I think I’ve had this feeling of déjà-vu before! · PDF file ·...
Transcript of I think I’ve had this feeling of déjà-vu before! · PDF file ·...
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I think I’ve had this feeling of déjà-vu before!
Making the most of a
structural id database
ACD Labs, Cambridge Symposium
27th September 2016
Steve Thomas
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Challenges
Laboratory Informatics 2016 2
How do I handle knowledge at the rate it is
being generated today?
How do I best share my knowledge with my
colleagues and gain access to theirs?
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Laboratory Informatics 2016 3
Outline
o Challenges in my research areao Data jigsaw
o Why we cannot rely on memoryo Staff turnover
o Building a databaseo Building a data cube!
o Metadata
o Embed and Grow
o Uptake and reviewo AAR
o Benefitso Accuracy and time
o Spread the word
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David Jack Centre for R&D, Ware
1898 - Allen and Hanburys,
formerly Plough Court
Pharmacy (est. 1715) built on
the site of the old mill at Ware,
Hertfordshire UK
R&DPlatform
Technology
Science
Global
Spectroscopy
Product
Development
and Supply
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Metabolite ID
Urine
Bile
Blood
We are generating data faster than ever, how can we hope to efficiently use legacy knowledge?
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Safety implications
The implications of passing a unsafe
drug into the clinic are severe.
Getting it wrong is not an option.
What’s on our side?
•Top end equipment
•Experience
•Historical data
•Ability to smell a structural alert
from 20 yards!
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Historical data storage
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A good memory
Grand wizard of metabolism –
Frank
GSK employee:
Late Jurassic - Feb 2009
Contingency plan on Frank’s
retirement!
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Drill down from a biotransformation map
D
E
T
A
I
L
I
M
P
A
C
T
O
OOH
OH
H
OHO
OH
OH
OH
OOH
O
OH
OH
OH
O
O
OO
H
O
O
O
OOH
OH
H
OHO
OH
OOH
O
OH
OH
OH
O
O
OOH
H
OHO
O
OOH
OH
H
OO
OH
O
OOH
OH
H
OHO
OH
O
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OH
H
OHO
O
OO
OH O
H
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Not a database, a data cube
Search from any point of interest
Variety of
customers leads to
a wide range of
ideas as to which
data is most
important.
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ACD/Chemfolder Enterprise
A B C D+ +
Initially designed as a tool for synthetic chemists:
– CFE allows users to database reactions
– Links to data supporting structure assignments
– Structures searchable
–“Has this been made before?”
– Data searchable
–“What have I made?”
To be of use in metabolism, the system must cope with 50+ products?
Your workflows?
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Success criteria
1. How easy is it to get the data into the database?
2. Can it help us move away from relying on the power of memory to solve
tricky problems if seen before and gain access to other associated
information?
3. Can we speed up the process of interpretation?
4. Can we have greater confidence in the elucidations and structural ID?
5. Can it help us avoid mistaken elucidations?
6. Will the proposed solution offer advantages in communication of data?
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Subtracted
spectrum
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User data entry form
How to ensure your
data is easily found.
Auto triggered on
update.
Fully customisable
• Auto fill e.g. Date
• Combiboxes
• Radio (choice)
• Mandatory entry
• Free text
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Screen space and unknowns
Enzyme: CYP3A4
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Merger of ACD/Chemfolder and ACD/SpecDB
ACD/Spectrus Processor and ACD/Chemfolder Enterprise now together as a
single Spectrus Database.
CFESpecDB SpectrusDB
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Change management curve
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Momentum and speed bumps
X
Speech recognition
X
3D
Printing
X
Wearable user interfaces
X
Big Data
XQuantum
Computing
Gartner “Hype cycle”
Expectations of novel technology
over time
“The most frequent point of failure is the
chasm between early adopters ‘The
visionaries’ and early majority, ‘The
pragmatists’.” John Trigg
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Scripting 1. - Map comparison
Rat and dog
data for
illustrative
purposes only
Safety cover?
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Scripting 1. - Map comparison
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Scripted table in word summarising where each metabolite was found
Scripting 2. - Matrix report
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Outreach – disseminating the knowledge
Avoid “Silo” mentality
• Users typically used to facile,
free access will not want access
restricted by logistics or cost.
• Without barriers our data will
reach everyone it can help
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Dissemination strategies
ACD/Web Librarian
Local super users
Requests!
Helium
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Scripting 3. – Automated reporting (scripting)
Peak ID P
Retention Time 8.6
Formula m/z Calc. Difference (Da)
m/z Exp.
