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Article

Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics

by
Matthew A. Koc
,
Senait Asmellash
,
Patrick Norman
,
Steven Rightmyer
,
Joanna Roder
,
Robert W. Georgantas III
and
Heinrich Roder
*
Biodesix Inc., Boulder, CO 80301, USA
*
Author to whom correspondence should be addressed.
Molecules 2022, 27(3), 997; https://doi.org/10.3390/molecules27030997
Submission received: 1 December 2021 / Revised: 21 December 2021 / Accepted: 22 December 2021 / Published: 1 February 2022
(This article belongs to the Special Issue Advances and Future Perspective of Mass Spectrometry Analysis in Proteomics)
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Abstract

Accurate and precise measurement of the relative protein content of blood-based samples using mass spectrometry is challenging due to the large number of circulating proteins and the dynamic range of their abundances. Traditional spectral processing methods often struggle with accurately detecting overlapping peaks that are observed in these samples. In this work, we develop a novel spectral processing algorithm that effectively detects over 1650 peaks with over 3.5 orders of magnitude in intensity in the 3 to 30 kD m/z range. The algorithm utilizes a convolution of the peak shape to enhance peak detection, and accurate peak fitting to provide highly reproducible relative abundance estimates for both isolated peaks and overlapping peaks. We demonstrate a substantial increase in the reproducibility of the measurements of relative protein abundance when comparing this processing method to a traditional processing method for sample sets run on multiple matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) instruments. By utilizing protein set enrichment analysis, we find a sizable increase in the number of features associated with biological processes compared to previously reported results. The new processing method could be very beneficial when developing high-performance molecular diagnostic tests in disease indications.
Keywords: proteomics; mass spectrometry; spectral processing; set enrichment analysis; peak detection proteomics; mass spectrometry; spectral processing; set enrichment analysis; peak detection
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MDPI and ACS Style

Koc, M.A.; Asmellash, S.; Norman, P.; Rightmyer, S.; Roder, J.; Georgantas, R.W., III; Roder, H. Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics. Molecules 2022, 27, 997. https://doi.org/10.3390/molecules27030997

AMA Style

Koc MA, Asmellash S, Norman P, Rightmyer S, Roder J, Georgantas RW III, Roder H. Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics. Molecules. 2022; 27(3):997. https://doi.org/10.3390/molecules27030997

Chicago/Turabian Style

Koc, Matthew A., Senait Asmellash, Patrick Norman, Steven Rightmyer, Joanna Roder, Robert W. Georgantas, III, and Heinrich Roder. 2022. "Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics" Molecules 27, no. 3: 997. https://doi.org/10.3390/molecules27030997

APA Style

Koc, M. A., Asmellash, S., Norman, P., Rightmyer, S., Roder, J., Georgantas, R. W., III, & Roder, H. (2022). Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics. Molecules, 27(3), 997. https://doi.org/10.3390/molecules27030997

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