A5070102563- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Stellar, planetary, and galactic studies
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Astrophysical Phenomena and Observations
- RNA and protein synthesis mechanisms
- Scientific Computing and Data Management
- Astronomy and Astrophysical Research
- Gene expression and cancer classification
- Gamma-ray bursts and supernovae
- Molecular Biology Techniques and Applications
- Astronomical Observations and Instrumentation
- vaccines and immunoinformatics approaches
- Research Data Management Practices
- Genetics, Bioinformatics, and Biomedical Research
- Ubiquitin and proteasome pathways
- Identification and Quantification in Food
- RNA modifications and cancer
- Bacterial Identification and Susceptibility Testing
- Astrophysics and Star Formation Studies
- Peptidase Inhibition and Analysis
Institute for Systems Biology
2016-2025
North Seattle College
2012-2025
InSysBio (Russia)
2002-2025
University of Groningen
2015
Fondazione Santa Lucia
2015
Seattle University
1993-2015
University of Liverpool
2013
SIB Swiss Institute of Bioinformatics
2013
European Bioinformatics Institute
2013
Wellcome Trust
2007-2013
The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination mass spectrometry worldwide. We give an overview the current consortium activities describe advances past few years. Augmenting PX founding members (PRIDE PeptideAtlas, including PASSEL resource), two new have joined consortium: MassIVE jPOST. ProteomeCentral remains as common access portal, providing ability search for...
Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With rapid advances mass technology methods, it has become imperative to provide standard output format data that will facilitate sharing analysis. Initially, efforts develop resulted multiple formats, each designed with different underlying philosophy. To resolve issues associated having vendors, researchers, software developers convened under banner of HUPO PSI single standard. The new incorporated...
Abstract The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination mass spectrometry worldwide since 2012. In this paper, we describe the main developments previous update manuscript was published in Nucleic Acids Research 2017. Since then, addition to four PX existing members at time (PRIDE, PeptideAtlas including PASSEL resource, MassIVE jPOST), two new have joined PX: iProX (China) Panorama Public (USA)....
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...
A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery same identifiable peptides by sequence database searching methods, which often are time-consuming and error-prone. more precise efficient method, in previously observed identified peptide MS/MS spectra catalogued condensed into searchable spectral libraries to allow new identifications matching, seen as a promising alternative. To that end, an open-source, functionally complete, high-throughput readily...
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on ability generate reliable assays that uniquely confidently identify target peptides a sample. Unfortunately, there wide range criteria being applied say an assay has been successfully developed. There no consensus what are acceptable little understanding impact variable...
Meaningful exchange of microarray data is currently difficult because it rare that published provide sufficient information depth or are even in the same format from one publication to another. Only when can be easily exchanged will entire biological community able derive full benefit such studies. To this end we have developed three key ingredients towards standardizing storage and data. First, created a minimal for annotation experiment (MIAME)-compliant conceptualization experiments...
Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog is important starting point for discovery disease biomarkers. In 2005, we showed that different proteomics measurements using sample preparation analysis techniques identify significantly sets proteins, a comprehensive proteome compiled only by combining data many experiments. Applying advanced computational methods...
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,...
Abstract Mass spectrometry is the method of choice for deep and reliable exploration (human) proteome. Targeted mass reliably detects quantifies pre-determined sets proteins in a complex biological matrix used studies that rely on quantitatively accurate reproducible measurement across multiple samples. It requires one-time, priori generation specific assay each targeted protein. SWATH-MS spectrometric combines data-independent acquisition (DIA) data analysis vastly extends throughput can be...
After the successful completion of Human Genome Project, Proteome Organization has recently officially launched a global Project (HPP), which is designed to map entire human protein set. Given lack protein-level evidence for about 30% estimated 20,300 protein-coding genes, systematic effort will be necessary achieve this goal with respect abundance, distribution, subcellular localization, interaction other biomolecules, and functions at specific time points. As general experimental strategy,...
A compendium of SRM assays for cancer-associated proteins provides a resource accelerating and planning biomarker verification studies.