Rapid Assessment of Contaminants and Interferences in Mass Spectrometry Data Using Skyline

  • Matthew J. RardinEmail author
Application Note


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, I 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.

Graphical Abstract


Contaminants Interferences Skyline MS1 filtering Proteomics 

Supplementary material

13361_2018_1940_MOESM1_ESM.xlsx (50 kb)
Supplemental Table S1 (XLSX 49 kb)


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Copyright information

© American Society for Mass Spectrometry 2018

Authors and Affiliations

  1. 1.Discovery Attribute SciencesAmgenSouth San FranciscoUSA

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