What is aView? <ul><li>CBIP Tool for capturing LC-MS results and a chemist’s assessment of each sample’s suitability for s...
What CB Processes are Controlled? <ul><li>DOS Library Production & Summary Statistics </li></ul><ul><li>Compound Registrat...
Mother Tube Sort Samples to Purify or Discard Samples in Screening Set DOS Library Production All Compound Samples DOS Int...
What are the Annotations? Three Components: Component Description Use “ Purity” Semi-quantitative estimate of actual purit...
What is “Purity” in aView? <ul><li>Peak Area% - NOT mass or mole based </li></ul>
Was the Target Mass (Compound) Found? <ul><li>Based on Mass Spectral Data Processing </li></ul><ul><li>Green = target mass...
Summary Assessment Matrix <ul><li>Analytical or Sample Directed </li></ul><ul><li>“ Terminal” or “non-Terminal” </li></ul>...
aView & DOS Library Production <ul><li>Control Library Production Workflow </li></ul><ul><ul><li>Intermediate Synthetic St...
aView & DOS Intermediate QC Analytical Method OK? Analytical Processing  OK? Complete Incomplete Re-run LC-MS Insufficient...
aView & Compound Registration Inform Compound Registration Dashboard
aView & Sample QC <ul><li>Capture Chemist’s Assessment of Sample Suitability for Screening </li></ul><ul><ul><li>Compound ...
“ Purity” Role in Annotation –  Business Rules for Sample QC Add “Other” Considerations Classify based on Purity > 70% < 4...
Classify based on Purity > 70% < 40% 40%< Purity < 70% Accept Purify Reject Comment required Summary Assessment  Requires ...
aView & DOS Library Production Statistics Inform Library Production Summary
aView & Compound Selection
aView Mechanics <ul><li>Data Collection Process Overview </li></ul><ul><li>MassLynx Folder & File naming standard </li></u...
LC-MS Data Collection Process CBIP SDMS Network File  Server MassLynx Input Files Raw Data Local PC Pipleline Pilot MassLy...
MassLynx Folder Structure & File Names masslynx LIB.pro sampleDB LIB_PLT_RUN#_RUN.txt LIB_PLT_RUN#_INT#_STD.txt LIB_PLT_RU...
Create MassLynx sample List in Pipeline Pilot <ul><li>Creating a sample list in MassLynx using the Import feature requires...
SDMS Picks Up Data from Instruments –  Archive Agent Template & MetaData
CBIP Collector Picks Up MetaData from SDMS
CBIP Collector – Status States Inform Users <ul><li>Standard Flow:  </li></ul><ul><ul><li>WaitingForRawData  </li></ul></u...
aView Reliability <ul><li>System Diagram </li></ul><ul><li>File Queue Monitoring </li></ul><ul><li>Storage Capacity Monito...
SDMS System Diagram
File Queue Monitoring- FileBoss <ul><li>04-Nov-2008 at 12:00:05:  </li></ul><ul><li>started log file &quot;C:Documents and...
Storage Capacity Monitoring - LetUKnow
Error Log Monitoring - LogMeister
aView Performance <ul><li>Schedule Monitoring with AA Log </li></ul>CBIP Collector SDMS LC-MS PP aView Directory Structure...
Adherence to Pickup Schedule –  1 Full Cycle (24 hr.) from AA Log Scheduled Pickup Time Actual Pickup Time Growing Delay C...
