This github repo most of the input files and the analyses used in the manuscript. Any files not located here are freely and openly accessible on the PanoramaWeb. MS data files can also be found on ProteomeXchange under the unique identifier PXD064536.
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HeLa_IsoWindow_Figs2-5_FigS1-2_S6-7_TableS1-2.Rmd: This file contains the processing for Figures 2-5, S1-2, S6-7, and Tables S1-2.
- Figure 2: Acquisition rate and cycle time comparisons between the Orbitrap Astral and prototype Orbitrap Astral Zoom mass spectrometers
- Figure 3: Detections of precursors and protein numbers between the Orbitrap Astral and prototype Orbitrap Astral Zoom MS
- Figure 4: Coefficient of variance (CV) comparison between the Orbitrap Astral and prototype Orbitrap Astral Zoom MS
- Figure 5: Ion counting for ions per peptide
- Figure S1: Injection time analysis comparing different isolation windows and input HeLa material
- Figure S2: Lower abundance proteins and precursors are gained at higher amounts of HeLa material
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EV_MMCC_Fig6_FigS8.Rmd: This files contains the processing for Figures 6 and S8.
- Figure 6: Extracellular vesicle (EV) matrix-matched calibration comparing the Orbitrap Astral and prototype Orbitrap Astral Zoom MS
- Figure S8: Detections of protein and precursors, CV, and other ion statistics
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Ion_Calibration_Table1_FigS3-5.Rmd: This file contains the code for calibrating the number of ions between different instruments
- Table 1: Comparison of calibration to ions/sec for various ThermoFisher Scientific MS instruments and analyzers
- Figure S3: Fragmentation pattern of various compounds used for calibration
- Figure S4: Plots of Glu[1]-Fibrinopeptide B signal intensity of various fragment ions and number of ions for calibration
- Figure S5: Comparison of calibration between the Orbitrap Astral and prototype Orbitrap Astral Zoom with various compounds
Any questions regarding the ion calibration code or manuscript, please feel free to contact (maccoss@uw.edu).
We are currently working on a GUI or Skyline external tool for quick and easy use for calibration.