MS-DAP Platform for Downstream Data Analysis of Label-Free Proteomics Uncovers Optimal Workflows in Benchmark Data Sets and Increased Sensitivity in Analysis of Alzheimer's Biomarker Data.

ABSTRACT: In the rapidly moving proteomics field, a diverse patchwork of data analysis pipelines and algorithms for data normalization and differential expression analysis is used by the community. We generated a mass spectrometry downstream analysis pipeline (MS-DAP) that integrates both popular and recently developed algorithms for normalization and statistical analyses. Additional algorithms can be easily added in the future as plugins. MS-DAP is open-source and facilitates transparent and reproducible proteome science by generating extensive data visualizations and quality reporting, provided as standardized PDF reports. Second, we performed a systematic evaluation of methods for normalization and statistical analysis on a large variety of data sets, including additional data generated in this s

SUBMITTER: Koopmans F 

PROVIDER: S-EPMC9903323 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature