Uncertainty estimation plays an important role in source apportionment models such as the positive matrix factorization (PMF) model. In this study, synthetic datasets were generated and analyzed using PMF with specified uncertainties at different levels to investigate the impact of uncertainty inputs on the results of PMF model, as well as the benefits and risks of emphasizing on certain species. The results showed that: (1) uncertainties for the PMF model should be estimated based on characteristics of the dataset being analyzed; (2) emphasizing on correct tracers will improved model performance; and (3) emphasizing on unsuitable tracers may lead to disruptive consequences that might not be captured by the Q metric. Tests were also performed on collected ambient PM2.5 samples and similar conclusions were drawn: emphasizing on correct tracers was shown to improve the separation of important source categories from mixed sources. When emphasizing on incorrect tracers, a counterfeit factor of Fe industrial source was extracted, which are inconsistent with field observations. Results from this study provide insights on how uncertainties should be estimated for the PMF model.