These data are the supplementary information for the technical report: In-gel sample preparation prior to proteomic analysis of bovine faeces increases protein identifications by removal of high molecular weight glycoproteins, which is published in Journal of Proteomics. Supplementary Figure 1: Comparisons between filter-aided sample preparation (FASP) and in-gel sample preparation (IGSP) in the bovine faecal sample identifications: (a) bovine proteins; (b) barley proteins and (c) bacterial proteins (Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Prevotellaceae, Bacterioidaceae, Spirochaetaceae). Proteins compared here were all master proteins Supplementary Table 1: Excel file of the proteome of bovine faecal extracts with bovine, barley and bacterial proteins identified following FASP and IGSP.