Figure 1

• Figure folder
• Supplementary Files (Includes figure components)

Figure 2

• Figure folder
• Raw Files
• Supplementary Files (Includes figure components)
• System Suitability AutoQC folder
• Skyline document (PRM)

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)

 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)

 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)

 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)

 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)

 Supplemental
Figure 1

• Figure folder
• Data shared with Figure 4
• Supplementary Files
  

Supplemental
Figure 2

• Figure folder
• Data shared with Figure 6
• Supplementary Files

Reference
Information

• Supplementary Files
• Supplemental Material
• FASTA
• Skyline report (.skyr) files
• Skyline document templates for QC