Proteomic Analysis of Biological Samples

The mass spectrometry system used for the proteomic approach was a nanoAcquity UPLC-Xevo QTof MS system (Waters, Manchester, UK), using the Protein Lynx Global Server (PLGS) software, after downloading the Uniprot database. The difference in expression between the groups was analyzed by t-test (p < 0.05), using the PLGS software. After protein identification and categorization, Cytoscape 3.6.1 (Java^®) software was used for bioinformatics analyses with the ClusterMarker plugin for protein-protein interaction networks and the ClueGO plugin for the determination of biological process groups (Bindea et al., 2009 (link)).

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Puty B., Bittencourt L.O., Lima L.A., Plaça J.R., Dionizio A., Buzalaf M.A., Gomes B.D., de Oliveira E.H, & Lima R.R. (2023). Unraveling molecular characteristic of fluoride neurotoxicity on U87 glial-like cells: insights from transcriptomic and proteomic approach. Frontiers in Cellular Neuroscience, 17, 1153198.

Publication 2023

nanoAcquity UPLC-Xevo QTof MS system

Biological determination Lynx Mass spectrometry Protein

Corresponding Organization : Universidade Federal do Pará

Other organizations : Instituto Evandro Chagas, National Council for Scientific and Technological Development, Fundação de Amparo à Pesquisa do Estado de São Paulo, Universidade de São Paulo

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Variable analysis

independent variables

Protein expression

dependent variables

Difference in protein expression between groups

control variables

Uniprot database used for protein identification
PLGS software used for protein identification and categorization
Cytoscape 3.6.1 (Java®) software used for bioinformatics analyses
ClusterMarker plugin used for protein-protein interaction networks
ClueGO plugin used for determination of biological process groups

controls

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

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