The continued technological advances in protein mass spectrometry has enabled unprecedented analytical resolution and sample throughput. So called SWATH™ acquisition is a relatively recent mass spectrometry approach which effectively digitises and collects quantitative information on all detectable peptides in each tissue sample following standardised sample preparation protocols. Simultaneous generation of a sample type specific peptide library facilitates the concomitant identification and quantification of all the peptides in each of the test samples in one experiment. We have utilised SWATH™ acquisition to evaluate the wound fluid microenvironment proteome of chronic leg ulcers and a small number of acute burn wounds. The identification and relative abundance measures of over 1000 proteins were obtained from the chronic wound fluid of healing vs non-healing chronic wounds. Subsequent gene ontology analysis revealed over represented biological processes and molecular functions when examining healing versus non-healing chronic wounds. Furthermore, a similar preliminary analysis of paediatric burn blister fluid, collected at time of patient presentation, revealed a panel of 70 proteins which could stratify those wounds which were grafted from those which were not thus reflecting the clinical decision making. Further verification work is continuing; however, these data suggest that SWATH™ acquisition is a powerful tool for the investigation of the complexities of the wound microenvironment.