Protocol detail

Peptide Analysis by Q-Exactive MS

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Mass spectrometry analysis of each sample’s peptides was performed using the Q-Exactive quadrupole-Orbitrap (Thermo Fisher Scientific, Waltham, Massachusetts, United States), which was coupled with a Dionex Ultimate 3000 nano-UPLC system as described before by Rossouw.^{12 (link)} Using Xcalibur^TM (version 4.2) (Thermo Fisher, Waltham, Massachusetts, United States), spectral data was collected in a data-dependent manner and details are shown in Supplementary document – Table S1.

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Rossouw S., Bendou H., Bell L., Rigby J, & Christoffels A. (2021). Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa. African Journal of Laboratory Medicine, 10(1), 1122.

Publication 2021

Q-Exactive quadrupole-Orbitrap Dionex Ultimate 3000

Mass spectrometry Peptides

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Variable analysis

independent variables

Mass spectrometry analysis of each sample's peptides

dependent variables

Spectral data collected in a data-dependent manner

control variables

Q-Exactive quadrupole-Orbitrap (Thermo Fisher Scientific, Waltham, Massachusetts, United States)
Dionex Ultimate 3000 nano-UPLC system

controls

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

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