C1: SDMS Locate and Repurpose Laboratory Information

C1: SDMS Locate and Repurpose Laboratory Information

C1: SDMS
Locate and Repurpose Laboratory Information
Ralf Schröder
Informatics Solution Consultant
©2011 Waters Corporation
Requirements
q
Retrieval
Capture
Instruments
Users
automatic capture — easy retrieval
©2011 Waters Corporation 2
Data Capture
Data Retrieval
Data Re-use
Publishing
Data Capture
©2011 Waters Corporation 3
Disparate
Data Sources
p
Data Capture
Data Retrieval
Data Re-use
Varian - CaryUV
Shimadzu FTIR
Parlez-vous
français?
00I0I0I00I0
I000I0I0II0
I0I0I00I00I
II0I00I00I0
Does anybody
speak a
common
language?!
¿Habla
Español?
Sprechen
Sie
Deutsch?
вы говорите
по-русски?
Bruker - NMR
Agilent - HPLC
Publishing
Waters - UPLC/MS
MDC-FLIPR
©2011 Waters Corporation 4
Life Cycle
of Analytical
Data
y
y
Data Capture
Data Retrieval
Publishing
Data Re-use
p g
Sampling
Instruments
Raw Data
File Capture
Data System
Report Content
Print Capture
Decision
©2011 Waters Corporation 5
Analytical
Data Management
y
g
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 6
Print Capture
p
Data Capture
Source
Data Retrieval
Publishing
Data Re-use
Process
Printer
- like Windows printer
- template based
metadata extraction
- interaction possible
- automated PDF
generation (optional)
Storage
Print Project
Metadata Catalogue
...
...
©2011 Waters Corporation 7
Catalogue
Automatically
g
y
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 8
Catalogue
Automatically
g
y
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 9
File Capture
p
Data Capture
Data Retrieval
Process
Source
Printer
- like Windows printer
- template based
metadata extraction
- interaction possible
- automated PDF
generation (optional)
Agent
010010010010010
010010010010010
010010010101000
100100101110100
100101001001001
000100100100100
Publishing
Data Re-use
- fully automated
- rule based metadata
extraction for ASCII files
- metadata via format
specific data adapter
- preprocessing and
conversion possible
Capture
Print Project
Metadata Catalogue
...
File Project
Metadata Catalogue
...
©2011 Waters Corporation 10
File Capture
p
Data Capture
Data Retrieval
Data Re-use
Publishing
g
- Original
folder/files
/
- Converted to JCAMP.dx
Folder
Lactose_50_7476.raw
L t
Lactose_50_7476.dx
50 7476 d
Files
C:\QC\Acquity\Purification\Lactose_50_7476.raw
_expment.inf
_func001.dat
func001 dat
_func001.idx
_func002.dat
_func002.idx
_functns.inf
_header.txt
h d t t
_history.inf
_inlet.inf
©2011 Waters Corporation 11
Data Capture
Data Retrieval
Data Re-use
Publishing
Data Retrieval
©2011 Waters Corporation 12
File Indexing
g
Data Capture
Data Retrieval
Data Re-use
Publishing
SDMS automated capture extracts system and fixed metadata
plus
metadata
l
t d t ffrom file
fil name and
d folder
f ld structure
t
t
and metadata from file content via data adapter
Folder
C:\QC\Acquity\Purification\Lactose_50_7476.raw
010010010010010010010010
010010010010010101001001
010010010101000100111001
100100101110100100100100
100101001001001001000111
000100100100100100100101
.raw
Lactose_50_7476.raw
Unique ID
Date/Time
Source
236F 2536 4509 …
01.01.2006/18:25:47
PC2222
Batch
Dosage
Compound
P oject
Project
Instrument
Department
7476
50
Lactose
Purification
Acquity
QC
Channel
Vial
Method
1143
B04
3/116
©2011 Waters Corporation 13
Browser with Metadata
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 14
View Printed Data
Without Original
Software
g
Data Capture
Data Retrieval
Data Re-use
Publishing
HPLC
Mass Spec
NMR
Gel
Images
©2011 Waters Corporation 15
Mass Spectrometry
p
y
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 16
Protein Chip
p Data
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 17
Images
g
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 18
View File Data
With Original
Software
g
