6533b7dbfe1ef96bd1270195

RESEARCH PRODUCT

Label-free profiling of skeletal muscle using high-definition mass spectrometry

subject

description

We report automated and time efficient (2 h per sample) profiling of muscle using ultra-performance liquid chromatography (LC) coupled directly with high-definition mass spectrometry (HDMSE). Soluble proteins extracted from rat gastrocnemius (n=10) were digested with trypsin and analysed in duplicate using a 90 min RPLC gradient. Protein identification and label-free quantitation were performed from HDMSE spectra analysed using TransOmics Informatics for Proteomics software. In total 1,514 proteins were identified. Of these, 811 had at least 3 unique peptides and were subsequently used to assess the dynamic range and precision of LC-HDMSE label-free profiling. Proteins analysed by LC-HDMSE encompass the entire complement of glycolytic, beta-oxidation and tricarboxylic acid enzymes. In addition, numerous components of the electron transport chain and protein kinases involved in skeletal muscle regulation were detected. The dynamic range of protein abundances spanned 4 orders of magnitude. The correlation between technical replicates of the 10 biological samples was R2 = 0.9961 ± 0.0036 (95 % CI = 0.9940 – 0.9992) and the technical coefficient of variation averaged 7.3 ± 6.7 % (95 % CI = 6.87 – 7.79 %). This represents the most sophisticated label-free profiling of skeletal muscle to date.