PeptideWitch-A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data.
David C L HandlerFlora ChengAbdulrahman M ShathiliPaul A HaynesPublished in: Proteomes (2020)
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output from peptide-to-spectrum matching search engines for 'control' and 'treated' samples. Through a combination of spectral count summation and inner joins, PeptideWitch processes low stringency data, and outputs high stringency data that are suitable for downstream quantitation. Data quality metrics are generated, and a series of statistical analyses and graphical representations are presented, aimed at defining and presenting the difference between the two sample proteomes.
Keyphrases
- label free
- electronic health record
- mass spectrometry
- big data
- data analysis
- magnetic resonance imaging
- computed tomography
- ms ms
- high throughput
- case report
- working memory
- magnetic resonance
- machine learning
- wastewater treatment
- deep learning
- binding protein
- newly diagnosed
- liquid chromatography
- peripheral blood
- contrast enhanced