PT  - JOURNAL ARTICLE
AU  - Johannes Griss
AU  - Goran Vinterhalter
AU  - Veit Schwämmle
TI  - IsoProt: A fully reproducible one-stop-shop for the analysis of iTRAQ/TMT data
AID  - 10.1101/446070
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 446070
4099  - http://biorxiv.org/content/early/2018/10/17/446070.short
4100  - http://biorxiv.org/content/early/2018/10/17/446070.full
AB  - Mass spectrometry coupled with isobaric labelling provides fast large-scale comparison of protein abundances over multiple conditions. To date, no one-stop-shop software solution exists that enables non-bioinformatics experts to carry out the full analysis of the acquired raw data with minimal intervention. Mostly, pipelines for such analyses are based on a combination of different software tools and in-house programs. In addition, different and often new versions of used tools and issues with the compatibility of apparently interoperable tools make it very difficult to ensure reproducible data analysis in the proteomics realm. We present a 100% reproducible software protocol to fully analyse data from one of the most popular types of proteomics experiments. The protocol uses only open source tools installed on a portable container environment and provides a user-friendly and interactive browser interface for configuration and execution of the different operations. An example use case is provided that can be used for testing and adaptation of own data sets. This setup will yield identical results on any computer analysing isobaric labelled MS data.AbbreviationsEuBICEuropean Bioinformatics CommunityFDRFalse Discovery RateyiTRAQMultiplexed Isobaric Tagging Technology for Relative QuantitationPbAPlasmodium Berghei ANKAPSMPeptide Spectrum MatchRMSERoot-Mean-Square ErrorTMTTandem Mass Tag