Quantitative Proteomic Analysis of Sweat Glands

Sweat glands from DC tissue samples (n = 9) and sweat glands isolated from normal palmar skin (n = 9) were denatured, alkylated, and digested as previously described [41 (link)]. Samples were injected into Thermo ScientificTM DionexTM UltimateTM 3000 RSLCnano systems equipped with NCS-3500RS (microflow) module and Q Exactive Plus—OrbitrapTM spectrometer (Thermo Fisher Scientific) operated in Data-Independent Acquisition (DIA) mode for peptide and protein quantification. Raw data was processed and analyzed by DIA-NN software [42 (link)] using default parameters. Q value (FDR) cut-off on precursor and protein level was applied 1%. All selected precursors that passed the filters were used for quantification. Proteomic data was analyzed using the Perseus software platform version 1.6.15.0 (www.perseus-framework.org (accessed on 10 November 2022) [43 (link)]). Samples with few data (names in manuscript: Control 7–9, DC 7–9; names in protein dataset: N1, N2 and N8, DD0, DD5 and DD7) as well as keratins, and immunoglobulins were removed. Data was filtered for at least 70% of the total valid values, and missing values were imputed from normal distribution width 0.3, down-shift 1.8. Up- or down-regulation was considered significant when p value < 0.05. The Kyoto Encyclopedia of Genes and Genomes (KEGG) mapper was used to visualize the signaling pathways involved, and enrichment analysis was performed using EnrichR tool (www.maayanlab.cloud/Enrichr/ (accessed on 10 November 2022)).

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Cárdenas-León C.G., Mäemets-Allas K., Klaas M., Maasalu K, & Jaks V. (2023). Proteomic Analysis of Dupuytren’s Contracture-Derived Sweat Glands Revealed the Synthesis of Connective Tissue Growth Factor and Initiation of Epithelial-Mesenchymal Transition as Major Pathogenetic Events. International Journal of Molecular Sciences, 24(2), 1081.

Publication 2023

Down Down regulation Genes Genomes Immunoglobulins Keratins Palmar Peptide Protein Signaling pathways Skin Sweat glands Tissue

Corresponding Organization : Tartu University Hospital

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Variable analysis

independent variables

Tissue samples: Sweat glands from DC tissue (n = 9) and sweat glands isolated from normal palmar skin (n = 9)

dependent variables

Peptide and protein quantification

control variables

Samples with few data (names in manuscript: Control 7–9, DC 7–9; names in protein dataset: N1, N2 and N8, DD0, DD5 and DD7) as well as keratins, and immunoglobulins were removed

controls

No positive or negative controls were explicitly mentioned in the protocol.

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