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Lab Informatics - NuGenesis SDMS interfaced with Compound QC Web App for Chemical Biology Library Production - David J. Howe

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Lab Informatics - NuGenesis SDMS interfaced with Compound QC Web App for Chemical Biology Library Production - David J. Howe

  1. 1. What is aView? <ul><li>CBIP Tool for capturing LC-MS results and a chemist’s assessment of each sample’s suitability for screening. </li></ul><ul><li>Standardization notation enables control logic for CB workflows. </li></ul><ul><li>Links back to RAW analytical data </li></ul>
  2. 2. What CB Processes are Controlled? <ul><li>DOS Library Production & Summary Statistics </li></ul><ul><li>Compound Registration Dashboard </li></ul><ul><li>Compound Selection for Screening </li></ul><ul><li>The Analytical Process itself </li></ul><ul><ul><li>Future: </li></ul></ul><ul><ul><li>Compound purification </li></ul></ul><ul><ul><li>Compound Library Quality Monitoring </li></ul></ul>
  3. 3. Mother Tube Sort Samples to Purify or Discard Samples in Screening Set DOS Library Production All Compound Samples DOS Intermediate QCs Sample QCs CBIP Collector SDMS LC-MS PP aView Directory Structure Raw LC-MS Data META Data Annotations DOS Library Production Stats Sample Reg. Dashboard RAW Data
  4. 4. What are the Annotations? Three Components: Component Description Use “ Purity” Semi-quantitative estimate of actual purity, based on peak area% Can be used to compare samples or drive logic of CBIP Tools Summary Assessment <ul><li>Standardized Notation Indicating: </li></ul><ul><ul><li>LC-MS Analysis Suitability </li></ul></ul><ul><ul><li>Sample Suitability </li></ul></ul>Drives logic of CBIP tools (Comments) Allows capture of relevant details regarding summary assessment Allows review of chemist’s key decision making considerations behind summary assessments
  5. 5. What is “Purity” in aView? <ul><li>Peak Area% - NOT mass or mole based </li></ul>
  6. 6. Was the Target Mass (Compound) Found? <ul><li>Based on Mass Spectral Data Processing </li></ul><ul><li>Green = target mass “found” Red = “not found” </li></ul>
  7. 7. Summary Assessment Matrix <ul><li>Analytical or Sample Directed </li></ul><ul><li>“ Terminal” or “non-Terminal” </li></ul>LC-MS Insufficient Re-run/Re-integrate Re-run (Acidic) Re-run (Basic) Re-run (Solvent Front) Re-integrate DOS Library Production: Complete Incomplete (Re-subject) Compound Selection: Accept Purify (<40%) Reject Incorrect Structure Analytical Sample Terminal Non-Terminal
  8. 8. aView & DOS Library Production <ul><li>Control Library Production Workflow </li></ul><ul><ul><li>Intermediate Synthetic Step </li></ul></ul><ul><ul><li>Representative Sample lantern from reaction flask </li></ul></ul><ul><ul><li>QC Plate made & Run on LC-MS </li></ul></ul><ul><ul><li>aView - Chemist Reviews Analytical Results and Annotates </li></ul></ul>
  9. 9. aView & DOS Intermediate QC Analytical Method OK? Analytical Processing OK? Complete Incomplete Re-run LC-MS Insufficient Incorrect Structure Re-integrate
  10. 10. aView & Compound Registration Inform Compound Registration Dashboard
  11. 11. aView & Sample QC <ul><li>Capture Chemist’s Assessment of Sample Suitability for Screening </li></ul><ul><ul><li>Compound sample – DOS or non-DOS (Vendor/Legacy) </li></ul></ul><ul><ul><li>Representative aliquot </li></ul></ul><ul><ul><li>QC Plate made & Run on LC-MS </li></ul></ul><ul><ul><li>aView - Chemist Reviews Analytical Results and Annotates </li></ul></ul>
  12. 12. “ Purity” Role in Annotation – Business Rules for Sample QC Add “Other” Considerations Classify based on Purity > 70% < 40% 40%< Purity < 70% Accept Purify Reject Analytical Method OK? Analytical Processing OK? Re-run LC-MS Insufficient Incorrect Structure Re-integrate No No Yes Yes
  13. 13. Classify based on Purity > 70% < 40% 40%< Purity < 70% Accept Purify Reject Comment required Summary Assessment Requires Chemist’s Knowledge Analytical Method OK? Analytical Processing OK? Re-run LC-MS Insufficient Incorrect Structure Re-integrate No No Yes Yes
  14. 14. aView & DOS Library Production Statistics Inform Library Production Summary
  15. 15. aView & Compound Selection
  16. 16. aView Mechanics <ul><li>Data Collection Process Overview </li></ul><ul><li>MassLynx Folder & File naming standard </li></ul><ul><li>Pipeline Pilot sample list generation </li></ul><ul><li>SDMS Archive Template – metadata extraction </li></ul><ul><li>CBIP Collector </li></ul>CBIP Collector SDMS LC-MS PP aView Directory Structure Raw LC-MS Data META Data
