A5101918119- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- Mass Spectrometry Techniques and Applications
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Telomeres, Telomerase, and Senescence
- Data Management and Algorithms
- Advanced Biosensing Techniques and Applications
- Research Data Management Practices
- Spectroscopy and Chemometric Analyses
- Protein Degradation and Inhibitors
- Genetics, Aging, and Longevity in Model Organisms
- Gene expression and cancer classification
- GDF15 and Related Biomarkers
- Biomedical Text Mining and Ontologies
- Data Quality and Management
- Advanced Nanomaterials in Catalysis
- Machine Learning in Bioinformatics
- Data Visualization and Analytics
- Geographic Information Systems Studies
- Protein Structure and Dynamics
- Leaf Properties and Growth Measurement
- Fungal and yeast genetics research
- Advanced biosensing and bioanalysis techniques
University of Washington
2015-2025
Panjab University
2022
Buck Institute for Research on Aging
2014
Purdue University West Lafayette
2014
Broad Institute
2014
Seattle University
2008
Institute for Systems Biology
2008
The senescence-associated secretory phenotype (SASP) has recently emerged as a driver of and promising therapeutic target for multiple age-related conditions, ranging from neurodegeneration to cancer. complexity the SASP, typically assessed by few dozen secreted proteins, been greatly underestimated, small set factors cannot explain diverse phenotypes it produces in vivo. Here, we present "SASP Atlas," comprehensive proteomic database soluble proteins exosomal cargo SASP originating...
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)....
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,...
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 address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers readers immediate visual access data behind conclusions, we present Panorama Public (https://panoramaweb.org/public.url), repository Skyline documents supporting results. is built on Panorama, an open source management system mass spectrometry targeted environment. The web application facilitates viewing, sharing, disseminating contained in via web-browser....
Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created refined with Skyline,1 an increasingly popular Windows client software tool proteomics experiments. allows laboratories to store organize curated results contained in Skyline documents fine-grained permissions, which facilitates distributed collaboration secure sharing of published unpublished data via web-browser interface. It fully integrated the workflow supports publishing document directly...
Although the value of proteomics has been demonstrated, cost and scale are typically prohibitive, gene expression profiling remains dominant for characterizing cellular responses to perturbations. However, high-throughput sentinel assays provide an opportunity contribute at a meaningful scale. We present systematic library resource (90 drugs × 6 cell lines) proteomic signatures that measure changes in reduced-representation phosphoproteome (P100) epigenetic marks on histones (GCP). A...
We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC–MS/MS runs are automatically imported into Skyline and multiple identification-free metrics extracted from targeted peptides. These data then uploaded Panorama document repository where can be viewed web-based interface using powerful process control techniques, including Levey–Jennings Pareto plots. The is versatile takes user input, which allows significant over...
A thorough evaluation of the quality, reproducibility, and variability bottom-up proteomics data is necessary at every stage a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures assess sample preparation, system function, quantitative System suitability samples are repeatedly measured longitudinally with targeted methods, we examples where they used on three instrument platforms identify severe failures track function over months years....
A thorough evaluation of the quality, reproducibility, and variability bottom-up proteomics data is necessary at every stage a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures assess sample preparation, system function, quantitative System suitability samples are repeatedly measured longitudinally with targeted methods, we examples where they used on three instrument platforms identify severe failures track function over months years....
Abstract Background Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they generally not comparable to each other in terms functionality, user interfaces, information input/output, do readily...
As large-scale cross-linking data becomes available, new software tools for processing and visualization are required to replace manual analysis. XLink-DB serves as a storage site tool results. accepts generated with any cross-linker stores them in relational database. Cross-linked sites automatically mapped onto PDB structures if results compared existing protein interaction databases. A network is also the entire set. The server, including examples, help page available noncommercial use at...
Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. The document model contains extensive mass spectrometry from experiments performed using selected reaction monitoring, parallel monitoring data-independent data-dependent acquisition methods. Researchers have developed software tools that perform statistical analysis of the experimental contained within documents. new external framework allows researchers to integrate...
The Library of Integrated Network-based Cellular Signatures (LINCS), an NIH Common Fund program, has cataloged and analyzed cellular function molecular activity profiles in response to >80,000 perturbing agents that are potentially disruptive cells. Because the importance proteins their modifications specific perturbations, four six LINCS centers have included significant proteomics efforts characterization resulting phenotype. This manuscript aims describe this effort data harmonization...
Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the complexity are only increasing with time. There exist many software pipelines for analyzing these data (each its own file formats), as technology improves, formats change new developed. Files produced from myriad programs may accumulate on hard disks or tape drives over time, older files rendered progressively more obsolete...
Abstract The senescence-associated secretory phenotype (SASP) has recently emerged as a driver of, and promising therapeutic target for, multiple age-related conditions, ranging from neurodegeneration to cancer. complexity of the SASP, typically assessed by few dozen secreted proteins, been greatly underestimated, small set factors cannot explain diverse phenotypes it produces in vivo . Here, we present ‘SASP Atlas’, comprehensive proteomic database soluble exosome SASP originating...
Abstract Fragment ion indexing has significantly improved the efficiency of proteomics database search tools. This work implements fragment in Comet, a widely-used, open-source engine. We demonstrate that this enhancement maintains scoring and identification accuracy while substantially increasing peptide spectral matching speeds across multiple applications, including open modification searches, immunopeptidomics, real-time searches. Comet-FI reduced by up to 94% enabling rapid analysis...
Electron-transfer dissociation (ETD) induces fragmentation along the peptide backbone by transferring an electron from a radical anion to protonated peptide. In contrast with collision-induced dissociation, side chains and modifications such as phosphorylation are left intact through ETD process. Because precursor charge state is important input MS/MS sequence database search tools, ability accurately determine helpful for identification Furthermore, because can be applied large, highly...
Regulation of protein abundance is a critical aspect cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms gene products where the each proteoform independently regulated. Understanding how abundances these distinct change essential understanding underlying mechanisms many biological processes. Bottom-up proteomics mass spectrometry techniques be used estimate indirectly by sequencing quantifying peptides that are later mapped...
Skyline Batch is a newly developed Windows forms application that enables the easy and consistent reprocessing of data with Skyline. has made previous advances in this direction; however, none enable seamless automated local remote files. keeps log all steps were taken document; reproducing these takes time allows room for human error. also command-line interface, enabling it to be run from batch script, but using program way requires expertise editing scripts. By formalizing workflow highly...
Skyline is a Windows application for targeted mass spectrometry method creation and quantitative data analysis. Like most graphical user interface (GUI) tools, it has complex with many ways users to edit their files which makes the task of logging actions challenging reason why audit every change not common in GUI tools. We present an object comparison-based approach that extensible other The new system keeps track all document modifications made through or command line displays them...
Summary Though the added value of proteomic measurements to gene expression profiling has been demonstrated, on its own remains dominant means understanding cellular responses perturbation. Direct protein are typically limited due issues cost and scale; however, recent development high-throughput, targeted sentinel mass spectrometry assays provides an opportunity for proteomics contribute at a meaningful scale in high-value areas drug development. To demonstrate feasibility systematic...