IsoMS: Automated Processing of LC-MS Data Generated
by a Chemical Isotope Labeling Metabolomics Platform
- Publication date
- Publisher
Abstract
A chemical isotope labeling or isotope
coded derivatization (ICD)
metabolomics platform uses a chemical derivatization method to introduce
a mass tag to all of the metabolites having a common functional group
(e.g., amine), followed by LC-MS analysis of the labeled metabolites.
To apply this platform to metabolomics studies involving quantitative
analysis of different groups of samples, automated data processing
is required. Herein, we report a data processing method based on the
use of a mass spectral feature unique to the chemical labeling approach,
i.e., any differential-isotope-labeled metabolites are detected as
peak pairs with a fixed mass difference in a mass spectrum. A software
tool, IsoMS, has been developed to process the raw data generated
from one or multiple LC-MS runs by peak picking, peak pairing, peak-pair
filtering, and peak-pair intensity ratio calculation. The same peak
pairs detected from multiple samples are then aligned to produce a
CSV file that contains the metabolite information and peak ratios
relative to a control (e.g., a pooled sample). This file can be readily
exported for further data and statistical analysis, which is illustrated
in an example of comparing the metabolomes of human urine samples
collected before and after drinking coffee. To demonstrate that this
method is reliable for data processing, five <sup>13</sup>C<sub>2</sub>-/<sup>12</sup>C<sub>2</sub>-dansyl labeled metabolite standards
were analyzed by LC-MS. IsoMS was able to detect these metabolites
correctly. In addition, in the analysis of a <sup>13</sup>C<sub>2</sub>-/<sup>12</sup>C<sub>2</sub>-dansyl labeled human urine, IsoMS detected
2044 peak pairs, and manual inspection of these peak pairs found 90
false peak pairs, representing a false positive rate of 4.4%. IsoMS
for Windows running R is freely available for noncommercial use from www.mycompoundid.org/IsoMS