Windows Scanning Multiomics: Integrated Metabolomics and Proteomics

Metabolomics and proteomics offer
significant advantages in understanding
biological mechanisms at two hierarchical levels. However, conventional
single omics analysis faces challenges due to the high demand for
specimens and the complexity of intrinsic associations. To obtain
comprehensive and accurate system biological information, we developed
a multiomics analytical method called Windows Scanning Multiomics
(WSM). In this method, we performed simultaneous extraction of metabolites
and proteins from the same sample, resulting in a 10% increase in
the coverage of the identified biomolecules. Both metabolomics and
proteomics analyses were conducted by using ultrahigh-performance
liquid chromatography mass spectrometry (UPLC-MS), eliminating the
need for instrument conversions. Additionally, we designed an R-based
program (WSM.R) to integrate mathematical and biological correlations
between metabolites and proteins into a correlation network. The network
created from simultaneously extracted biomolecules was more focused
and comprehensive compared to those from separate extractions. Notably,
we excluded six pairs of false-positive relationships between metabolites
and proteins in the network established using simultaneously extracted
biomolecules. In conclusion, this study introduces a novel approach
for multiomics analysis and data processing that greatly aids in bioinformation
mining from multiomics results. This method is poised to play an indispensable
role in systems biology research.