Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment

Jade K. Macdonald; Cassandra L. Clift; Janet Saunders; Stephen C. Zambrzycki; Anand S. Mehta; Richard R. Drake; Peggi M. Angel

doi:10.1021/jasms.3c00366

Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment

Jade K. Macdonald, Cassandra L. Clift, Janet Saunders, Stephen C. Zambrzycki, Anand S. Mehta, Richard R. Drake, Peggi M. Angel

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Circulating extracellular matrix (ECM) proteins are serological biomarkers of interest due to their association with pathologies involving disease processes such as fibrosis and cancers. In this study, we investigate the potential for serum biomarker research using differential protease specificity (DPS), leveraging alternate protease specificity as a targeting mechanism to selectively digest circulating ECM protein serum proteins. A proof-of-concept study is presented using serum from patients with cirrhotic liver or hepatocellular carcinoma. The approach uses collagenase DPS for digestion of deglycosylated serum and liquid-chromatography-trapped ion mobility-tandem mass spectrometry (LC-TIMS-MS/MS) to enhance the detection of ECM proteins in serum. It requires no sample enrichment and minimizes the albumin average precursor intensity readout to less than 1.2%. We further demonstrate the capabilities for using the method as a high-throughput matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS) assay coupled with reference library searching. A goal is to improve the depth and breadth of biofluid proteomics for noninvasive assays.

Original language	English
Pages (from-to)	487-497
Number of pages	11
Journal	Journal of the American Society for Mass Spectrometry
Volume	35
Issue number	3
DOIs	https://doi.org/10.1021/jasms.3c00366
State	Published - Mar 6 2024
Externally published	Yes

Funding

J.K.M. was supported by the Cellular, Biochemical and Molecular Sciences Training Program 5T32GM132055 (NIH/NIGMS). P.M.A. was supported by NIH/NCI R21CA263464, R01CA253460; and in part by pilot research funding, Hollings Cancer Center’s Cancer Center Support Grant P30 CA138313 at the Medical University of South Carolina. Supported in part by MUSC Digestive Disease Research Core Center (P30DK123794) and the Biorepository & Tissue Analysis Shared Resource and the Translational Science Laboratory, Hollings Cancer Center, Medical University of South Carolina. The FT was supported by the provost office and Hollings Cancer Center. Additional support was provided by the South Carolina Centers of Economic Excellence SmartState program to RRD and ASM. The Mass Spectrometry Facility and Redox Proteomics Core is supported by the University and P20GM103542 (NIH/NIGMS) with shared instrumentation S10 OD010731 & S10 OD025126 (NIH/OD) to LEB and S10 0D030212 to PMA. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH or NCATS.

Funders	Funder number
Hollings Cancer Center’s Cancer Center	P30 CA138313
MUSC Digestive Disease Research Core Center	P30DK123794
NIH/OD	S10 0D030212
South Carolina Centers
Translational Science Laboratory
University	P20GM103542, S10 OD025126
National Institutes of Health
National Cancer Institute	R01CA253460, R21CA263464
National Institute of General Medical Sciences
National Center for Advancing Translational Sciences
Hollings Cancer Center, Medical University of South Carolina
Medical University of South Carolina

Keywords

collagen
extracellular matrix
proteomics
serum
trapped ion mobility

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1021/jasms.3c00366

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Macdonald, J. K., Clift, C. L., Saunders, J., Zambrzycki, S. C., Mehta, A. S., Drake, R. R., & Angel, P. M. (2024). Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment. Journal of the American Society for Mass Spectrometry, 35(3), 487-497. https://doi.org/10.1021/jasms.3c00366

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title = "Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment",

abstract = "Circulating extracellular matrix (ECM) proteins are serological biomarkers of interest due to their association with pathologies involving disease processes such as fibrosis and cancers. In this study, we investigate the potential for serum biomarker research using differential protease specificity (DPS), leveraging alternate protease specificity as a targeting mechanism to selectively digest circulating ECM protein serum proteins. A proof-of-concept study is presented using serum from patients with cirrhotic liver or hepatocellular carcinoma. The approach uses collagenase DPS for digestion of deglycosylated serum and liquid-chromatography-trapped ion mobility-tandem mass spectrometry (LC-TIMS-MS/MS) to enhance the detection of ECM proteins in serum. It requires no sample enrichment and minimizes the albumin average precursor intensity readout to less than 1.2%. We further demonstrate the capabilities for using the method as a high-throughput matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS) assay coupled with reference library searching. A goal is to improve the depth and breadth of biofluid proteomics for noninvasive assays.",

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Macdonald, JK, Clift, CL, Saunders, J, Zambrzycki, SC, Mehta, AS, Drake, RR & Angel, PM 2024, 'Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment', Journal of the American Society for Mass Spectrometry, vol. 35, no. 3, pp. 487-497. https://doi.org/10.1021/jasms.3c00366

Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment. / Macdonald, Jade K.; Clift, Cassandra L.; Saunders, Janet et al.
In: Journal of the American Society for Mass Spectrometry, Vol. 35, No. 3, 06.03.2024, p. 487-497.

Research output: Contribution to journal › Article › peer-review

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AU - Zambrzycki, Stephen C.

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AU - Drake, Richard R.

AU - Angel, Peggi M.

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Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment

Abstract

Funding

Keywords

UN SDGs

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