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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.

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Common Uses of PEAKS

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  1. Common Uses of PEAKS Dan Maloney Bioinformatics Solutions Inc.

  2. Insure Accurate Reporting • Must understand what makes a good result • avoid false positives and negatives.

  3. Agenda • Walk through a PEAKS Search • Project creation • Search configuration • PEAKS DB results • de novo results

  4. Project Creation Select enzyme for each sample Add multiple samples

  5. Multiple Enzyme Approach Multiple Enzyme Project Glu C Lys C Trypsin

  6. Multiple Enzyme Approach Select ‘use enzyme specified in the sample’

  7. PEAKS Complete Analysis Launch everything from one screen

  8. PEAKS Complete Analysis

  9. Target + decoy database plotted # of hits false true score

  10. An Idea to Improve Score Function

  11. Effect of similarity on scoring function false after before true score

  12. PEAKS DB Result

  13. PEAKS DB Result PTM Mutation

  14. PEAKS DB Result Set false discovery rate threshold Pick a cut off

  15. PEAKS DB Result You may still have many hits below the threshold

  16. PEAKS DB Result

  17. PEAKS DB Result Cannot actually count this protein

  18. Confident PTMs and Mutations

  19. de novo only view

  20. Filtering de novo results Only trust the highly confident amino acids

  21. Filtering de novo results Press this button to bring up the local confidence filter

  22. Filtering de novo results Set a local confidence cut off

  23. Filtering de novo results Amino acids below cut off will not be displayed, mass shown instead

  24. De Novo Enabled PTM Discovery good scan missed by protein ID

  25. De Novo Enabled PTM Discovery Was not found because dehydration was overlooked

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