title: Evaluation of dimethyl sulfoxide (DMSO) as a mobile phase additive during top 3 label-free quantitative proteomics.
abstract: Dimethyl sulfoxide (DMSO) has been advocated as a beneficial additive to electrospray solvents for peptide analysis due to the improved ionisation efficiency conferred. Previous reports have shown that the resultant improvements in peptide ion signal intensities are non-uniform. As a result, it was hypothesised that inclusion of DMSO in electrospray solvents could be detrimental to the outcome of intensity-based label-free absolute quantification approaches, specifically the top 3 method. The effect of DMSO as a mobile phase additive in top 3 label-free quantification was therefore evaluated. We show that inclusion of DMSO enhances data quality, improving the precision and number of proteins quantified, with no significant change to the quantification values observed in its absence.
authors: Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland; Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
authors: Dominika
authors: D
authors: Strzelecka
authors: Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
authors: Stephen W
authors: SW
authors: Holman
authors: Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
authors: Claire E
authors: CE
authors: Eyers
keywords: DIA, data-independent acquisition; DMSO; DMSO, dimethyl sulfoxide; ESI, electrospray ionisation; HDMSE, ion mobility-assisted MSE; LC, liquid chromatography; LC–MS; Label-free; MS, mass spectrometry; MS/MS, tandem mass spectrometry; MSE, mass spectrometry with elevated energy (a form of data-independent tandem mass spectrometry); Peptide; Proteomics; Q-ToF, quadrupole-time-of-flight; Quantification; SWATH, sequential window acquisition of all theoretical fragment ion spectra; cpc, copies per cell