Cell line dependence of metabolite leakage in metabolome analyses of adherent normal and cancer cell lines

Journal: Metabolomics

Rahul Vijay Kapoore · Rachael Coyle ·Carolyn A Staton ·Nicola J Brown ·Seetharaman Vaidyanathan

Rahul Vijay Kapoore · Seetharaman Vaidyanathan

ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom

Corresponding author email:

Ph.: +44 (0)114 222 7526

Fax: +44 (0)114 222 7501

Rachael Coyle ·Carolyn A Staton ·Nicola J Brown

Microcirculation Research Group, Department of Oncology, Faculty of Medicine, Dentistry and Health, The University of Sheffield, Sheffield, S10 2RX, United Kingdom

Table S1 List of metabolites identified by GC-MS along with their retention time from twelve metabolite mixture used for validation of AMDIS parameters

Fig.S1Overlay of total ion chromatograms after retention time correction using XCMS online (web-based platform) of all trypsinized and cell scraped samples from MDA-MB-436 cell line. X-axis represents total ion current (TIC) and Y-axis represents retention time in minutes, where Tryp = Trypsinization (straight lines); Csr = Cell scraping treatment (dotted lines); 436 = MDA-MB-436 cell line and A, B and C = biological replicates.

Fig.S2 Overlay of total ion chromatograms after retention time correction using XCMS online (web-based platform) of all trypsinized and cell scraped samples from HMEC-1 cell line. X-axis represents total ion current (TIC) and Y-axis represents retention time in minutes, where Tryp = Trypsinization (straight lines); Csr = Cell scraping treatment (dotted lines); Hmec = HMEC-1 cell line and A, B and C = biological replicates.

Fig.S3 Overlay of total ion chromatograms after retention time correction using XCMS online (web-based platform) of all trypsinized and cell scraped samples from MCF-7 cell line. X-axis represents total ion current (TIC) and Y-axis represents retention time in minutes, where Tryp = Trypsinization (straight lines); Csr = Cell scraping treatment (dotted lines); Mcf7 = MCF-7 cell line and A, B and C = biological replicates.

Fig. S4 PCA analysis of metabolomics data displaying clustering of MDA-MB-436 samples after trypsinization and cell scraping treatment. PCA is calculated using the feature intensities from all samples. The colours (red/blue) are assigned based on the sample class, where red colour = trypsinized samples; blue colour = cell scraped samples; Tryp = Trypsinization; Csr = Cell scraping treatment; MDA = MDA-MB-436 cell line and A, B and C = biological replicates.

Fig. S5 PCA analysis of metabolomics data displaying clustering of HMEC-1 samples after trypsinization and cell scraping treatment. PCA is calculated using the feature intensities from all samples. The colours (red/blue) are assigned based on the sample class, where red colour = trypsinized samples; blue colour = cell scraped samples; Tryp = Trypsinization; Csr = Cell scraping treatment; Hmec = HMEC-1 cell line and A, B and C = biological replicates.

Fig. S6 PCA analysis of metabolomics data displaying clustering of MCF-7 samples after trypsinization and cell scraping treatment. PCA is calculated using the feature intensities from all samples. The colours (red/blue) are assigned based on the sample class, where red colour = trypsinized samples; blue colour = cell scraped samples; Tryp = Trypsinization; Csr = Cell scraping treatment; Mcf7 = MCF-7 cell line and A, B and C = biological replicates.

Table S2 List of putatively identified metabolites in MDA-MB-436, HMEC-1 and MCF-7 cell lines across different applied sampling protocols

Table S2 (continued) List of putatively identified metabolites in MDA-MB-436, HMEC-1 and MCF-7 cell lines across different applied sampling protocols