Comprehensive Proteomic Analysis of RC-LH1 Complex

Pure RC-LH1 core complex (50 µg) was solubilised and digested with pepsin, and the resulting peptides were analysed by nano-flow liquid chromatography coupled to a Q Exactive HF quadrupole-Orbitrap (Thermo Scientific) mass spectrometer as described in our previous work [10 (link),38 (link)]. Protein identification was performed by database searching using Byonic (v2.9.38, Protein Metrics) operating with the default parameters except that methionine sulfoxide (+15.19949 Da) was specified as a common variable modification (with a maximum of two per peptide). Cleavage sites were specified as N- and C-terminal to F, Y, W and L (semi-specific). The database was the Rba. sphaeroides reference proteome (www.uniprot.org/proteomes/ UP000002703) downloaded on 28 April 2021 and edited by adding the putative protein-Z sequence derived by the re-annotation of the Rsp_2385 locus (see Supplementary Figure S2).

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Qian P., Croll T.I., Hitchcock A., Jackson P.J., Salisbury J.H., Castro-Hartmann P., Sader K., Swainsbury D.J, & Hunter C.N. (2021). Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation. Biochemical Journal, 478(21), 3923-3937.

Publication 2021

Q Exactive HF quadrupole-Orbitrap Byonic

Cleavage Liquid chromatography Methionine sulfoxide Pepsin Peptide Protein Protein sequence Proteomes

Corresponding Organization : University of Sheffield

Other organizations : Thermo Fisher Scientific (Netherlands), University of Cambridge

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Variable analysis

independent variables

Solubilisation and digestion of Pure RC-LH1 core complex (50 µg) with pepsin

dependent variables

Resulting peptides analysed by nano-flow liquid chromatography coupled to a Q Exactive HF quadrupole-Orbitrap (Thermo Scientific) mass spectrometer

control variables

Protein identification performed by database searching using Byonic (v2.9.38, Protein Metrics) operating with the default parameters except that methionine sulfoxide (+15.19949 Da) was specified as a common variable modification (with a maximum of two per peptide)
Cleavage sites were specified as N- and C-terminal to F, Y, W and L (semi-specific)
The database used was the Rba. sphaeroides reference proteome (www.uniprot.org/proteomes/ UP000002703) downloaded on 28 April 2021 and edited by adding the putative protein-Z sequence derived by the re-annotation of the Rsp_2385 locus

Annotations

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