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2025-04-19

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This paper includes 7 figures and 2 Supplemental Figures. The mass spectrometry data was collected between 2014 and 2023 in the MacCoss laboratory. The public GitHub Repository manuscript-qc-system-suitability includes R scripts and R Markdown documents that were used to generate Figures 3-7 and Supplementary Figures 1 and 2.

Folder	Data and Supplementary File Locations	Script to generate figure
Figure 1	Figure folder Supplementary Files (Includes figure components)	N/A
Figure 2	Figure folder Raw Files Supplementary Files (Includes figure components) System Suitability AutoQC folder Skyline document (PRM)	N/A
Figure 3	Figure folder Raw Files Supplementary Files FASTA Script input files (Including those >25 MB that are not available on github) Metadata PRM data DDA data output Skyline report (.skyr) files Skyline document (PRM) Limelight project: ID 131 (DDA)	maccoss_qc_figures_3_4_5_6_S1_S2.Rmd
Figure 4	Figure folder Raw Files Supplementary Files FASTA Script input files (Including those >25 MB that are not available on github) Metadata PRM data DDA data Skyline Report Files Skyline documents (DIA and PRM)	maccoss_qc_figures_3_4_5_6_S1_S2.Rmd
Figure 5	Figure folder Raw Files Supplementary Files FASTA Script input files (Including those >25 MB that are not available on github) Metadata PRM data DIA data Skyline report (.skyr) files Skyline documents (DIA and PRM)	maccoss_qc_figures_3_4_5_6_S1_S2.Rmd
Figure 6	Figure folder Raw Files PRM DIA Supplementary Files FASTA Script input files (Including those >25 MB that are not available on github) Metadata PRM data DIA data Skyline report (.skyr) files System Suitability AutoQC folder Skyline document (PRM) Sample AutoQC Folder Skyline document (DIA)	maccoss_qc_figures_3_4_5_6_S1_S2.Rmd
Figure 7	Figure folder Raw Files Supplementary Files FASTA Script input files (Including those >25 MB that are not available on github) Metadata PRM data DIA data Skyline report (.skyr) files System Suitability AutoQC folder Skyline document (PRM)	plot_7a.r and plot_7b.r
Supplemental Figure 1	Figure folder Data shared with Figure 4 Supplementary Files	maccoss_qc_figures_3_4_5_6_S1_S2.Rmd
Supplemental Figure 2	Figure folder Data shared with Figure 6 Supplementary Files	maccoss_qc_figures_3_4_5_6_S1_S2.Rmd
Reference Information	Supplementary Files Supplemental Material FASTA Skyline report (.skyr) files Skyline document templates for QC	N/A

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