Proper sample preparation in proteomic workflows is essential to the success of modern mass spectrometry experiments. Complex workflows often require reagents which are incompatible with MS analysis (e.g. detergents) necessitating a variety of sample cleanup methods. Efforts to understand and mitigate sample contamination are a continual source of distraction with respect to both time and resources. To improve the ability to rapidly assess sample contamination from a diverse array of sources, we developed a molecular library in Skyline for rapid extraction of contaminant precursor signals using MS1 Filtering. This contaminant template library is easily managed and can be modified for a diverse array of mass spectrometry sample preparation workflows. Utilization of this template allows the assessment of sample integrity and indicates potential sources of contamination.