphoproteomics has transformed investigations of cell signaling, but it remains challenging to scale the technology for high-throughput analyses. Here we report a rapid and reproducible approach analyze hundreds phosphoproteomes using data-independent acquisition (DIA) with an accurate site localization score incorporated into Spectronaut. DIA-based achieves order magnitude broader dynamic range, higher reproducibility identification, improved sensitivity accuracy...
Targeted mass spectrometry by selected reaction monitoring (S/MRM) has proven to be a suitable technique for the consistent and reproducible quantification of proteins across multiple biological samples wide dynamic range. This performance profile is an important prerequisite systems biology biomedical research. However, method limited measurements few hundred peptides per LC-MS analysis. Recently, we introduced SWATH-MS, combination data independent acquisition targeted analysis that vastly...
Comprehensive, high throughput analysis of the plasma proteome has potential to enable holistic health state an individual. Based on our own experience and evaluation recent large-scale mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow delicate nano-flow liquid chromatography (LC) irreproducibility identification data-dependent acquisition (DDA). We determined optimal solution reducing these limitations with robust capillary-flow data-independent...
Comprehensive proteome quantification is crucial for a better understanding of underlying mechanisms diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method choice comprehensive due to its power and versatility. Even though great advances have been made in recent years, full coverage complex samples remains challenging high dynamic range protein expression. Additionally, when studying disease regulatory proteins, biomarkers or potential drug targets are often low...
The MSstats R-Bioconductor family of packages is widely used for statistical analyses quantitative bottom-up mass spectrometry-based proteomic experiments to detect differentially abundant proteins. It applicable a variety experimental designs and data acquisition strategies compatible with many processing tools identify quantify spectral features. In the face ever-increasing complexities strategies, core package family, same name MSstats, has undergone series substantial updates. Its new...
Targeted analysis of data-independent acquisition (DIA) data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires spectral library, which contains all considered peptide precursor ions empirically determined fragment ion intensities their predicted retention time (RT). RTs, however, are not comparable on an absolute scale, especially if heterogeneous measurements combined. Here, we present method high-precision prediction...
Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA by extending widely used software, Spectronaut, also accommodate cross-link data. A mixture of seven proteins...
Abstract Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI‐related proteome changes is critical prevention and development of novel therapeutics to recover function mitigate susceptibility recurrent AKI or chronic disease. In this study, mouse kidneys were subjected ischemia‐reperfusion injury, contralateral remained uninjured enable comparison assess injury‐induced in proteome. A ZenoTOF 7600 mass spectrometer was optimized...
Abstract Human leukocyte antigen (HLA) molecules are critical mediators of immune surveillance, functioning to present antigenic peptides derived from self and non-self proteins T cells. By facilitating the recognition pathogenic or abnormal cells, such as cancer HLA play a pivotal role in guiding responses enabling targeted interventions. In oncology clinical trials, use peripheral blood mononuclear cells (PBMCs) offers significant advantages for immunopeptidomics (IMPX) potential...
recently been shown that targeted analysis of data independently acquired (DIA) peptide fragment ion spectra (SWATH-MS) has the potential to combine scale shotgun proteomics with analytical accuracy MRM [1]. We have developed software Spectronaut for high content datasets which are typically produced in DIA mode. adapts algorithms mProphet [2] providing fast and efficient processing accurate error statistics.
Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances mass spectrometry have enabled the cataloging of thousands sites throughout cell; however, identifying regulatory marks proven to be daunting task. Knowledge kinetics and stoichiometry site-specific an important factor uncover function. Here, improved method quantifying was developed validated, providing detailed landscape dynamic within compartments. The nature response...
Data-independent acquisition mass spectrometry is essential for comprehensive quantification of proteomes, enabling deeper insights into cellular processes and disease mechanisms. On the timsTOF platform, diagonal-PASEF methods have recently been introduced to directly continuously cover observed diagonal shape peptide precursor ion distributions. Although has shown great promise, its broad adoption as a routine workflow hampered by lack available algorithmic solutions paucity demonstrated...
Summary Measuring protein turnover is essential for understanding cellular biological processes and advancing drug discovery. The multiplex DIA mass spectrometry (DIA-MS) approach, combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC), has proven to be a reliable method analyzing degradation kinetics. Previous DIA-MS workflows have employed various strategies, including leveraging the highest isotopic channels of peptides enhance detection MS signal pairs clusters. In this study, we...
Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical prevention and development of novel therapeutics to recover function mitigate susceptibility recurrent AKI or chronic disease. In this study, mouse kidneys were subjected ischemia-reperfusion injury, contralateral remained uninjured enable comparison assess injury-induced in proteome. A fast-acquisition rate ZenoTOF 7600 mass spectrometer was...
ABSTRACT Quantitative phosphoproteomics has in recent years revolutionized understanding of cell signaling, but it remains a challenge to scale the technology for high-throughput analyses. Here we present rapid and reproducible approach systematically analyze hundreds samples by fast liquid chromatography tandem mass spectrometry using data independent acquisition (DIA). To overcome inherent issue positional phosphopeptide isomers DIA-based phosphoproteomics, developed employed an accurate...
Abstract Major histocompatibility complex (MHC) molecules play a central role in orchestrating immune responses by presenting antigenic peptides derived from both self and foreign proteins. In the context of cancer, understanding repertoire tumor-associated antigens (TAAs) presented MHC (or HLA human) is crucial for deciphering how system recognizes responds to malignant cells. The identification neoantigens, unique individual tumors due somatic mutations, has become focal point...
Protein extracts of the human HEK-293 cell line were spiked with HRM Kit and measured in six replicates on a Thermo Scientific Q Exactive mass spectrometer 2h gradient mode analyzed Spectronaut. To perform fair analysis library was combined E. coli such that software did not know about positive negative control. This then tested three common decoy approaches.
ABSTRACT Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances mass spectrometry have enabled the cataloging of thousands sites throughout cell, however identifying regulatory marks proven to be daunting task. Knowledge kinetics and stoichiometry site-specific are important factors uncover function. Here, an improved method quantifying was developed validated, providing detailed landscape dynamic within compartments. The...
The “Profiling Standard Sample Set” consisted of eight sam-ples with a constant background (HEK-293 cells) and 12 non-human proteins spiked in three master mix groups. Master 1 2 were at small concentration changes on two ranges. 3 was as four fold dilution series. lowest set to the value 1.