A5050639345- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Salivary Gland Disorders and Functions
- Coral and Marine Ecosystems Studies
- Protein Interaction Studies and Fluorescence Analysis
- Biosensors and Analytical Detection
- Cancer, Hypoxia, and Metabolism
- Cancer Cells and Metastasis
- Photochemistry and Electron Transfer Studies
- Gene expression and cancer classification
- Oral microbiology and periodontitis research
- Peptidase Inhibition and Analysis
- Marine Biology and Environmental Chemistry
- Hemoglobin structure and function
- Cancer Research and Treatments
- Environmental Toxicology and Ecotoxicology
- Probiotics and Fermented Foods
Vassar College
2012
National Institutes of Health
2011
National Cancer Institute
2011
Sciex (Canada)
2010
University of California, Berkeley
2002
The Paragon™ Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using sequence tag algorithm, allowing degree implication by an MS/MS spectrum each region to be determined on continuum. Counter conventional approaches, features such as modifications, substitutions, and cleavage events modeled with probabilities rather than discrete user-controlled settings consider or not...
False discovery rate (FDR) analyses of protein and peptide identification results using decoy database searching conventionally report aggregate or global FDRs for a whole set identifications, which are often not very informative about the error rates individual members in set. We describe nonlinear curve fitting method calculating local FDR, estimates chance that an (or peptide) is incorrect, present simple tool implements this analysis. The goal to offer extension now commonplace...
Large databases (>10 6 sequences) used in metaproteomic and proteogenomic studies present challenges matching peptide sequences to MS/MS data using database‐search programs. Most notably, strict filtering avoid false‐positive matches leads more false negatives, thus constraining the number of matches. To address this challenge, we developed a two‐step method wherein derived from primary search against large database were create smaller subset database. The second was performed...
Epithelial-mesenchymal transition (EMT) is an important contributor to the invasion and metastasis of epithelial-derived cancers. While considerable effort has focused in regulators involved process, we have on consequences EMT prosurvival signaling. Changes distinct metastable 'epigentically-fixed' states were measured by correlation protein, phosphoprotein, phosphopeptide RNA transcript abundance. The assembly 1167 modulated components into functional systems or machines simplified...
We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by Proteomics Standards Initiative. The format was developed Initiative in collaboration with instrument software vendors, developers major open-source projects proteomics. Software implementations have been to enable conversion from most popular proprietary formats, mzIdentML will soon be supported public repositories. These developments proteomics scientists start working...
Policies supporting the rapid and open sharing of proteomic data are being implemented by leading journals in field. The proteomics community is taking steps to ensure that made publicly accessible high quality, a challenging task requires development deployment methods for measuring documenting quality metrics. On September 18, 2010, United States National Cancer Institute convened "International Workshop on Proteomic Data Quality Metrics" Sydney, Australia, identify address issues facing...
The human salivary proteome is extremely complex, including proteins from glands, serum, and oral microbes. Much has been learned about the host component, but little known microbial component. Here we report a metaproteomic analysis of supernatant pooled six healthy subjects. For deep interrogation proteome, combined protein dynamic range compression ( DRC ), multidimensional peptide fractionation, high‐mass accuracy MS / with novel two‐step identification method using database plus those...
We present an MS/MS database search algorithm with the following novel features: (1) a protein structure containing extensive preindexing and (2) zone modification searching, which enables rapid discovery of modifications known (i.e., user-specified) unanticipated delta masses. All these features are implemented in Interrogator, engine that runs behind Pro ID, ICAT, QUANT software products. Speed benchmarks demonstrate our modification-tolerant is 100-fold faster than traditional algorithms...
Policies supporting the rapid and open sharing of proteomic data are being implemented by leading journals in field. The proteomics community is taking steps to ensure that made publicly accessible high quality, a challenging task requires development deployment methods for measuring documenting quality metrics. On September 18, 2010, U.S. National Cancer Institute (NCI) convened "International Workshop on Proteomic Data Quality Metrics" Sydney, Australia, identify address issues facing use...
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...
An earlier investigation of the temperature dependencies rates and kinetic isotope effects (KIEs) in glucose oxidase (GO) used variants that differed extent glycosylation at surface protein. Kohen et al. [Kohen, A., Jonsson, T., Klinman, J. P. (1997) Biochemistry 36, 2603−2611] presented evidence KIE on Arrhenius prefactor varied as a function protein modification, concluding degree hydrogen tunneling active site was dependent changes mass surface. We now examine GO proteins containing...
Inferring which protein species have been detected in bottom-up proteomics experiments has a challenging problem for solutions maturing over the past decade.While many inference approaches now function well isolation, comparing and reconciling results generated across different tools remains difficult.It presently stands as one of greatest barriers collaborative efforts such Human Proteome Project public repositories like PRoteomics IDEntifications (PRIDE) database.Here we present framework...
LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw processing, which utilizes precursor-level high mass accuracy for peak processing and MGF creation. In particular, results from MaxQuant-processed peaklists sets resulted in spectral utilization due to an peaklist quality higher precision precursor (HPMA). The output postsearch analysis tools of both workflows were utilized previously unexplored features a three-dimensional fractionated hexapeptide library...
Abstract Policies supporting the rapid and open sharing of proteomic data are being implemented by leading journals in field. The proteomics community is taking steps to ensure that made publicly accessible high quality, a challenging task requires development deployment methods for measuring documenting quality metrics. On September 18, 2010, U.S. National Cancer Institute (NCI) convened “International Workshop on Proteomic Data Quality Metrics” Sydney, Australia, identify address issues...
Policies supporting the rapid and open sharing of proteomic data are being implemented by leading journals in field. The proteomics community is taking steps to ensure that made publicly accessible high quality, a challenging task requires development deployment methods for measuring documenting quality metrics. On September 18, 2010, U.S. National Cancer Institute (NCI) convened "International Workshop on Proteomic Data Quality Metrics" Sydney, Australia, identify address issues facing use...
The theme of the third annual Spring workshop HUPO-PSI was “proteomics and beyond” its underlying goal to reach beyond boundaries proteomics community interact with groups working on similar issues developing interchange standards minimal reporting requirements. Significant developments in many XML formats, requirements accompanying controlled vocabularies were reported, these now feeding into broader efforts Functional Genomics Experiment (FuGE) data model Ontology (FuGO) ontologies.