A5079842634- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Wine Industry and Tourism
- Horticultural and Viticultural Research
- Genomics and Phylogenetic Studies
- Fermentation and Sensory Analysis
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Genomics and Rare Diseases
- Studies on Chitinases and Chitosanases
- Genetics, Bioinformatics, and Biomedical Research
- Photosynthetic Processes and Mechanisms
- Water Quality Monitoring and Analysis
- vaccines and immunoinformatics approaches
- Soil Carbon and Nitrogen Dynamics
- Anaerobic Digestion and Biogas Production
- Forest Biomass Utilization and Management
- Postharvest Quality and Shelf Life Management
- Edible Oils Quality and Analysis
- Mitochondrial Function and Pathology
- Luminescence Properties of Advanced Materials
Institute for Systems Biology
2015-2025
InSysBio (Russia)
2022-2025
North Seattle College
2014-2018
Tecnológico de Estudios Superiores de Jocotitlán
2017
Hong Kong University of Science and Technology
2009
University of Zurich
2009
ETH Zurich
2009
University of Hong Kong
2009
The combination of tandem mass spectrometry and sequence database searching is the method choice for identification peptides mapping proteomes. Over last several years, volume data generated in proteomic studies has increased dramatically, which challenges computational approaches previously developed these data. Furthermore, a multitude search engines have been that identify different, overlapping subsets sample from particular set spectra. We present iProphet, new addition to widely used...
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination public MS data. It now 10 years since initial workflow implemented. In this manuscript, we describe main developments PX previous update manuscript Nucleic Acids Research published 2020. six members Consortium are PRIDE,...
The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet ProteinProphet, were published 20 years ago. current release provides a large complement of tools for spectrum processing, searching, search validation, abundance computation, protein inference, more. Many the include machine-learning modeling to extract most information from sets build robust statistical models compute probabilities...
Public repositories for proteomics data have accelerated research by enabling more efficient cross‐analyses of datasets, supporting the creation protein and peptide compendia experimental results, development testing new software tools, facilitating manuscript review process. The available to date been designed accommodate either shotgun experiments or generic proteomic files. Here, we describe a kind repository collection representation from selected reaction monitoring ( SRM )...
Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide ions, and in addition, possible ions carrying post-translational modifications (PTMs), but most do not provide confidence metrics for the exact localization of those PTMs when several sites are available. Localization is absolutely required downstream molecular cell biology analysis PTM function vitro vivo. Therefore, we developed PTMProphet, a free...
Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun spectrometry methods when applied to proteome analyses. However, it involves selective measurement predetermined analytes, which requires more preparation in the form selecting appropriate signatures for proteins peptides that are be targeted. There growing number software programs resources...
The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected many different laboratories, all reanalyzed through uniform processing pipeline. latest 2015-03 build contains substantially more input data than past releases, mapped to recent version our merged reference proteome, and uses improved informatics development AtlasProphet provide results. Within set ∼20,000 neXtProt primary entries,...
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about thaliana proteome, such as significance of protein splice forms and post-translational modifications (PTMs), or simply obtain reliable information specific proteins. is based on published mass spectrometry (MS) data collected through ProteomeXchange reanalyzed uniform processing metadata annotation pipeline. All matched MS-derived peptide are linked spectral,...
Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery new therapeutic targets modalities. The NCATS Data Translator project working federate autonomous agents providers within a distributed system for answering questions. Within that the broader field, there need framework can efficiently reproducibly build an integrated,...
Multiple reaction monitoring mass spectrometry (MRM-MS) is a targeted analysis method that has been increasingly viewed as an avenue to explore proteomes with unprecedented sensitivity and throughput. We have developed software tool, called MaRiMba, automate the creation of explicitly defined MRM transition lists required program triple quadrupole spectrometers in such analyses. MaRiMba creates from downloaded or custom-built spectral libraries, restricts output specified proteins peptides,...
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023–10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were to Araport11 annotation, identifying ∼0.6 unique peptides 18,267 proteins at highest confidence level 3396 lower proteins, together representing 78.6% predicted proteome. Additional identified not in should be...
Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants post-translational modifications (PTMs) in biological samples. However, most workflows require that such variations be included search space used to analyze data, doing so remains challenging with analysis tools. In order facilitate for known PTMs, Proteomics Standards Initiative (PSI) has designed implemented PSI extended FASTA format (PEFF). PEFF is...
This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for collected from ProteomeXchange were reanalyzed through a uniform processing and metadata annotation pipeline. These are wide range of genetic backgrounds many sample types experimental conditions. The protein search space included different genome annotations B73 inbred line MaizeGDB, UniProtKB,...
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that used for further downstream analysis new spectra. There many different formats encoding libraries, but none have undergone a standardization process to ensure broad applicability applications. As part Human Proteome Organization Proteomics Standards Initiative (PSI), we developed standardized format called mzSpecLib...
Abstract Electron transfer dissociation (ETD) is an alternative fragmentation technique to CID that has recently become commercially available. ETD several advantages over CID. It less prone fragmenting amino acid side chains, especially those are modified, thus yielding fragment ion spectra with more uniform peak intensities. Further, precursor ions of longer peptides and higher charge states can be fragmented identified. However, analysis a few important differences require the...
Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide isolated mass spectrometer; however, in reality spectrometers often isolate more than one within window isolation contribute to additional peaks many spectra. We present new tool called reSpect, implemented Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby identified round sequence searching or spectral library...
Label-free quantification has grown in popularity as a means of obtaining relative abundance measures for proteomics experiments. However, easily accessible and integrated tools to perform label-free have been lacking. We describe StPeter, an implementation Normalized Spectral Index wide availability through integration into the widely used Trans-Proteomic Pipeline. This specifically designed reproducibility ease use. demonstrate that StPeter outperforms other state-of-the art packages using...
Proteomics data-dependent acquisition data sets collected with high-resolution mass-spectrometry (MS) can achieve very high-quality results, but nearly every analysis yields results that are thresholded at some accepted false discovery rate, meaning a substantial number of incorrect. For study conclusions rely on small peptide-spectrum matches being correct, it is thus important to examine least crucial spectra ensure they not one the incorrect identifications. We present Quetzal, peptide...
HIV-1 is taken up by immature monocyte derived dendritic cells (iMDDCs) into tetraspanin rich caves from which the virus can either be transferred to T lymphocytes or enter endosomes resulting in degradation. binding and fusion with DC membrane results low level de novo infection that also at a later stage. We have previously reported induce partial maturation of iMDDCs both stages trafficking. Here we show CD45⁺ microvesicles (MV) contaminate purified inocula due similar size density,...