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 19
View File Data
With the Analytical
Data Viewer
y
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 20
View File Data
With InSpector
p
Data Capture
Data Retrieval
Data Re-use
Publishing
©2011 Waters Corporation 21
Data Capture
Data Retrieval
Data ReRe-use
Publishing
Data Re-use
©2011 Waters Corporation 22
Data Export/Re-use
p /
Data Capture
Data Retrieval
Data ReRe-use
Publishing
Data Sources
NuGenesis SDMS
Data Consumers
©2011 Waters Corporation 23
Re-use Report
Content
p
Data Capture
Data Retrieval
Data ReRe-use
Publishing
©2011 Waters Corporation 24
Re-using
g Data in SDMS
Data Retrieval
Data Capture
Publishing
Data ReRe-use
ƒ No transcription or cut and paste or checking
ƒ Apply on printed reports with the same layout
ƒ Automation of calculations in destination document
Quantify Sample Report
MassLynx 4.1
Page 16 of 20
Dataset:
C:\Daten\2006_003.PRO\intervetapciFges.qld
Signature:
Not signed
Quantify Sample Report
MassLynx 4.1
41
Page 16 of 20
Last Altered: Monday, March 13, 2006 18:38:30 Eastern Standard Time
Printed:
At
Monday, March 13, 2006 18:39:07 Eastern Standard Time
Dataset:
C:\Daten\2006_003.PRO\intervetapciFges.qld
By
WATERS-62X73KYU\Micromass (Mass Spectrometer Instrument)
Signature:
Not signed
Quantify Sample Report
MassLynx 4.1
16 of 20 4.1
Quantify Sample Report PageMassLynx
Page 16 of 20
Last Altered: Monday, March 13, 2006 18:38:30 Eastern Standard Time
Printed:
At
Monday, March 13, 2006 18:39:07 Eastern Standard Time
Dataset:
C:\Daten\2006_003.PRO\intervetapciFges.qld
Dataset: Date:C:\Daten\2006_003.PRO\intervetapciFges.qld
Name: intervetapci060309055,
10-Mar-2006, Time: 02:52:52, (Mass
ID: , Description:
F Instrument)
5000
By
WATERS-62X73KYU\Micromass
Spectrometer
Signature:
Not signed
Signature:
Not signed
Quantify Sample Report
MassLynx 4.1
Page 16 of 20
Last Altered: Monday, March 13, 2006 18:38:30 Eastern Standard
Time
PMT
Last Altered: Monday, March 13, 2006 18:38:30 Eastern Standard Time
Printed:
At
Monday, March 13, 2006 18:39:07 Eastern Standard TimeF1:MRM
of 3 channels,AP+
Printed:
At
Monday, March 13, 2006 18:39:07 Eastern Standard Time
Dataset:
C:\Daten\2006_003.PRO\intervetapciFges.qld
Name:
intervetapci060309055,
10-Mar-2006, Time: 02:52:52, (Mass
ID: , Description:
F Instrument)
5000
By
WATERS-62X73KYU\Micromass (Mass Spectrometer
Instrument)
734.55
> 174.1
By Date:
WATERS-62X73KYU\Micromass
Spectrometer
Signature:
Not signed
3.217e+006
PMT
Quantify Sample Report
MassLynx 4.1
Page 16 of 20
100
PMT 1.62
Last Altered: Monday, March 13, 2006 18:38:30 Eastern Standard Time
242364.91
F1:MRM of 3 channels,AP+
At
Monday, March 13, 2006 18:39:07 Eastern Standard Time
Name: intervetapci060309055, Date: 10-Mar-2006, Time: 02:52:52, ID: , Description:
F 5000 Printed: Dataset:
C:\Daten\2006_003.PRO\intervetapciFges.qld
10-Mar-2006, Time: 02:52:52, (Mass
ID: , Description:
F Instrument)
5000
2.42e5Name: intervetapci060309055,
734.55 > 174.1
By Date:
WATERS-62X73KYU\Micromass
Spectrometer
Signature:
Not signed
3.217e+006
PMT
%
100
PMT
PMT 1.62
Last Altered: Monday, March 13, 2006 18:38:30 Eastern Standard Time
F1:MRM of 3 channels,AP+
242364.91
F1:MRM
of 3 channels,AP+
Printed:
At
Monday, March 13, 2006 18:39:07 Eastern Standard Time
734.55 > 174.1
10-Mar-2006, Time: 02:52:52, (Mass
ID: , Description:
F Instrument)
5000
2.42e5Name: intervetapci060309055,
734.55 > 174.1
By Date:
WATERS-62X73KYU\Micromass
Spectrometer
100
3.217e+006
PMT
1.62
242364.91
2.42e5
0
%
1
2
0
min
2.00
Name:
4.00
%
2.00
1004.00
min
PMT
RT
5000
ISTD
Area Sec.Area
1 ISTD
1.62
329714
2
2 PMT
1.62
2022242
Value
CQ102
CQ102
CQ102
CQ102
CQ102
CQ102
13,27
14,89
12,72
13,04
13,49
14,13
Average
13.59
3.217e+006
%
2.00
242364.91
Response Detecti...
ng/g# Name
%DevPMT
Ion Ratio
Area Sec.Area
Response Detecti...
