1. PCCSE Project Peculiar P100 Peak Picking Puzzles
LINCS PCCSE Meeting
11 Feb 2016

2. Data QC Pipeline
Import .raw files into heavy checker during acquisition to verify optimal instrument performance
Import .raw files into full DIA analysis file with precursors
Import .raw files into QC DIA file to determine enrichment efficiency
Manually pick correct peak range using full DIA file (“Peptide ID”)
Manually refine boundaries and transitions while removing precursors (“Quant”)
Add metadata into Document Grid View
Export into .gct file for data analysis

3. “Peptide ID”

4. “Quant”

5. Peak Boundaries: KIAA1844 Can’t consistently find right peak
2 examples of this

6. Peak Boundaries: KIAA0701 This is integrated poorly
Many more examples of this

7. Peak Boundaries: KIAA0701
Automatic Manual

8. Transition Refinement: AHNAK

9. Transition Refinement: BAF155

10. Transition Refinement: A2D Sample B1

11. Transition Refinement: A2D Sample B12

12. Transition Refinement: CDC2 Sample D8

13. Transition Refinement: CDC2 Sample H2