akhileshkaushal / Metabolomics-I

Untargeted LC/MS-based metabolomics data analysis.

🧬Metabolomics-I🧬

LC/MS metabolomics data pre-processing using xcms

• LC/MS-featured oriented metabolomics data analysis pipeline based on xcms.

💾Data

• Download the following data subset (https://drive.google.com/drive/folders/1iocIVSCMTDflmRJhyvnVN5xJH3orKV_s) consisting of 4 .mzML files from human serum samples in MTBLS103 study (https://www.ebi.ac.uk/metabolights/MTBLS103) by (Samino et al. 2015).
• Acquisition: UHPLC system (1290 Agilent) coupled to a quadrupole time of flight (QTOF) mass spectrometer (6550 Agilent Technologies) / HILIC-based chromatography / ESI(+) mode.

🔬XCMS Analysis

• The xcms analysis has been performed considering on-line xcms parameters (https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage) optimized for UPLC with ~15 min gradient, high-resolution ESI-QTOF-MS (e.g. Agilent UHD Q-TOF 6538).

📑References

• Prince, John T., and Edward M. Marcotte. 2006. “Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping.” Analytical Chemistry 78 (17): 6140–52. https://doi.org/10.1021/ac0605344.

• Samino, Sara, Maria Vinaixa, Marta Díaz, Antoni Beltran, Miguel A Rodríguez, Roger Mallol, Mercedes Heras, et al. 2015. “Metabolomics reveals impaired maturation of HDL particles in adolescents with hyperinsulinaemic androgen excess.” Scientific Reports 5 (January): 11496. https://doi.org/10.1038/srep11496.

• Smith, Colin A., Elizabeth J. Want, Grace O’Maille, Ruben Abagyan, and Gary Siuzdak. 2006. “XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification.” Anal. Chem. 78 (3): 779–87. https://doi.org/10.1021/ac051437y.

• Tautenhahn, Ralf, Christoph Bottcher, and Steffen Neumann. 2008. “Highly sensitive feature detection for high resolution LC/MS.” BMC Bioinformatics 9: 1–16. https://doi.org/10.1186/1471-2105-9-504.