Surgical treatment of early rectal cancer (RC) (Stage I/IIA) is commonly curative, although infrequently some patients recur with dire prognoses. It would be beneficial to identify prognostic biomarkers in primary rectal tumours to detect aggressive tumours, where at-risk patients could consider adjuvant chemotherapy. To undertake this study primary specimens of Stage I/IIA rectal tumours were used. The cohort included 7 patients with distant recurrence, matched with 11 patients with no recurrence after 3 years from surgery. Tumour regions were isolated by laser microdissection of FFPE sections, heated at 95oC for 30 minutes with 1% SDC, 100mM Tris-HCl, digested overnight with trypsin, then desalted using StageTips. Peptides were analysed by LC-MS/MS using DIA on a Orbitrap HF-X MS over a 140-minute run time. DIA-NN was used to identify and quantify peptides to 1% FDR. PRM was conducted to confirm some protein expression levels. 7977 proteins were identified in the tumour specimens, of which 5508 proteins were quantified in all samples. 161 proteins showed 2-fold or more differential expression between patient groups. Gene set enrichment analysis identified the epithelial-mesenchymal transition (EMT) and coagulation pathways as enriched in the recurrent patient group. Our PRM assay showed good quantitative consistency between MS methods for 6 out of 8 proteins. Immunohistochemistry revealed that patients with recurrence had lower density of CD3+CD8+ T lymphocytes in their primary tumours compared to patients without recurrence. These biomarkers may be validated in a larger cohort to determine their functional significance in driving recurrence, and as biomarkers to identify patients at higher risk of recurrence with distant metastasis.