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What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?
Open AccessFeature PaperArticle

PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data

1
Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
2
Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, NSW 2109, Australia
*
Author to whom correspondence should be addressed.
Proteomes 2020, 8(3), 21; https://doi.org/10.3390/proteomes8030021
Received: 24 July 2020 / Revised: 13 August 2020 / Accepted: 18 August 2020 / Published: 21 August 2020
(This article belongs to the Special Issue Proteomics: Technologies and Their Applications)
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. View Full-Text
Keywords: label-free shotgun proteomics; false discovery rate; data quality; protein quantitation; spectral counting label-free shotgun proteomics; false discovery rate; data quality; protein quantitation; spectral counting
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MDPI and ACS Style

Handler, D.C.L.; Cheng, F.; Shathili, A.M.; Haynes, P.A. PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data. Proteomes 2020, 8, 21. https://doi.org/10.3390/proteomes8030021

AMA Style

Handler DCL, Cheng F, Shathili AM, Haynes PA. PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data. Proteomes. 2020; 8(3):21. https://doi.org/10.3390/proteomes8030021

Chicago/Turabian Style

Handler, David C.L.; Cheng, Flora; Shathili, Abdulrahman M.; Haynes, Paul A. 2020. "PeptideWitch–A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data" Proteomes 8, no. 3: 21. https://doi.org/10.3390/proteomes8030021

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