Advantages of label free method in comparison with 2DE proteomic analysis of <i>Butyrivibrio fibrisolvens</i> 3071 grown on different carbon sources

The aim of this study was the comparison label-free method with 2DE to other analytical bacterium Butyrivibrio fibrisolvens extracellular protein samples. Label-free quantification (LF) performed in work compared previously obtained results proteomic analysis using two-dimensional electrophoresis (2DE) and nano-liquid chromatography coupled mass spectroscopy (nLC/MS). B. as an important plant fibre degrader cultivated on four different carbon sources (including xylan, xylose, glucose, a mixture xylan glucose). impact growth substrate profile assessed by six pair-wise comparisons evaluating significantly differently abundant proteins. Gel-free gel-based methods resulted substantially dissimilar results. LC-MS/MS approach detected substrate-dependent differences transport binding membrane proteins (TBP) nucleotidase, while effect included synthesis butyrate synthesis. On hand, both observed differentially regulated involved glycolytic pathway, however, only shared enzyme (protein approach) fructose-bisphosphate aldolase. high abundance separated peptides. However, it cannot be easily considered supreme analysis. Both differ sample preparation, their advantages limitations. findings indicate these can complement each together they elucidate better metabolic functions fibrisolvens.HIGHLIGHTSComparison LF showed limitations connected narrow optimised pH interval number affected contrary results.Butyrivibrio culture same changes presence saccharides whole rumen fluid vivo.Selected could used for monitoring polysaccharides fermentation optimisation hemicellulose degradation overall feed utilisation.