What is aView?What is aView?

• CBIP Tool for capturing LC-MS results and a chemist’s assessment of each sample’s suitability for screening.

• Standardization notation enables control logic for CB workflows.

• Links back to RAW analytical data

What CB Processes are Controlled?What CB Processes are Controlled?

• DOS Library Production & Summary Statistics

• Compound Registration Dashboard

• Compound Selection for Screening

• The Analytical Process itself

Future:– Compound purification– Compound Library Quality Monitoring

Mother Tube Sort

Samples toPurify or Discard

Samples inScreening Set

DOS LibraryProduction

All CompoundSamples

DOSIntermediate

QCs

SampleQCsCBIP Collector

SDMS

LC-MS

PP

aView

Directory Structure

Raw LC-MS Data

META Data

DOS LibraryProduction

Stats

Sample Reg. Dashboard

RAW Data

What are the Annotations?What are the Annotations?

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

Standardized Notation Indicating:

• LC-MS Analysis Suitability • Sample Suitability

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

Three Components:

What is “Purity” in aView?What is “Purity” in aView?

• Peak Area% - NOT mass or mole based

Was the Target Mass (Compound) Was the Target Mass (Compound) Found?Found?

• Based on Mass Spectral Data Processing• Green = target mass “found” Red = “not found”

Summary Assessment MatrixSummary Assessment Matrix

• Analytical or Sample Directed

• “Terminal” or “non-Terminal”

Analytical SampleTerminal

Non-Terminal

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

aView & DOS Library ProductionaView & DOS Library Production

Control Library Production Workflow

• Intermediate Synthetic Step• Representative Sample lantern from reaction flask • QC Plate made & Run on LC-MS• aView - Chemist Reviews Analytical Results and Annotates

aView & DOS Intermediate QCaView & DOS Intermediate QC

Analytical Method

OK?

Analytical Processing

OK?

Complete

Incomplete

Re-runLC-MS InsufficientIncorrect Structure

Re-integrate

aView & Compound RegistrationaView & Compound Registration

Inform Compound Registration Dashboard

aView & Sample QCaView & Sample QC

Capture Chemist’s Assessment of Sample Suitability for Screening

• Compound sample – DOS or non-DOS (Vendor/Legacy)• Representative aliquot • QC Plate made & Run on LC-MS• aView - Chemist Reviews Analytical Results and Annotates

““Purity” Role in Annotation – Purity” Role in Annotation – Business Rules for Sample QCBusiness 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-runLC-MS InsufficientIncorrect Structure

Re-integrate

No No

YesYes

Classify based on

Purity

> 70%

< 40%

40%< Purity < 70%

Accept

Purify

Reject

Comment required

Summary Assessment Summary Assessment Requires Chemist’s KnowledgeRequires Chemist’s Knowledge

Analytical

Method OK?

Analytical Processing

OK?

Re-runLC-MS InsufficientIncorrect Structure

Re-integrate

No No

YesYes

aView & DOS Library aView & DOS Library Production StatisticsProduction Statistics

Inform Library Production Summary

aView & Compound SelectionaView & Compound Selection

aView MechanicsaView Mechanics

• Data Collection Process Overview

• MassLynx Folder & File naming standard

• Pipeline Pilot sample list generation

• SDMS Archive Template – metadata extraction

• CBIP CollectorCBIP Collector

SDMS

LC-MS

PP

aView

Directory Structure

Raw LC-MS Data

META Data

CBIP

SDMS

NetworkFile

ServerMassLynx

InputFiles

RawData

Local PCPipleline

PilotMassLynxLocal PC

MassLynxLocal PC

CompositePurity

Report (text)

aView

Individual“Print” Reports

(graphic)

SDMSFile Capture

AnalyticalChemist’s

Input Params

QC Plate Map

SDMS Print Capture

Extracted Metadata:• Sample ID• DAD Image• Purity

Annotation&

DefinitiveInjection

SDMSSDK

Acquire Data Process Data

Review Data

Link s to Raw Data:• JCAMP (SpectrixX)

• RPT (Openlynx Browser)

MassLynxInputFiles

CBIPCollector

LC-MS Data LC-MS Data Collection ProcessCollection Process

\\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#\

*.olpSample 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

MassLynx Folder Structure & File NamesMassLynx Folder Structure & File Names

Create MassLynx sample List in Pipeline PilotCreate MassLynx sample List in Pipeline Pilot

• 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 "Create QC Plates" tool in CBIP.  Once this barcoded plate is recieved by the analytical chemist, the sample list can be generated as described below.

• 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.

• To access protocols in the

• Pipelein Pilot Webport, use Internet Explorer: 

• http://fuller.broad.mit.edu:9944/webport/main.htm

SDMS Picks Up Data from Instruments – SDMS Picks Up Data from Instruments – Archive Agent Template & MetaDataArchive Agent Template & MetaData

CBIP Collector Picks Up MetaData from SDMS CBIP Collector Picks Up MetaData from SDMS

CBIP Collector – Status States Inform UsersCBIP Collector – Status States Inform Users

Standard Flow:

•WaitingForRawData

• WaitingForPrintedReports

• WaitingForPurityReport

• WaitingForCollection

Warnings:

• Warning______

• Warning______

• Warning______

aView ReliabilityaView Reliability

• System Diagram• File Queue Monitoring• Storage Capacity Monitoring• Application Server Monitoring

CBIP Collector

SDMS

LC-MS

PP

aView

Directory Structure

Raw LC-MS Data

META Data

SDMS System DiagramSDMS System Diagram

File Queue Monitoring- FileBossFile Queue Monitoring- FileBoss04-Nov-2008 at 12:00:05:

started log file "C:\Documents and Settings\sdmsadmin.GP33D-0B6\My Documents\FileBoss Data\FileBoss Summary.log"

• 2,067 folders searched

• Files found: 964 (300,824,199 bytes)

• Results from UPLC_MassLynx

• 2008-11-04 12-02-34

• 10,064 folders searched

• Files found: 1 (0 bytes)

• Results from UPLC_DOS

• 2008-11-04 12-30-38

• 2,973 folders searched

• Files found: 2 (3,476 bytes)

• Results from New_UPLC_DOS

• 2008-11-04 12-30-35

• 66,855 folders searched

• Files found: 4,614 (1,046,403,921 bytes)

• Results from UPLC_Screening

• 2008-11-04 13-23-31

• 1 folders searched

• Files found: 1 (0 bytes)

• Results from New_UPLC_Screening

• 2008-11-04 13-00-06

Storage Capacity Monitoring - Storage Capacity Monitoring - LetUKnowLetUKnow

Error Log Monitoring - LogMeisterError Log Monitoring - LogMeister

aView PerformanceaView Performance

CBIP Collector

SDMS

LC-MS

PP

aView

Directory Structure

Raw LC-MS Data

META Data

• Schedule Monitoring with AA Log

Adherence to Pickup Schedule – 1 Full Cycle (24 hr.) from AA Log

Scheduled Pickup Time

Actual P

ickup Tim

e

Growing Delay

Catch Up

On schedule (slope = 1)