Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics
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 o...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-02-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/27/3/997 |
| _version_ | 1827659756366462976 |
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| author | Matthew A. Koc Senait Asmellash Patrick Norman Steven Rightmyer Joanna Roder Robert W. Georgantas Heinrich Roder |
| author_facet | Matthew A. Koc Senait Asmellash Patrick Norman Steven Rightmyer Joanna Roder Robert W. Georgantas Heinrich Roder |
| author_sort | Matthew A. Koc |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T23:27:49Z |
| format | Article |
| id | doaj.art-f06fbb42e8a2433bb5d757fb65b5d1c2 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T23:27:49Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-f06fbb42e8a2433bb5d757fb65b5d1c22023-11-23T17:15:56ZengMDPI AGMolecules1420-30492022-02-0127399710.3390/molecules27030997Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular DiagnosticsMatthew A. Koc0Senait Asmellash1Patrick Norman2Steven Rightmyer3Joanna Roder4Robert W. Georgantas5Heinrich Roder6Biodesix Inc., Boulder, CO 80301, USABiodesix Inc., Boulder, CO 80301, USABiodesix Inc., Boulder, CO 80301, USABiodesix Inc., Boulder, CO 80301, USABiodesix Inc., Boulder, CO 80301, USABiodesix Inc., Boulder, CO 80301, USABiodesix Inc., Boulder, CO 80301, USAAccurate 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.https://www.mdpi.com/1420-3049/27/3/997proteomicsmass spectrometryspectral processingset enrichment analysispeak detection |
| spellingShingle | Matthew A. Koc Senait Asmellash Patrick Norman Steven Rightmyer Joanna Roder Robert W. Georgantas Heinrich Roder Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics Molecules proteomics mass spectrometry spectral processing set enrichment analysis peak detection |
| title | Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics |
| title_full | Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics |
| title_fullStr | Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics |
| title_full_unstemmed | Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics |
| title_short | Semi-Quantitative MALDI Measurements of Blood-Based Samples for Molecular Diagnostics |
| title_sort | semi quantitative maldi measurements of blood based samples for molecular diagnostics |
| topic | proteomics mass spectrometry spectral processing set enrichment analysis peak detection |
| url | https://www.mdpi.com/1420-3049/27/3/997 |
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