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 procedures. Efforts to understand and mitigate sample contamination are a continual source of disruption 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 rapid assessment of sample integrity, and indicates potential sources of contamination

To insert a non-protein transition list into Skyline (v4.1.0.11714) requires the following information: molecule list name, precursor name, molecular formula, adducts (M+H, M+NH4, etc) precursor m/z and charge state. For polymers such as PEG the molecular list name remains constant while the precursor name varies with polymer length. Total PEG contamination, as with other polymers, is then viewed by highlighting only the molecular list name in the Skyline transition tree. Full Scan (MS1) features such as resolution and scan range can be adjusted in Skyline depending on the mass spectrometer used.