ng/g
%Dev Ion Ratio
2.42e5 RT
F1:MRM
F1:MRM
3 channels,AP+
329713.625
011 ISTD16.3
1 bbof 3 channels,AP+
1.62ofmin
329714
329713.625
bb
1
16.3
% 10-Mar-2006, Time:
Name:
intervetapci060309056,
Date:
03:01:01,
> 108.1 -5.2
734.55 >ID:
98.1, Description: Acetonitril
2.00 8.34 4.00
242365
6.133 2 bb 744.55
4739
2 PMT
1.62
2022242
242365
6.133
bb
4739
-5.2
8.34
0.32
0.32
2.506e+004
1.042e+005
100
100
ISTD
ISTD
PMT
# Name PMT
RT
Area Sec.Area
Response Detecti...
ng/g
%Dev Ion Ratio
1.62
1.62
F1:MRM
of 3 channels,AP+
F1:MRM
ofmin
3 channels,AP+
0
1
1
ISTD
1.62
329714
329713.625
bb
1
16.3
935.58
Name: intervetapci060309056, Date: 10-Mar-2006, Time: 03:01:01, ID: , Description:
Acetonitril
Name:
intervetapci060309056,
Date:
Time: 03:01:01,
3626.74
744.55 > 108.1
734.55 >ID:
98.1, Description: Acetonitril
2.0010-Mar-2006,
4.00
9.36e2 0.32
2
2 PMT
1.62
2022242
242365
6.133
bb
4739
-5.2
8.34
3.63e3 0.32
2.506e+004
1.042e+005
%
%
100
100
ISTD
PMT
ISTD
ISTD
PMT
# Name PMT
RT
Area Sec.Area
Response Detecti...
ng/g
%Dev Ion Ratio
F1:MRM of 3 channels,AP+
F1:MRM of 3 channels,AP+ 1.62
1.62
F1:MRM
F1:MRM
1 of 3 channels,AP+
1 ISTD
1.62of 3 channels,AP+
329714
329713.625
bb
1
16.3
744.55 > 108.1
734.55 > 98.1 935.58
Name: intervetapci060309056,
Date:
10-Mar-2006,
Time:
03:01:01,
ID:
,
Description:
Acetonitril
3626.74
744.55 > 108.1
734.55 > 98.1
0.32
0.32
2 0
2 PMT
1.62
2022242
242365
6.133
bb
4739
-5.2
8.34
2.506e+004
1.042e+005 9.36e2 0.32
0
min
min
3.63e3 0.32
2.506e+004
1.042e+005
%
%
100
100
ISTD
1004.00
1004.00
ISTD
2 00
2.00
4 00
2 00
2.00
4 00
PMT
ISTD
PMT
PMT
1.62
1.62
1.62
1.62
F1:MRM of 3 channels,AP+
F1:MRM of 3 channels,AP+
935.58
935.58
3626.74 PMT
Name:
intervetapci060309056,
Date:
10-Mar-2006,
Time:
03:01:01,
ID:
,
Description:
Acetonitril
3626.74
744.55
>
108.1
734.55
>
98.1
9.36e2
9.36e2 0.32
3.63e3
0
0
min
min
3.63e3 0.32
2.506e+004
1.042e+005
%
%
F1:MRM%of 3 channels,AP+
%
1004.00
ISTD
2.00734.55100
2.00
ISTD
PMT
>4.00
174.1
PMT
1.62
0.32
1.361e+004
1.62
F1:MRM of 3 channels,AP+
F1:MRM of 3 channels,AP+
935.58
100
PMT
3626.74
744.55 > 108.1
734.55 > 98.1
PMT
9.36e2
0
0
min
0.32
0
0
min
min
3.63e3 0.32
2.506e+004
1.042e+005
1.62 min
F1:MRM%of 3 channels,AP+
%
2.00
4.00
2.00
4.00
1004.00
ISTD
2.00734.55100
2.00
437.76
>4.00
174.1
PMT
1.62
4.38e2 0.32
1.361e+004
1.62
%
935.58
100
PMT
PMT
3626.74
PMT
9.36e2
0
0
F1:MRM of 3 channels,AP+
min
min
3.63e3
1.62
F1:MRM%of 3 channels,AP+
%
734.55 > 174.1
2.00734.55 >4.00
2.00
4.00
437.76
174.1
0.32
1.361e+004
0
min
1.361e+004
4.38e2 0.32
%
100
1004.00
2.00
PMT
PMT
PMT
0
0
1.62
min
min
1.62
F1:MRM of 3 channels,AP+
437.76
# Name
RT
Area
2.00734.55
Sec.Area
Response Detecti...
