Evaluation of Spectral Counting for Relative Quantitation of Proteoforms in Top-Down Proteomics
| dc.contributor.author | Geis-Asteggiante, Lucía | |
| dc.contributor.author | Ostrand-Rosenberg, Suzanne | |
| dc.contributor.author | Fenselau, Catherine | |
| dc.contributor.author | Edwards, Nathan J. | |
| dc.date.accessioned | 2019-03-04T16:44:42Z | |
| dc.date.available | 2019-03-04T16:44:42Z | |
| dc.date.issued | 2018-10-09 | |
| dc.description.abstract | Spectral counting is a straightforward label-free quantitation strategy used in bottom-up proteomics workflows. The application of spectral counting in label-free top-down proteomics workflows can be similarly straightforward but has not been applied as widely as quantitation by chromatographic peak areas or peak intensities. In this study, we evaluate spectral counting for quantitative comparisons in label-free top down proteomics workflows by comparison with chromatographic peak areas and intensities. We tested these quantitation approaches by spiking standard proteins into a complex protein background and comparing relative quantitation by spectral counts with normalized chromatographic peak areas and peak intensities from deconvoluted extracted ion chromatograms of the spiked proteins. Ratio estimates and statistical significance of differential abundance from each quantitation technique are evaluated against the expected ratios and each other. In this experiment, spectral counting was able to detect differential abundance of spiked proteins for expected ratios ≥2, with comparable or higher sensitivity than normalized areas and intensities. We also found that while ratio estimates using peak areas and intensities are usually more accurate, the spectral-counting-based estimates are not substantially worse. Following the evaluation and comparison of these label-free top down quantitation strategies using spiked proteins, spectral counting, along with normalized chromatographic peak areas and intensities, were used to analyze the complex protein cargo of exosomes shed by myeloid-derived suppressor cells collected under high and low conditions of inflammation, revealing statistically significant differences in abundance for several proteoforms, including the active pro-inflammatory proteins S100A8 and S100A9. | en_US |
| dc.description.sponsorship | This project was funded by the National Institutes of Health grants GM021248 and OD019938. We thank Virginia Clements for animal husbandry. | en_US |
| dc.description.uri | https://pubs.acs.org/doi/10.1021/acs.analchem.6b02151 | en_US |
| dc.format.extent | 17 pages | en_US |
| dc.genre | journal articles postprints | en_US |
| dc.identifier | doi:10.13016/m2ulux-csqb | |
| dc.identifier.citation | Lucía Geis-Asteggiante, Suzanne Ostrand-Rosenberg, Catherine Fenselau, and Nathan J. Edwards, Evaluation of Spectral Counting for Relative Quantitation of Proteoforms in Top-Down Proteomics, Anal. Chem., 2016, 88 (22), pp 10900–10907 DOI: 10.1021/acs.analchem.6b02151 | en_US |
| dc.identifier.uri | https://dx.doi.org/10.1021%2Facs.analchem.6b02151 | |
| dc.identifier.uri | http://hdl.handle.net/11603/12910 | |
| dc.language.iso | en_US | en_US |
| dc.publisher | American Chemical Society | en_US |
| dc.relation.isAvailableAt | The University of Maryland, Baltimore County (UMBC) | |
| dc.relation.ispartof | UMBC Biological Sciences Department Collection | |
| dc.relation.ispartof | UMBC Faculty Collection | |
| dc.rights | This item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author. | |
| dc.rights | This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://pubs.acs.org/doi/10.1021/acs.analchem.6b02151 | |
| dc.subject | proteomics workflows | en_US |
| dc.subject | chromatographic peak areas | en_US |
| dc.subject | cargo of exosomes | en_US |
| dc.subject | myeloid-derived suppressor cells | en_US |
| dc.title | Evaluation of Spectral Counting for Relative Quantitation of Proteoforms in Top-Down Proteomics | en_US |
| dc.type | Text | en_US |