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Novel “omics” approach for study of low-abundance, low-molecular-weight components of a complex biological tissue: regional differences between chorionic and basal plates of the human placenta

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Abstract

Tissue proteomics has relied heavily on two-dimensional gel electrophoresis, for protein separation and quantification, then single protein isolation, trypsin digestion, and mass spectrometric protein identification. Such methods are predominantly used for study of high-abundance, full-length proteins. Tissue peptidomics has recently been developed but is still used to study the most highly abundant species, often resulting in observation and identification of dozens of peptides only. Tissue lipidomics is likewise new, and reported studies are limited. We have developed an “omics” approach that enables over 7,000 low-molecular-weight, low-abundance species to be surveyed and have applied this to human placental tissue. Because the placenta is believed to be involved in complications of pregnancy, its proteomic evaluation is of substantial interest. In previous research on the placental proteome, abundant, high-molecular-weight proteins have been studied. Application of large-scale, global proteomics or peptidomics to the placenta have been limited, and would be challenging owing to the anatomic complexity and broad concentration range of proteins in this tissue. In our approach, involving protein depletion, capillary liquid chromatography, and tandem mass spectrometry, we attempted to identify molecular differences between two regions of the same placenta with only slightly different cellular composition. Our analysis revealed 16 species with statistically significant differences between the two regions. Tandem mass spectrometry enabled successful sequencing, or otherwise enabled chemical characterization, of twelve of these. The successful discovery and identification of regional differences between the expression of low-abundance, low-molecular weight biomolecules reveals the potential of our approach.

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Acknowledgments

This work was supported by the Department of Chemistry and Biochemistry, Brigham Young University. The authors would like to extend their gratitude to several individuals who participated in parts of this study: Dr Moana Hopoate-Sitake, Bruce Jackson, Jody Jones, Dr M. Sean Esplin, and the Mass Spectrometry Facility at BYU. We gratefully acknowledge the support provided by Intermountain Health Care (IHC) hospitals in making placental tissue samples available.

Conflict of interest

The authors declare no competing financial considerations or other conflicts of interest.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Brigham Young University, BNSN C-212, Provo, UT, 84602, USA

    Komal Kedia, Caitlin A. Nichols & Steven W. Graves

  2. Department of Chemistry, Utah Valley University, 800 W. University Parkway, Orem, UT, 84058, USA

    Craig D. Thulin

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  1. Komal Kedia
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  2. Caitlin A. Nichols
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Correspondence to Steven W. Graves.

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Kedia, K., Nichols, C.A., Thulin, C.D. et al. Novel “omics” approach for study of low-abundance, low-molecular-weight components of a complex biological tissue: regional differences between chorionic and basal plates of the human placenta. Anal Bioanal Chem 407, 8543–8556 (2015). https://doi.org/10.1007/s00216-015-9009-3

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