PMID- 35245044
OWN - NLM
STAT- MEDLINE
DCOM- 20220408
LR  - 20220408
IS  - 1520-6882 (Electronic)
IS  - 0003-2700 (Linking)
VI  - 94
IP  - 10
DP  - 2022 Mar 15
TI  - Paramounter: Direct Measurement of Universal Parameters To Process Metabolomics 
      Data in a "White Box".
PG  - 4260-4268
LID - 10.1021/acs.analchem.1c04758 [doi]
AB  - Choosing appropriate data processing parameters is critical in processing liquid 
      chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics data. The 
      conventional design of experiments (DOE) approach is time-consuming and provides 
      no intuitive explanation why the selected parameters generate the best results. 
      After studying commonly used metabolomics data processing software, this work 
      summarized a set of universal parameters, including mass tolerance, peak height, 
      peak width, and instrumental shift. These universal parameters are shared among 
      different feature extraction programs and are critical to metabolic feature 
      extraction. We then developed Paramounter, an R program that automatically 
      measures these universal parameters from raw LC-MS-based metabolomics data prior 
      to metabolic feature extraction. This is made possible through novel concepts of 
      rank-based intensity sorting, zone of interest, and many others. Paramounter also 
      translates universal parameters to software-specific parameters for data 
      processing in different programs. Applying Paramounter is demonstrated to provide 
      a threefold increase in the extracted metabolites compared to using default 
      parameters in MS-DIAL-based feature extraction. Furthermore, the comparison 
      between Paramounter, AutoTuner, and IPO showed that Paramounter generates 3.7- 
      and 1.6-fold more true positive features than AutoTuner and IPO, respectively. 
      Further validation of Paramounter on 11 datasets covering different sample types, 
      data acquisition modes, and MS vendors proved that Paramounter is a convenient 
      and robust program. Overall, the proposed universal parameters and the 
      development of Paramounter address a critical need in metabolomics data 
      processing, transforming metabolomics feature extraction from a "black box" to a 
      "white box." Paramounter is freely available on GitHub 
      (https://github.com/HuanLab/Paramounter).
FAU - Guo, Jian
AU  - Guo J
AD  - Department of Chemistry, Faculty of Science, University of British Columbia, 
      Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.
FAU - Shen, Sam
AU  - Shen S
AD  - Department of Chemistry, Faculty of Science, University of British Columbia, 
      Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.
FAU - Huan, Tao
AU  - Huan T
AUID- ORCID: 0000-0001-6295-2435
AD  - Department of Chemistry, Faculty of Science, University of British Columbia, 
      Vancouver Campus, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20220304
PL  - United States
TA  - Anal Chem
JT  - Analytical chemistry
JID - 0370536
SB  - IM
MH  - Chromatography, Liquid/methods
MH  - Mass Spectrometry/methods
MH  - *Metabolomics/methods
MH  - *Software
EDAT- 2022/03/05 06:00
MHDA- 2022/04/09 06:00
CRDT- 2022/03/04 17:10
PHST- 2022/03/05 06:00 [pubmed]
PHST- 2022/04/09 06:00 [medline]
PHST- 2022/03/04 17:10 [entrez]
AID - 10.1021/acs.analchem.1c04758 [doi]
PST - ppublish
SO  - Anal Chem. 2022 Mar 15;94(10):4260-4268. doi: 10.1021/acs.analchem.1c04758. Epub 
      2022 Mar 4.