Proteomic Profiling of Epicardial Adipose Tissue

Proteins and their peptides were extracted from both the EAT and EAT secretome of 3 patients with and 3 without AF by liquid chromatography-tandem mass spectrometry using an Ultimate 3000 Nano LC–MS/MS system (Dionex LC-Packings, Amsterdam, The Netherlands) and identified as described previously [20 (link), 29 (link)]. Specific to this study, secretome extracted from ± 20 1 mm EAT cubes per sample were concentrated approximately 40 times using ultrafiltration devices (Amicon Ultra-4 Centrifugal Filter Unit, millipore, UFC801024), and EAT samples were cryo-milled and solubilized before protein denaturation and fixation (gels: Additional file 1: Fig. S1). For protein identification, MS/MS spectra were searched against the Swiss-Prot human FASTA file (canonical and isoforms, downloaded March 2017, 42161 entries) using MaxQuant version 1.5.4.1.[9 (link)]. Proteomes from EAT and EAT secretome were uploaded to the ProteomeXchange Consortium via the proteomics identification database PRIDE with accession number PXD013230.

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Meulendijks E.R., Al-Shama R.F., Kawasaki M., Fabrizi B., Neefs J., Wesselink R., Ernault A.C., Piersma S., Pham T.V., Jimenez C.R., Knol J.C., van Boven W.J., Driessen A.H., de Vries T.A., van der Leeden B., Niessen H.W., de Boer O.J., Krul S.P, & de Groot J.R. (2023). Atrial epicardial adipose tissue abundantly secretes myeloperoxidase and activates atrial fibroblasts in patients with atrial fibrillation. Journal of Translational Medicine, 21, 366.

Publication 2023

Ultra-4 Centrifugal Filter Unit

Cubes Devices Gels Human Isoforms Liquid chromatography Ms ms Patients Peptides Protein Protein denaturation Proteomes Secretome Ultra Ultrafiltration

Corresponding Organization : Amsterdam University Medical Centers

Other organizations : Amsterdam UMC Location VUmc, Isala

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Variable analysis

independent variables

Presence or absence of atrial fibrillation (AF) in patients

dependent variables

Proteins and peptides extracted from epicardial adipose tissue (EAT) and EAT secretome

control variables

Use of the same liquid chromatography-tandem mass spectrometry (LC-MS/MS) system and protocol for all samples
Concentration of secretome samples using ultrafiltration devices
Cryomilling and solubilization of EAT samples before protein denaturation and fixation
Searching MS/MS spectra against the same Swiss-Prot human FASTA file using MaxQuant version 1.5.4.1

controls

Positive control: Not specified
Negative control: Not specified

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