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Biology 2014, 3(2), 383-402; doi:10.3390/biology3020383
Article

Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments

1
, 2
 and 1,*
Received: 17 March 2014; in revised form: 16 April 2014 / Accepted: 10 May 2014 / Published: 5 June 2014
(This article belongs to the Special Issue Advances in Proteomics Methods)
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Abstract: Multiple Reaction Monitoring (MRM) conducted on a triple quadrupole mass spectrometer allows researchers to quantify the expression levels of a set of target proteins. Each protein is often characterized by several unique peptides that can be detected by monitoring predetermined fragment ions, called transitions, for each peptide. Concatenating large numbers of MRM transitions into a single assay enables simultaneous quantification of hundreds of peptides and proteins. In recognition of the important role that MRM can play in hypothesis-driven research and its increasing impact on clinical proteomics, targeted proteomics such as MRM was recently selected as the Nature Method of the Year. However, there are many challenges in MRM applications, especially data pre‑processing where many steps still rely on manual inspection of each observation in practice. In this paper, we discuss an analysis pipeline to automate MRM data pre‑processing. This pipeline includes data quality assessment across replicated samples, outlier detection, identification of inaccurate transitions, and data normalization. We demonstrate the utility of our pipeline through its applications to several real MRM data sets.
Keywords: multiple reaction monitoring; label-free; quality assessment; data normalization; proteomics; peptide; transition multiple reaction monitoring; label-free; quality assessment; data normalization; proteomics; peptide; transition
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Chung, L.M.; Colangelo, C.M.; Zhao, H. Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments. Biology 2014, 3, 383-402.

AMA Style

Chung LM, Colangelo CM, Zhao H. Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments. Biology. 2014; 3(2):383-402.

Chicago/Turabian Style

Chung, Lisa M.; Colangelo, Christopher M.; Zhao, Hongyu. 2014. "Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments." Biology 3, no. 2: 383-402.



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