Proteome Profiling of Plasma and Muscle

Here, we briefly summarise the 2-DE procedure as the procedure was described in detail earlier [10 (link),23 (link),50 (link)]. Proteomic analysis of depleted plasma samples and prepared muscle biopsies was carried out using Ettan IPGphor 3 IEF System (GE Healthcare, Buckinghamshire, UK) (first dimension) and Ettan DALTsix Electrophoresis Unit (Amersham, Pharmacia, Uppsala, Sweden) (second dimension). The fluorescent stain SYPRO Ruby (Bio-Rad Laboratories, Hercules, CA, USA) was applied to plasma protein gels, and silver stain was applied to muscle biopsy gels. The stained protein pattern was visualized using a charge coupled device camera (VersaDoc Imaging system 4000 MP, Bio-Rad). The PDQuest Advanced (v. 8.0.1, Bio-Rad) software was used to analyse and quantify the protein pattern. The amount of protein in a certain spot was assessed as background corrected optical density integrated over all pixels in the spot and expressed as integrated optical density (IOD). The parts per million (ppm) values for all proteins were generated and used for further statistical analysis.

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Gerdle B., Wåhlén K., Gordh T, & Ghafouri B. (2021). Thermal Pain Thresholds Are Significantly Associated with Plasma Proteins of the Immune System in Chronic Widespread Pain—An Exploratory Pilot Study Using Multivariate and Network Analyses. Journal of Clinical Medicine, 10(16), 3652.

Publication 2021

Ettan IPGphor 3 IEF System Ettan DALTsix Electrophoresis Unit SYPRO Ruby VersaDoc Imaging system 4000 MP

Biopsy Device Electrophoresis Gels Muscle Plasma Plasma protein Proteins Silver Sypro ruby

Corresponding Organization : Linköping University

Other organizations : Uppsala University

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Protein expression pattern in plasma and muscle biopsy samples
Quantification of protein expression (integrated optical density, IOD)
Parts per million (ppm) values for all proteins

control variables

Ettan IPGphor 3 IEF System (GE Healthcare, Buckinghamshire, UK) for the first dimension of 2-DE
Ettan DALTsix Electrophoresis Unit (Amersham, Pharmacia, Uppsala, Sweden) for the second dimension of 2-DE
Fluorescent stain SYPRO Ruby (Bio-Rad Laboratories, Hercules, CA, USA) for plasma protein gels
Silver stain for muscle biopsy gels
Charge coupled device camera (VersaDoc Imaging system 4000 MP, Bio-Rad) for visualizing the stained protein pattern
PDQuest Advanced (v. 8.0.1, Bio-Rad) software for protein pattern analysis and quantification

controls

No positive or negative controls were explicitly mentioned in the provided information.

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