Download - Common Uses of PEAKS
Common Uses of PEAKS
Dan MaloneyBioinformatics Solutions Inc.
Insure Accurate Reporting
• Must understand what makes a good result– avoid false positives and negatives.
Agenda
• Walk through a PEAKS Search– Project creation– Search configuration– PEAKS DB results– de novo results
Project Creation
Add multiple samples
Select enzyme for each sample
Multiple Enzyme Approach
Multiple Enzyme Project
Glu C
Lys C
Trypsin
Multiple Enzyme Approach
Select ‘use enzyme specified in the sample’
PEAKS Complete Analysis
Launch everything from one screen
PEAKS Complete Analysis
Target + decoy database plotted
score
false
true
FDR#reported false hits
# reported hits
# of hits
An Idea to Improve Score Function
score
false
true
before after
Effect of similarity on scoring function
PEAKS DB Result
PEAKS DB Result
PTM Mutation
PEAKS DB Result
Set false discovery rate threshold
Pick a cut off
PEAKS DB Result
You may still have many hits below the threshold
PEAKS DB Result
PEAKS DB Result
Cannot actually count this protein
Confident PTMs and Mutations
de novo only view
Filtering de novo results
Only trust the highly confident amino acids
Filtering de novo results
Press this button to bring up the local confidence filter
Filtering de novo results
Set a local confidence cut off
Filtering de novo results
Amino acids below cut off will not be displayed, mass shown instead
De Novo Enabled PTM Discovery
good scan missed by protein ID
De Novo Enabled PTM Discovery
Was not found because dehydration was overlooked