MilQuant: a free, generic software tool for isobaric tagging-based quantitation |
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Authors: | Zou Xiao Zhao Minzhi Shen Hongyan Zhao Xuyang Tong Yuanpeng Wang Qingsong Wei Shicheng Ji Jianguo |
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Affiliation: | State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China. marinzou@gmail.com |
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Abstract: | Isobaric tagging techniques such as iTRAQ and TMT are widely used in quantitative proteomics and especially useful for samples that demand in vitro labeling. Due to diversity in choices of MS acquisition approaches, identification algorithms, and relative abundance deduction strategies, researchers are faced with a plethora of possibilities when it comes to data analysis. However, the lack of generic and flexible software tool often makes it cumbersome for researchers to perform the analysis entirely as desired. In this paper, we present MilQuant, mzXML-based isobaric labeling quantitator, a pipeline of freely available programs that supports native acquisition files produced by all mass spectrometer types and collection approaches currently used in isobaric tagging based MS data collection. Moreover, aside from effective normalization and abundance ratio deduction algorithms, MilQuant exports various intermediate results along each step of the pipeline, making it easy for researchers to customize the analysis. The functionality of MilQuant was demonstrated by four distinct datasets from different laboratories. The compatibility and extendibility of MilQuant makes it a generic and flexible tool that can serve as a full solution to data analysis of isobaric tagging-based quantitation. |
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Keywords: | ETD, Electron transfer dissociation HCD, High energy collision dissociation IT, Ion trap iTRAQ, Isobaric tags for relative and absolute quantitation MS, Mass spectrometry PQD, Pulsed Q dissociation PSM, Peptide-spectrum match SILAC, Stable isotope labeling by amino acids in cell culture TMT, Tandem mass tags. |
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