The accuracy of any analytical method is highly dependent on the selection of an appropriate calibration model. Here, we present CCWeights, an R package for automated assessment and selection of weighting factors for accurate quantification using linear calibration curve. Additionally, CCWeights includes a web application that allows users to analyze their data using an interactive graphical user interface, without any programming requirements. The workflow and features of CCWeights are illustrated by the analyses of two datasets acquired by liquid chromatography-mass spectrometry (LC-MS). The resulting quantification table can be directly utilized for further model assessment and subsequent data analysis.;CCWeights is publicly available on CRAN repository (https://cran.r-project.org/web/packages/CCWeights), with source code available on GitHub (https://github.com/YonghuiDong/CCWeights) under a GPL-3 license. The web application can be run locally from R console using a simple command "runGui()". Alternatively, the web application can be freely accessed for direct online use at https://bcdd.shinyapps.io/CCWeights/.;Supplementary data are available at Bioinformatics Advances online.