  17. 17. LC-MS Data Collection Process CBIP SDMS Network File Server MassLynx Input Files Raw Data Local PC Pipleline Pilot MassLynx Local PC MassLynx Local PC Composite Purity Report (text) aView Individual “ Print” Reports (graphic) SDMS File Capture Analytical Chemist’s Input Params QC Plate Map SDMS Print Capture <ul><li>Extracted Metadata: </li></ul><ul><li>Sample ID </li></ul><ul><li>DAD Image </li></ul><ul><li>Purity </li></ul>Annotation & Definitive Injection SDMS SDK Acquire Data Process Data Review Data <ul><li>Link s to Raw Data: </li></ul><ul><li>JCAMP (SpectrixX) </li></ul><ul><li>RPT (Openlynx Browser) </li></ul>MassLynx Input Files CBIP Collector
  18. 18. MassLynx Folder Structure & File Names masslynx LIB.pro sampleDB LIB_PLT_RUN#_RUN.txt LIB_PLT_RUN#_INT#_STD.txt LIB_PLT_RUN#_INT#_INT.txt *.rpt *.spl Data LIB_PLT_WELL_VIRTID_RUN# *.olp Sample Run Lists Standard Processing Lists Sample Processing Lists OpenLynx Purity Reports Sample Lists (converted from text lists above) Raw data Folders MassLynx “Project” corresponding to a given DOS Librar, LIB Folder on local instrument’s computer OpenLynx Processing parameters files
  19. 19. Create MassLynx sample List in Pipeline Pilot <ul><li>Creating a sample list in MassLynx using the Import feature requires that the imported text file follow certain formatting conventions, described in this document , taken from the MassLynx application manual.  All of these formatting tasks are performed by a Pipeline Pilot Webport application.  The Webport requires that the samples for QC analysis are present in a barcoded plate that is registered to CBIP.  Registered plates are created by the &quot;Create QC Plates&quot; tool in CBIP.  Once this barcoded plate is recieved by the analytical chemist, the sample list can be generated as described below. </li></ul><ul><li>Different sample lists currently drive the data aquisition process and the data analysis process, which currently occur at two different points in the sample workflow.  The Webport will create both sample lists at the same time, storing them under different names to the same location.  The analytical chemist must choose to import the file that is appropriate for the activity at hand. </li></ul><ul><li>To access protocols in the </li></ul><ul><li>Pipelein Pilot Webport, use Internet Explorer:  </li></ul><ul><li>http://fuller.broad.mit.edu:9944/webport/main.htm </li></ul>
  20. 20. SDMS Picks Up Data from Instruments – Archive Agent Template & MetaData
  21. 21. CBIP Collector Picks Up MetaData from SDMS
  22. 22. CBIP Collector – Status States Inform Users <ul><li>Standard Flow: </li></ul><ul><ul><li>WaitingForRawData </li></ul></ul><ul><ul><li>WaitingForPrintedReports </li></ul></ul><ul><ul><li>WaitingForPurityReport </li></ul></ul><ul><ul><li>WaitingForCollection </li></ul></ul><ul><li>Warnings: </li></ul><ul><ul><li>Warning______ </li></ul></ul><ul><ul><li>Warning______ </li></ul></ul><ul><ul><li>Warning______ </li></ul></ul>
  23. 23. aView Reliability <ul><li>System Diagram </li></ul><ul><li>File Queue Monitoring </li></ul><ul><li>Storage Capacity Monitoring </li></ul><ul><li>Application Server Monitoring </li></ul>CBIP Collector SDMS LC-MS PP aView Directory Structure Raw LC-MS Data META Data
  24. 24. SDMS System Diagram
  25. 25. File Queue Monitoring- FileBoss <ul><li>04-Nov-2008 at 12:00:05: </li></ul><ul><li>started log file &quot;C:Documents and Settingssdmsadmin.GP33D-0B6My DocumentsFileBoss DataFileBoss Summary.log&quot; </li></ul><ul><li>2,067 folders searched </li></ul><ul><li>Files found: 964 (300,824,199 bytes) </li></ul><ul><li>Results from UPLC_MassLynx </li></ul><ul><li>2008-11-04 12-02-34 </li></ul><ul><li>10,064 folders searched </li></ul><ul><li>Files found: 1 (0 bytes) </li></ul><ul><li>Results from UPLC_DOS </li></ul><ul><li>2008-11-04 12-30-38 </li></ul><ul><li>2,973 folders searched </li></ul><ul><li>Files found: 2 (3,476 bytes) </li></ul><ul><li>Results from New_UPLC_DOS </li></ul><ul><li>2008-11-04 12-30-35 </li></ul><ul><li>66,855 folders searched </li></ul><ul><li>Files found: 4,614 (1,046,403,921 bytes) </li></ul><ul><li>Results from UPLC_Screening </li></ul><ul><li>2008-11-04 13-23-31 </li></ul><ul><li>1 folders searched </li></ul><ul><li>Files found: 1 (0 bytes) </li></ul><ul><li>Results from New_UPLC_Screening </li></ul><ul><li>2008-11-04 13-00-06 </li></ul>
  26. 26. Storage Capacity Monitoring - LetUKnow
  27. 27. Error Log Monitoring - LogMeister
  28. 28. aView Performance <ul><li>Schedule Monitoring with AA Log </li></ul>CBIP Collector SDMS LC-MS PP aView Directory Structure Raw LC-MS Data META Data
  29. 29. Adherence to Pickup Schedule – 1 Full Cycle (24 hr.) from AA Log Scheduled Pickup Time Actual Pickup Time Growing Delay Catch Up On schedule (slope = 1)

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