BIOINFORMATICS SOLUTIONS INC. PEAKS Studio 5.1 User’s Manual © Bioinformatics Solutions Inc. 470 Weber St. N. Suite 204 Waterloo, Ontario, Canada N2L 6J2 Phone 519-885-8288 • Fax 519-885-9075 Please contact BSI for questions or suggestions for improvement. 1. Introduction to PEAKS 5.1 ................................................................................6 1.1 Main Features............................................................................................................. 6 1.2 New Features in the PEAKS 5 Product Line .......................................................... 6 1.3 Workflow .................................................................................................................... 7 1.4 Guidelines for Using this Manual............................................................................. 7 1.5 Scope............................................................................................................................ 7 1.6 Service and Support................................................................................................... 7 2. Getting Started with PEAKS 5.1 .......................................................................8 2.1 Package Contents....................................................................................................... 8 2.2 System Requirements ................................................................................................ 8 2.2.1 Adjusting the Amount of Memory that PEAKS Uses ............................. 8 2.3 Installation for Windows Users ................................................................................ 9 2.4 Registering PEAKS.................................................................................................. 10 2.4.1 Registration Instructions (Internet Connection).................................... 10 2.4.2 Registration Instructions (No Internet Connection).............................. 11 2.4.3 Re-registration Instructions..................................................................... 14 2.5 Set up PEAKS Preferences ..................................................................................... 14 2.6 Set up PEAKS Configuration ................................................................................. 14 3. Quick Walkthrough ..........................................................................................15 3.1 Create a Sample Database....................................................................................... 15 3.2 Create a Project........................................................................................................ 15 3.3 Perform Data Refinement ....................................................................................... 17 3.4 Run de novo Sequencing.......................................................................................... 18 3.5 Run Protein Identification ...................................................................................... 21 3.6 Run PTM Finder...................................................................................................... 23 3.7 Run an inChorus Search ......................................................................................... 25 3.8 Perform a SPIDER Search...................................................................................... 30 4. Load Data...........................................................................................................33 4.1 Data Formats............................................................................................................ 33 4.2 Data Conversion....................................................................................................... 33 4.2.1 PEAKS Project Converter ....................................................................... 33 4.2.2 Agilent Data............................................................................................... 34 4.2.3 Applied Biosystems (WIFF)Data............................................................. 34 4.2.4 Applied Biosystems (4700/4800)Data ...................................................... 35 4.2.5 Bruker Data............................................................................................... 35 4.2.6 Shimadzu Data .......................................................................................... 35 4.2.7 Thermo Data.............................................................................................. 36 4.2.8 Varian Data ............................................................................................... 36 4.2.9 Waters/Micromass (MassLynx) Data ..................................................... 36 4.3 Create a New Project............................................................................................... 37 4.4 Add Data to an Existing Project............................................................................. 38 4.5 Open / Close a Project ............................................................................................. 39 4.6 Delete and Hide Results............................................................................................ 39 4.7 Change the Location of Saved Projects ................................................................. 39 4.8 Orienting Yourself ................................................................................................... 40 2 4.8.1 Project View Panel.................................................................................... 40 4.8.2 Properties Panel ........................................................................................ 40 4.8.3 Raw Spectrum View ................................................................................. 41 5. Data Refinement.................................................................................................43 5.1 Run Data Refine....................................................................................................... 43 5.2 Data Refinement Parameters.................................................................................. 44 5.2.1 Merging Scans ........................................................................................... 44 5.2.2 Precursor Charge Correction .................................................................. 44 5.2.3 Filtering MS/MS Scans............................................................................. 44 5.2.4 Preprocessing MS/MS Scans.................................................................... 44 5.3 Data Preprocessing Results..................................................................................... 44 6. de novo Sequencing ...........................................................................................45 6.1 Setting up Auto de novo Sequencing Parameters.................................................. 45 6.1.1 Mass Options ............................................................................................. 46 6.1.2 Enzyme Options ........................................................................................ 46 6.1.3 PTM Options ............................................................................................. 46 6.1.4 General Options ........................................................................................ 46 6.2 de novo Sequencing Results..................................................................................... 47 6.2.1 Peptide Candidates Frame....................................................................... 48 6.2.2 Ion Table Frame........................................................................................ 50 6.2.3 Spectrum View Frame.............................................................................. 50 6.2.4 Spectrum Alignment Frame..................................................................... 51 6.2.5 Survey Scan ............................................................................................... 51 6.2.6 Error Map.................................................................................................. 51 6.3 Manual de novo Sequencing.................................................................................... 51 6.3.1 Manual de novo Graphical User Interface.............................................. 51 6.3.2 Manual de novo Operations ..................................................................... 53 7. Database Search ................................................................................................58 7.1 Setting up Protein Identification Parameters........................................................ 58 7.1.1 Mass Options ............................................................................................. 59 7.1.2 Enzyme Options ........................................................................................ 59 7.1.3 General Options ........................................................................................ 59 7.1.4 PTM Options ............................................................................................. 60 7.1.5 Database Options ...................................................................................... 61 7.1.6 Advanced Options..................................................................................... 61 7.2 Protein Identification Results ................................................................................. 62 7.2.1 Peptide View.............................................................................................