Briefly, DIA raw data files were converted in profile mode to mzXML using msconvert and analyzed using OpenSWATH (2.0.0) [14] (link) as described previously [13] (link). Retention time extraction window was set as 600 s (for 60 min LC) or 350 s (for 20 min LC), and m/z extraction was performed with 0.03 Da tolerance. Retention time was then calibrated using both SiRT and CiRT peptides. Peptide precursors that were identified by OpenSWATH and pyprophet with d_score > 0.01 were used as inputs for TRIC [52] (link). For each protein, the median MS2 intensity value of peptide precursor fragments that were detected to belong to the protein was used to represent the protein abundance.
Zhu T., Zhu Y., Xuan Y., Gao H., Cai X., Piersma S.R., Pham T.V., Schelfhorst T., Haas R.R., Bijnsdorp I.V., Sun R., Yue L., Ruan G., Zhang Q., Hu M., Zhou Y., Van Houdt W.J., Le Large T.Y., Cloos J., Wojtuszkiewicz A., Koppers-Lalic D., Böttger F., Scheepbouwer C., Brakenhoff R.H., van Leenders G.J., Ijzermans J.N., Martens J.W., Steenbergen R.D., Grieken N.C., Selvarajan S., Mantoo S., Lee S.S., Yeow S.J., Alkaff S.M., Xiang N., Sun Y., Yi X., Dai S., Liu W., Lu T., Wu Z., Liang X., Wang M., Shao Y., Zheng X., Xu K., Yang Q., Meng Y., Lu C., Zhu J., Zheng J., Wang B., Lou S., Dai Y., Xu C., Yu C., Ying H., Lim T.K., Wu J., Gao X., Luan Z., Teng X., Wu P., Huang S., Tao Z., Iyer N.G., Zhou S., Shao W., Lam H., Ma D., Ji J., Kon O.L., Zheng S., Aebersold R., Jimenez C.R, & Guo T. (2020). DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. Genomics, Proteomics & Bioinformatics, 18(2), 104-119.
Publication 2020
Cirt Peptide Protein Retention Sirt Tolerance
Corresponding Organization : Westlake University
Other organizations :
Fudan University, Thermo Fisher Scientific (Germany), Amsterdam UMC Location VUmc, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Thermo Fisher Scientific (China), The Netherlands Cancer Institute
Retention time calibration using SiRT and CiRT peptides
Peptide precursors identified by OpenSWATH and pyprophet with d_score > 0.01
controls
Positive control: SiRT and CiRT peptides used for retention time calibration
Negative control: Not explicitly mentioned
Annotations
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