Common Uses of PEAKS

Common Uses of PEAKS Dan Maloney Bioinformatics 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 Select enzyme for each sample Add multiple samples

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 # of hits false true score

An Idea to Improve Score Function

Effect of similarity on scoring function false after before true score

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

Common Uses of PEAKS