The risk assessment of chlorinated paraffins (CPs), chemicals of widespread industrial use, is struggling without standardized analytical methods to obtain reliable occurrence data. Indeed, scientists face analytical challenges that hinder the comparability of analytical methods, among them uncontrolled ionization efficiency and lack of quantification standards. In this study, our goal was to investigate potential issues faced when comparing data from different mass spectrometry platforms and quantification methods. First, the injection of the same set of single-chain length standards in three different instrumental mass spectrometry set-ups (liquid chromatography-electrospray-Orbitrap (LC/ESI-HRMS), liquid chromatography-electrospray-time-of-flight (LC/ESI-MS), and gas chromatography-electron capture negative ion-Orbitrap (GC/ECNI-HRMS)) revealed a shift of homologue response patterns even in-between LC/ESI-based set-ups, which was more pronounced for CPs of low chlorination degree. This finding emphasizes the need for a comprehensive description of instrument parameters when publishing occurrence data. Second, the quantification of a data set of samples with four quantification methods showed that quantification at the sum SCCP and MCCP levels presented good comparability, while quantification at the homologue level remained unsatisfactory. In light of those results, we suggest that (i) response pattern comparison should only be performed between similar instrumental set-ups, (ii) experimental chlorination degrees should be used when quantifying according to the %Cl (instead of those provided by the suppliers), and (iii) concentration results should be expressed as the sum of SCCPs and MCCPs primarily, with an indication on the match between samples and quantification standards (for example their chlorine content).