C25H39O6 435.2752 -0.1155 435.1597
min
Monoisotopic Mass 436.3Mol Weight:
1H NMR:
10
9
8
1
2
7
6
5
4
3 18
14O11
19
12
O13
20
21
22
26 27
15
16OH17
28
24
23
OH25
H2a
29OH30
O31
Atom Exp. Shift (ppm)
18 0.94
19 1.12
15 1.16
27 1.16
26 1.16
15 1.27
10 1.43
23 1.43
23 1.57
21 1.61
14 1.61
21 1.66
3 1.74
10 2.02
Atom Exp. Shift (ppm)
4 2.31
9 2.35
2a 2.41
28 2.45
28 2.46
16 3.74
24 4.13
1 5.36
8 5.53
5 5.83
6 6.01
MS Fragmentation:
Structure m/z Exp.
CH2-
28
29
OH30
O31
59
O-
11
12
O13
C20
26
27
85
O-
11
12
O13
20
21
22
26
27
115
CH-
1 2
3
4
5
6
7
8
9
10
14
15
CH16
OH17
18
19
H2a
215
Structure m/z Exp.
CH-
1 2
3
4
5
6
7
8
9
10
14
15
16
OH17
18
19
23
24
OH25
28
29
OH30
O31
H2a
319
1
2
3
4
5
6
7
8
9
10
O11
12
O13
14
15
16
OH17
18
19
20
21
22
23
24
OH25
26 27
28
29
O-
30O31
H2a
435
Comments:
O
OOH
OH
H
OHO
OH
OH
OH
OOH
O
OH
OH
OH
O
O
OO
H
O
O
O
OOH
OH
H
OHO
OHOOH
O
OH
OH
OH
O
O
OOH
H
OHO
O
OOH
OH
H
OO
OH
O
OOH
OH
H
OHO
OH
O
OOH
OH
H
OHOO
OO
OH O
H
O
O
OH
OH
H
OH
O
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Success criteria
1. How easy is it to get the data into the database?
Variable e.g MassLynx ACD/Labs button, Xcaliber, Unify
2. Can it help us move away from relying on the power of memory to solve
tricky problems if seen before and gain access to other associated
information?
Search on structure, substructure, peaks, metadata, arrows
3. Can we speed up the process of interpretation?
Ready access to similar analyses. Import assignments
4. Can we have greater confidence in the elucidations and structural ID?
Has anyone seen a metabolite like this?
5. Can it help us avoid mistaken elucidations?
Smart assignment
6. Will the proposed solution offer advantages in communication of data?
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What went well?1. Communication between sites has been good on occasions
2. 1:1 training has been excellent
3. Regular up-dates
4. The database searchability is starting to show promise – some
early adopters
5. Summer students – data entry (good use of resource)
6. Communicated well across boundaries and teams
What could be improved?1. Communication between sites has been poor on occasions
2. Training guide is obsolete - needs up-dating (seen as vital)
3. “Our site didn’t have a training guide, or at least weren't aware one
existed “(communication)
4. Lack of training has hindered uptake
5. Clarity and visibility on business rules (communication)
6. Lack of energy at times – felt like lost momentum , because
Spectrus upgrade was looming
7. Not easy to enter data - lack of training options?
8. Issues with processing software (automatic assignment) when
looking at real metabolites
9. Same for MS (duplication)
10. Big issue with re-learning (as long time gaps between use) – comes
back to provision of adequate training guide
11. Uncertainty about Spectrus – when, where and how
(communication)
12. Better visibility to a project plan – when, where, how and who
(communication)
13. Training set/tutorial should be available
14. Reporting and exporting issues – more energy in this space
15. Clarity around met id data reporting e.g. in report Appendix
16. Inconsistent message from ACD – different viewpoints from
different ACD experts/sales folk?
Empowering the users – After action review
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Spread the word
- Other groups facing similar challengess
A
B
C
DE
F
G
H
J
K
L
M
I
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Working across boundaries
Synthetic impurities
Metabolites
Forced degradants
A
B
C
DE
F
G
H
J
K
L
M
I
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Synergy – Metabolism and Degradation
NH
NN
N
NNH
N
NH
N
OH
N
NN
N
NN
OH
OO
OHOH
OH
N
N
H
N
OH
NN
O
N
N
O
H
N
N
O
H
OH
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Summary
– Get everyone on-board. Community of empowered users.
– Training, user guides
– Hooks
– Valuable way to store, search and share sets of related molecules
– Body (metabolites)
– Environment (stability)
– Chemist (reactions / impurities)
– Scripting capability
– Automated reporting
– Further enhancements constantly delivered
– ACD respond to new feature requests
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Thank you