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The relative degree of fluorotelomer-based acrylate polymers (FTACPs) fluorination was demonstrated to influence the sample preparation protocol for matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry. A homologous series of FTACPs were synthesized from fluorotelomer and hydrocarbon acrylates of different chain lengths, which varied the ratio of perfluorinated to hydrogenated carbons (RF/RH). The solubility of FTACPs in tetrahydrofuran (THF) and chloroform was observed to decrease for highly fluorinated FTACPs (RF/RH>0.5) promoting FTACP aggregation. No dependence on the degree of fluorination was observed for the solubility of FTACPs in the fluorinated solvents α,α,α-trifluorotoluene (TFT) or dichloropentafluoropropanes (HCFC-225). For FTACPs with a low degree of fluorination such as poly(8:2 FTAC-co-HDA) (RF/RH=0.375), MALDI-ToF analysis was successful using a conventional sample preparation protocol with THF, and dithranol (Dith) matrix. Conversely, the poor solubility of the highly fluorinated poly(8:2 FTAC-co-BA) (RF/RH=1.5) in THF resulted in mass discrimination. Several fluorinated sample preparation protocols were evaluated for poly(8:2 FTAC-co-BA) using TFT and HCFC-225, and decafluoroazobenzene (DFAB) or 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile (DCTB) matrices. The high volatility of HCFC-225 decreased FTACP pooling during solvent evaporation in comparison to the less volatile TFT, and improved the quantity of detectable signals. MALDI-ToF analysis of poly(8:2 FTAC-co-BA) in a 95:5 HCFC-225:methanol with DCTB being the best sample preparation protocol for highly fluorinated FTACPs in this study producing the highest number of observable signals. Employing a fluorinated sample preparation offers the capability of analyzing other highly fluorinated polymers that are not compatible with conventional sample preparations.