Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum

Nagib Ahsan; Luca Fornelli; Fares Z Najar; Sanjeewa Gamagedara; Mohammad Robiul Hossan; R Shyama Prasad Rao; Ujwal Punyamurtula; Andrew Bauer; Zhibo Yang; Steven B Foster; Maureen A Kane

doi:10.1002/pmic.202300150

Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases-specific biomarkers from blood serum

Proteomics. 2023 Oct;23(20):e2300150. doi: 10.1002/pmic.202300150. Epub 2023 May 18.

Authors

Nagib Ahsan^{1

2}, Luca Fornelli^{1

3}, Fares Z Najar⁴, Sanjeewa Gamagedara⁵, Mohammad Robiul Hossan⁶, R Shyama Prasad Rao⁷, Ujwal Punyamurtula⁸, Andrew Bauer⁹, Zhibo Yang¹, Steven B Foster^{1

2}, Maureen A Kane¹⁰

Affiliations

¹ Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA.
² Mass Spectrometry, Proteomics and Metabolomics Core Facility, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA.
³ Department of Biology, University of Oklahoma, Norman, Oklahoma, USA.
⁴ High-Performance Computing Center (HPCC), Oklahoma State University, Stillwater, Oklahoma, USA.
⁵ Department of Chemistry, University of Central Oklahoma, Edmond, Oklahoma, USA.
⁶ School of Engineering, University of Central Oklahoma, Edmond, Oklahoma, USA.
⁷ Center for Bioinformatics, NITTE deemed to be University, Mangaluru, Karnataka, India.
⁸ Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
⁹ Department of Neurosurgery, University of Oklahoma-Health Science Center, Oklahoma, Oklahoma, USA.
¹⁰ Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA.

PMID: 37199141
DOI: 10.1002/pmic.202300150

Abstract

Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%-19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics.

Keywords: abundant protein depletion; biomarkers; blood; comparative proteomics; pathogenesis; serum.

Grants and funding

R35 GM147397/GM/NIGMS NIH HHS/United States