Identification of putative protein biomarkers for SMA in skeletal muscle from 'severe’ SMA mice. (A) Scatter plot showing the process of filtering undertaken on the raw proteomics data in order to generate a final list of 23 proteins modified in SMA mouse skeletal muscle at P5, but unchanged at P1. The left column shows all proteins identified by the Progenesis label-free proteomics software (n = 540 proteins in total) in control and SMA (knockout (KO)) mouse LAL muscle at P5, with the relative expression levels between samples represented as a ratio (KO/Control). The red bars indicate the 20% cutoff threshold for being up-regulated or down-regulated in SMA mice compared to controls. The middle column shows the proteins remaining in the P5 dataset following filtering (for example, that were either up- or down-regulated by >20% and were identified by at least two peptides (n = 245 proteins in total)). The right column shows those proteins that were identified as being changed in SMA mouse skeletal muscle at P5, but that were unchanged in comparable muscle samples at P1 (n = 23 proteins in total). (B) Graph showing all 14 proteins that were unchanged at P1 in 'severe’ SMA mouse LAL muscle compared to littermate controls, but had increased levels >20% at P5. (C) Graph showing all nine proteins that were unchanged at P1 in 'severe’ SMA mouse LAL muscle compared to littermate controls, but had decreased levels >20% at P5. Dashed lines in B and C indicate 20% change cut-off thresholds.