SWATH-MS is a powerful mass spectrometry technique with the potential to become a clinical tool for biomarker discovery and diagnostics. However, clinical tissue samples can be prohibitively limited, with a biopsy as small as 1 mg of tissue. This small amount of tissue necessarily dictates a lower loading on a mass spectrometer, but the effect on protein and peptide quantification is unclear. Therefore, the relationship between sample loading and protein and peptide quantification was investigated. A large batch of rat brain was digested and pooled to form a stock digest. This digest was loaded on to a Sciex 6600 TripleTOF at three concentrations: low, medium and high; with 6 replicates per group. The SWATH-MS peaks were extracted in PeakView with MS/MSALL SWATH Acquisition with a moderate spectral reference library (~4,300 proteins with 5% FDR). Quantified peptides were analysed in R and R/Bioconductor using a 1% FDR with an additional requirement to be present in all 6 samples. There was a moderate gain in the number of proteins and peptides quantified from the low to the medium loading groups. However, there was a modest gain in the moderate to high groups. These results indicate a small compromise in quantified proteins when loading samples from limited sources, such as biopsies.