Please use this identifier to cite or link to this item:
http://doi.org/10.25358/openscience-8767
Authors: | Kwiatkowski, Marcel Hotze, Madlen Schumacher, Julia Asif, Abdul R. Miguel, Jose Pittol, Ramos Brenig, Bertram Ramljak, Sanja Zischler, Hans Herlyn, Holger |
Title: | Protein speciation is likely to increase the chance of proteins to be determined in 2-DE/MS |
Online publication date: | 7-Feb-2023 |
Year of first publication: | 2022 |
Language: | english |
Abstract: | Multiple spotting due to protein speciation might increase a protein's chance of being captured in a random selection of 2-DE spots. We tested this expectation in new (PXD015649) and previously published 2-DE/MS data of porcine and human tissues. For comparison, we included bottom-up proteomics studies (BU-LC/MS) of corresponding biological materials. Analyses of altogether ten datasets proposed that amino acid modification fosters multispotting in 2-DE. Thus, the number of 2-DE spots containing a particular protein more tightly associated with a peptide diversity measure accounting for amino acid modification than with an alternative one disregarding it. Furthermore, every 11th amino acid was a post-translational modification candidate site in 2-DE/MS proteins, whereas in BU-LC/MS proteins this was merely the case in every 21st amino acid. Alternative splicing might contribute to multispotting, since genes encoding 2-DE/MS proteins were found to have on average about 0.3 more transcript variants than their counterparts from BU-LC/MS studies. Correspondingly, resolution completeness as estimated from the representation of transcript variant-rich genes was higher in 2-DE/MS than BU-LC/MS datasets. These findings suggest that the ability to resolve proteomes down to protein species can lead to enrichment of multispotting proteins in 2-DE/MS. Low sensitivity of stains and MS instruments appears to enhance this effect. |
DDC: | 300 Sozialwissenschaften 300 Social sciences |
Institution: | Johannes Gutenberg-Universität Mainz |
Department: | FB 02 Sozialwiss., Medien u. Sport |
Place: | Mainz |
ROR: | https://ror.org/023b0x485 |
DOI: | http://doi.org/10.25358/openscience-8767 |
Version: | Published version |
Publication type: | Zeitschriftenaufsatz |
Document type specification: | Scientific article |
License: | CC BY-NC |
Information on rights of use: | https://creativecommons.org/licenses/by-nc/4.0/ |
Journal: | Electrophoresis 43 11 |
Pages or article number: | 1203 1214 |
Publisher: | John Wiley & Sons, Ltd |
Publisher place: | Weinheim |
Issue date: | 2022 |
ISSN: | 1522-2683 |
Publisher DOI: | 10.1002/elps.202000393 |
Appears in collections: | DFG-491381577-H |
Files in This Item:
File | Description | Size | Format | ||
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protein_speciation_is_likely_-20230206154158825.pdf | 1.35 MB | Adobe PDF | View/Open |