Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage

Abstract Mass spectrometry-based proteomics using isobaric labeling for multiplex quantitation has become a popular approach for proteomic studies. We present Multi-Q 2, an isobaric-labeling quantitation tool which can yield the largest quantitation coverage and improved quantitation accuracy compar...

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Autores principales:	Ching-Tai Chen, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, Ting-Yi Sung
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b627d80c53c64e4898b25d0d9adcf2e2
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spelling	oai:doaj.org-article:b627d80c53c64e4898b25d0d9adcf2e22021-12-02T13:57:26ZMulti-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage10.1038/s41598-021-81740-42045-2322https://doaj.org/article/b627d80c53c64e4898b25d0d9adcf2e22021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-81740-4https://doaj.org/toc/2045-2322Abstract Mass spectrometry-based proteomics using isobaric labeling for multiplex quantitation has become a popular approach for proteomic studies. We present Multi-Q 2, an isobaric-labeling quantitation tool which can yield the largest quantitation coverage and improved quantitation accuracy compared to three state-of-the-art methods. Multi-Q 2 supports identification results from several popular proteomic data analysis platforms for quantitation, offering up to 12% improvement in quantitation coverage for accepting identification results from multiple search engines when compared with MaxQuant and PatternLab. It is equipped with various quantitation algorithms, including a ratio compression correction algorithm, and results in up to 336 algorithmic combinations. Systematic evaluation shows different algorithmic combinations have different strengths and are suitable for different situations. We also demonstrate that the flexibility of Multi-Q 2 in customizing algorithmic combination can lead to improved quantitation accuracy over existing tools. Moreover, the use of complementary algorithmic combinations can be an effective strategy to enhance sensitivity when searching for biomarkers from differentially expressed proteins in proteomic experiments. Multi-Q 2 provides interactive graphical interfaces to process quantitation and to display ratios at protein, peptide, and spectrum levels. It also supports a heatmap module, enabling users to cluster proteins based on their abundance ratios and to visualize the clustering results. Multi-Q 2 executable files, sample data sets, and user manual are freely available at http://ms.iis.sinica.edu.tw/COmics/Software_Multi-Q2.html .Ching-Tai ChenJen-Hung WangCheng-Wei ChengWei-Che HsuChu-Ling KoWai-Kok ChoongTing-Yi SungNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ching-Tai Chen Jen-Hung Wang Cheng-Wei Cheng Wei-Che Hsu Chu-Ling Ko Wai-Kok Choong Ting-Yi Sung Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
description	Abstract Mass spectrometry-based proteomics using isobaric labeling for multiplex quantitation has become a popular approach for proteomic studies. We present Multi-Q 2, an isobaric-labeling quantitation tool which can yield the largest quantitation coverage and improved quantitation accuracy compared to three state-of-the-art methods. Multi-Q 2 supports identification results from several popular proteomic data analysis platforms for quantitation, offering up to 12% improvement in quantitation coverage for accepting identification results from multiple search engines when compared with MaxQuant and PatternLab. It is equipped with various quantitation algorithms, including a ratio compression correction algorithm, and results in up to 336 algorithmic combinations. Systematic evaluation shows different algorithmic combinations have different strengths and are suitable for different situations. We also demonstrate that the flexibility of Multi-Q 2 in customizing algorithmic combination can lead to improved quantitation accuracy over existing tools. Moreover, the use of complementary algorithmic combinations can be an effective strategy to enhance sensitivity when searching for biomarkers from differentially expressed proteins in proteomic experiments. Multi-Q 2 provides interactive graphical interfaces to process quantitation and to display ratios at protein, peptide, and spectrum levels. It also supports a heatmap module, enabling users to cluster proteins based on their abundance ratios and to visualize the clustering results. Multi-Q 2 executable files, sample data sets, and user manual are freely available at http://ms.iis.sinica.edu.tw/COmics/Software_Multi-Q2.html .
format	article
author	Ching-Tai Chen Jen-Hung Wang Cheng-Wei Cheng Wei-Che Hsu Chu-Ling Ko Wai-Kok Choong Ting-Yi Sung
author_facet	Ching-Tai Chen Jen-Hung Wang Cheng-Wei Cheng Wei-Che Hsu Chu-Ling Ko Wai-Kok Choong Ting-Yi Sung
author_sort	Ching-Tai Chen
title	Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
title_short	Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
title_full	Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
title_fullStr	Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
title_full_unstemmed	Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
title_sort	multi-q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b627d80c53c64e4898b25d0d9adcf2e2
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Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage

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