A5043959168- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mitochondrial Function and Pathology
- Bioinformatics and Genomic Networks
- Genetics, Aging, and Longevity in Model Organisms
- Microtubule and mitosis dynamics
- Adipose Tissue and Metabolism
- RNA and protein synthesis mechanisms
- Insect symbiosis and bacterial influences
- Analytical Chemistry and Chromatography
- Machine Learning in Bioinformatics
- Ubiquitin and proteasome pathways
- Genomics and Chromatin Dynamics
- Phytoplasmas and Hemiptera pathogens
- Plant Virus Research Studies
- Photosynthetic Processes and Mechanisms
- Sperm and Testicular Function
- Alzheimer's disease research and treatments
- Hormonal and reproductive studies
- Metabolism and Genetic Disorders
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Biosensing Techniques and Applications
- Protein Degradation and Inhibitors
- Fungal and yeast genetics research
University of Washington
2016-2025
Seattle University
2012-2024
Human Genome Sciences (United States)
2006-2024
Healthwise
2021
Cornell University
2013-2020
University of Stirling
2019
Buck Institute for Research on Aging
2014
Purdue University West Lafayette
2014
Broad Institute
2010-2014
Seattle Pacific University
2014
Abstract Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It open source freely available academic commercial use. The user interface simplifies the development of mass spectrometer methods analysis from experiments performed using selected reaction monitoring (SRM). supports creating MS/MS spectral libraries wide variety sources to choose SRM filters verify results based on previously observed ion trap data. exports...
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription occupancy events within regulatory regions, representing differential 8.4 distinct short elements. Here show that this small compartment, roughly twice size of exome, encodes an expansive repertoire conserved recognition sequences for DNA-binding proteins...
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)....
Large-scale genomics has enabled proteomics by creating sequence infrastructures that can be used with mass spectrometry data to identify proteins. Although protein sequences deduced from nucleotide sequences, posttranslational modifications proteins, in general, cannot. We describe a process for the analysis of is simple, robust, and applied complicated mixtures. A or mixture digested using three different enzymes: one cleaves site-specific manner two others cleave nonspecifically. The...
Multiple reaction monitoring ( MRM ) has recently become the method of choice for targeted quantitative measurement proteins using mass spectrometry. The method, however, is limited in number peptides that can be measured one run. This markedly increased by scheduling acquisition if accurate retention time RT each peptide known. Here we present i , an empirically derived dimensionless peptide‐specific value allows highly prediction. a fixed relative to standard set reference ‐peptides...
Data independent acquisition (DIA) mass spectrometry is a powerful technique that improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow uses this to construct chromatogram libraries capture fragment ion chromatographic peak shape retention time for every detectable peptide in experiment. These coordinates calibrate protein databases or spectrum specific spectrometer chromatography setup, facilitating DIA-only pipelines reuse global...
Background— Age is a major risk for cardiovascular diseases. Although mitochondrial reactive oxygen species have been proposed as one of the causes aging, their role in cardiac aging remains unclear. We previously shown that overexpression catalase targeted to mitochondria (mCAT) prolongs murine median lifespan by 17% 21%. Methods and Results— used echocardiography study function cohorts wild-type mCAT mice. Changes found mice recapitulate human aging: age-dependent increases left...
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,...
Despite advances in metabolic and postmetabolic labeling methods for quantitative proteomics, there remains a need improved label-free approaches. This is particularly pressing workflows that incorporate affinity enrichment at the peptide level, where isobaric chemical labels such as tags relative absolute quantitation tandem mass may prove problematic or stable isotope with amino acids cell culture cannot be readily applied. Skyline freely available, open source software tool data...
The accumulation of damaged mitochondria has been proposed as a key factor in aging and the pathogenesis many common age-related diseases, including Parkinson disease (PD). Recently, vitro studies PD-related proteins Parkin PINK1 have found that these factors act pathway to promote selective autophagic degradation (mitophagy). However, whether mitophagy under normal physiological conditions vivo is unknown. To address this question, we used proteomic approach Drosophila compare rates...
Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values posterior error probabilities, to peptides peptide-spectrum matches (PSMs) from experiments. Percolator's processing speed has been sufficient for typical data sets consisting of hundreds thousands PSMs. With our new scalable approach, we can now also analyze millions PSMs matter minutes on commodity computer. Furthermore,...
Aberrant WNT signal transduction is involved in many diseases. In colorectal cancer and melanoma, mutational disruption of proteins the degradation beta-catenin, key effector signaling pathway, results stabilization beta-catenin and, turn, activation transcription. We have used tandem-affinity protein purification mass spectrometry to define interaction network destruction complex. This assay revealed that WTX, a encoded by gene mutated Wilms tumors, forms complex with AXIN1, beta-TrCP2...
Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially targeted analysis workflows. Skyline is a freely available, open-source tool quantitative mass spectrometry method development data processing with 10 year history supporting six major instrument vendors. Designed initially proteomics analysis, we describe the expansion to molecule including selected reaction monitoring, high-resolution spectrometry, calibrated quantification. This...
To quantify proteins on a global level from mammalian tissue, method was developed to metabolically introduce 15N stable isotopes into the of Rattus norvegicus for use as internal standards. The long-term metabolic labeling rats with diet enriched in did not result adverse health consequences. average amino acid enrichments reflected relative turnover rates different tissues and ranged 74.3 mpe brain 92.2 plasma. Using 15N-enriched liver quantitative standard, changes individual protein...
Abstract As the speed with which proteomic labs generate data increases along scale of projects they are undertaking, resulting storage and processing problems will continue to challenge computational resources. This is especially true for shotgun techniques that can tens thousands spectra per instrument each day. One design factor leading many these caused by storing database identifications a given spectrum as individual files. While be addressed all search results in large relational...