ng/g 2.00
%Dev Ion 4.00
Ratio
437.76
>4.00
174.1
4.38e2
01 ISTD
4.38e2 0.32 1.62 min
%
1
936 1.361e+004
935.577
bb
0
-99.7
%
1004.00
2.00
PMT
2
2 PMT
1.62
3627
438
3.876
bd
2993
8.28
PMT
1.62
F1:MRM of 3 channels,AP+
# Name
RT
Area734.55
Sec.Area
Response Detecti...
ng/g
%Dev Ion Ratio
437.76
> 174.1
0
0 32 1.62 min
min
i
01 ISTD
4.38e2 0.32
1
936 1.361e+004
935.577
bb
0
-99.7
%
2.00
4.00
1004.00
2.00
2
2 PMT
1.62
3627
438
3.876
bd
2993
8.28
PMT
1.62
# Name
RT
Area Sec.Area
Response Detecti...
ng/g# Name
%Dev Ion Ratio
RT
Area
Sec.Area
Response
Detecti...
ng/g
%Dev Ion Ratio
437.76
1
1 ISTD
1.62
936
935.577 1 bb
-99.7
01 ISTD
min
4.38e2
1.62
936
935.577
bb
0
-99.7
%
2.00 8.28 4.00
2
2 PMT
1.62
3627
438
3.876 2 bd
29932 PMT
1.62
3627
438
3.876
bd
2993
8.28
# Name
1
Analyte
PMT 1.62
242364.91
F1:MRM of 3 channels,AP+
RT intervetapci060309055,
Area 734.55
Sec.Area
Date:
Response
10-Mar-2006,
Detecti...
Time:
ng/g 02:52:52,
%Dev Ion Ratio
ID: , Description: F
2.42e5Name:
> 174.1
1.62 min
bb
1
16.3
PMT 329714 3.217e+006 329713.625
1004.00
PMT
2 PMT
1.62 1.622022242
242365
6.133
bb
4739
-5.2
8.34
242364.91
F1:MRM of 3 channels,AP+
# Name
Area734.55
Sec.Area
Response Detecti...
ng/g
%Dev Ion Ratio
2.42e5 RT
> 174.1
01 ISTD
3.217e+006 329713.625
1
1.62 min
bb
1
16.3
PMT 329714
% 10-Mar-2006, Time:
intervetapci060309056, Date:
03:01:01,
ID:
,
Description:
Acetonitril
1004.00
2.00
2
2 PMT
1.62 1.622022242
242365
6.133
bb
4739
-5.2
8.34
# Name
01 ISTD
Subject
1
# Name
01 ISTD
2
2 PMT
RT
1.62 min
2.00
# Name
4.00
1.62
Area Sec.Area
936
3627
RT
438
Response Detecti...
bb
0
3.876
bd
2993
Area Sec.Area
1
1 ISTD
1.62
936
2
2 PMT
1.62
3627
ng/g
935.577
438
Response Detecti...
1232-S1
1232-C1
1232-S2
1232-C2
1232-S3
1232-C3
1232
C3
%Dev Ion Ratio
-99.7
8.28
ng/g
935.577
bb
0
3.876
bd
2993
%Dev Ion Ratio
-99.7
8.28
©2011 Waters Corporation 25
Table Mode Extraction
Data Capture
Data Retrieval
Publishing
Data ReRe-use
Output:
ƒ HTML
ƒ XML
ƒ Tabbed text
ƒ CSV
ƒ Images
©2011 Waters Corporation 26
Data Transfer LIMS
Data Capture
Data Retrieval
Publishing
Data ReRe-use
NuGenesis SDMS
- Batch ID
- Batch ID
- Sample ID
- Sample ID
- Worklist
- Reports
- Results
- Files
Instruments
-…
Extraction
Template
Print Data
Raw Data
©2011 Waters Corporation 27
Data Export/Re-use
p /
Data Capture
Data Retrieval
Data ReRe-use
Publishing
Data Sources
NuGenesis SDMS
Data Consumers
©2011 Waters Corporation 28
Data Capture
Data Retrieval
Data Re-use
Publishing
Publishing and ELN Functionality
©2011 Waters Corporation 29
Two Major
j Types
yp of Laboratory
y
Data Capture
Data Retrieval
Data Re-use
Publishing
ƒ Discovery, R&D
— Free-flow
— Geared towards new
scientific discoveries
— Seeks to protect
intellectual property rights
?
ƒ Process, QC
— Follows standard protocols
— Geared towards routine testing
— Often follows GxP such as
EPA regulations
Test
Test
Maze obtained from pbs.org
©2011 Waters Corporation 30
Templates
p
Data Capture
Data Retrieval
Data Re-use
Document
p
Template
Introduction
Experiments
Introduction
Publishing