In this study, microplastic samples from surface seawater of Tokyo Bay were collected, polyethylene (PE) microplastics were used to calculate carbonyl index (CI), and average spectra of PE were analyzed and compared with a previous study applying agitation during chemical treatment. It was found that PE and polypropylene (PP) were the predominant polymer type in the samples. Among PE samples, fragments were the most commonly observed shape, with white being the dominant color. Deviations were found in the average spectra among different shapes and colors when compared to the standard PE spectrum. A comparison of the average spectra between the two datasets suggests that pronounced peaks related to oxidation are most likely resulted from agitation during the chemical treatment. Additionally, it was found a closer spectral resemblance between the sample spectra and the spectrum of standard sample of oxidized PE (PEO) than with the standard PE spectrum, suggesting that using the oxidized PE as a reference spectrum might be more effective for identification. These findings highlight the complex factors affecting the spectral properties of microplastics and highlight the importance of understanding these variations to enhance the accuracy of microplastic identification workflows and understanding of environmental fate of microplastics.