PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization

BMC Research Notes
Jessica Da Gama DuarteJonathan M Blackburn

Abstract

Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4)...Continue Reading

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Citations

Sep 19, 2020·BMC Bioinformatics·Dmytro FishmanHedi Peterson
Jan 31, 2021·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Jennifer MooiNiall C Tebbutt
Jan 14, 2020·Journal of Proteome Research·Feng FengThomas B Kepler

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Methods Mentioned

BETA
protein array
PMA

Software Mentioned

PMA
gal
CT100 Analyser
ProteinMicroarrayAnalyser

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