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Title: Accurate Estimation of False Discovery Rates for Protein and Proteoform Identification in Top Down Proteomics Open Access Deposited

http://creativecommons.org/licenses/by/4.0/
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Abstract
  • Within the last five years, top down proteomics (TDP) has emerged as a high throughput technique for protein identification in addition to characterization and quantitation of thousands of modified proteoforms. Here, a framework for calculating an accurate false discovery rate (FDR) that considers both protein and proteoform levels was used to evaluate local dependencies when aggregating results from replicate LC-MS/MS runs searched with different search modes and parameters.Ê We find that proteoform identifications are not statistically independent of each other and that correcting the FDR locally within a given LC-MS/MS run is not sufficient to control FDR globally across a large experiment.Ê A series of corrections used previously in genomics was implemented to address these issues and produce a global FDR calculation that scales well. ÊThe validity of the system is assessed by analyzing two previously published experimental datasets.ÊWeb-based access via a new TDPORTAL to high-performance computation enables all steps necessary to create a set of results utilizing the accurate and scalable FDR estimation described here. Also, a new application called TOP DOWN VIEWER enables viewing, analyzing, and sharing result sets via .tdReport files and is available at  http://topdownviewer.northwestern.edu.
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  • 06/20/2024
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  • Forthcoming;
To Cite this Work:
Accurate Estimation of False Discovery Rates for Protein and Proteoform Identification in Top Down Proteomics [Data set]. Indiana University - DataCORE.

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Files (Count: 2; Size: 2.82 KB)

Thumbnail Title Original Upload Last Modified File Size Access Actions
DataSHAMSpaper.zip 2024-08-16 2024-08-16 Open Access
READMESHAMS.txt 2024-08-16 2024-08-16 2.82 KB Open Access

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