Dataset Information

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

ABSTRACT: The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected from many different laboratories, all reanalyzed through a uniform processing pipeline. The latest 2015-03 build contains substantially more input data than past releases, is mapped to a recent version of our merged reference proteome, and uses improved informatics processing and the development of the AtlasProphet to provide the highest quality results. Within the set of ?20,000 neXtProt primary entries, 14,070 (70%) are confidently detected in the latest build, 5% are ambiguous, 9% are redundant, leaving the total percentage of proteins for which there are no mapping detections at just 16% (3166), all derived from over 133 million peptide-spectrum matches identifying more than 1 million distinct peptides using AtlasProphet to characterize and classify the protein matches. Improved handling for detection and presentation of single amino-acid variants (SAAVs) reveals the detection of 5326 uniquely mapping SAAVs across 2794 proteins. With such a large amount of data, the control of false positives is a challenge. We present the methodology and results for maintaining rigorous quality along with a discussion of the implications of the remaining sources of errors in the build.

SUBMITTER: Deutsch EW

PROVIDER: S-EPMC4755269 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Deutsch Eric W EW Sun Zhi Z Campbell David D Kusebauch Ulrike U Chu Caroline S CS Mendoza Luis L Shteynberg David D Omenn Gilbert S GS Moritz Robert L RL

Journal of proteome research 20150724 9

The Human PeptideAtlas is a compendium of the highest quality peptide identifications from over 1000 shotgun mass spectrometry proteomics experiments collected from many different laboratories, all reanalyzed through a uniform processing pipeline. The latest 2015-03 build contains substantially more input data than past releases, is mapped to a recent version of our merged reference proteome, and uses improved informatics processing and the development of the AtlasProphet to provide the highest ...[more]

PMID: 26139527

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Project description:Background: Chronic obstructive pulmonary disease (COPD) remains a leading cause of disability and death in the United States. The "COPD in the United States" project gathered data about the impact of COPD to highlight variability across states and provide a single point of access to data for state decision makers, the public health community and advocates. This report provides a summary of COPD-related morbidity and mortality in the United States and individual states during 2014-2015 (some metrics contain data from other years). Methods: We used data from multiple sources ( the Behavioral Risk Factor Surveillance System [BRFSS], the Centers for Disease Control and Prevention (CDC) Wide-ranging ONline Data for Epidemiologic Research online database, the CDC's chronic disease indicators data, Centers from Medicare and Medicaid Services Chronic Conditions Data Warehouse, Medical Expenditures Panel Survey and the American Association of Cardiovascular and Pulmonary Rehabilitation Pulmonary Rehabilitation Directory) to estimate 10 national and state-specific COPD metrics (prevalence, hospitalizations and emergency department visits, 30-day hospital readmissions, mortality, vaccinations, smoking prevalence, per capita medical cost, and the number of COPD patients per a pulmonary rehabilitation program) and to calculate average score across the 10 metrics. Additionally, we used BRFSS data to calculate the prevalence of common comorbid diseases among people who also report having a diagnosis of COPD. Results: During 2014-2015, 5.9% of adults (more than 15.9 million) reported having been told by their health care professional that they had COPD. The age-adjusted prevalence ranged from 3.7% for Puerto Rico and Hawaii, to 12% for West Virginia. The average score, 1 being best and 5 being worst, of the overall COPD burden based on the 10 key metrics ranged from 1.5 for Puerto Rico and Utah to 4.6 for West Virginia. Conclusion: The level of COPD morbidity and mortality is severe throughout the United States. There is considerable variability in COPD metrics by state. These differences may be useful in identifying and addressing policy gaps in the public health approach to COPD and in implementing the COPD National Action Plan.

Dataset Information

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Publications

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Similar Datasets

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