Is there life after LIMS?
No, but thankfully there is
beer.
LIMS for Light Stable Isotopes
Created by T.B. Coplen, USGS Reston
Benjamin Harlow, Stable Isotope Core Facility at Washington
State University
Is LIMS for you?
• Do you process >100 samples per year?
• Do you process samples for multiple clients?
• Do you measure multiple isotopes?
• Do you use more than one instrument?
Is LIMS for you…
• Do you already have a database or spreadsheets that
work for you?
• LIMS by the USGS is not the only way to go
• LIMS by the USGS is the most readily available,
supported, and FREE software for Light Stable Isotopes
• If yes, start sooner rather than later!
Thankfully there is beer.
Benefits to using LIMS
• All your information in one place
• Rapid and consistent treatment of data
• Hourly drift corrections from multiple standards
• Linearity correction
• Data revision and safeguards
• Powerful search, average and export functions
• Report and Invoice generation
Limitations
• Can only have as many mass spectrometers or
lasers as letters in the English alphabet
• Normalization by linear regression is all that is
currently possible
• Some data manipulations may still be required
via spreadsheet, etc. prior to importing
First things first
• MS Access supported versions
– MS Office 2007, 2010, 32 bit only
• Required Security settings
– Add LIMS backend database to “trusted locations”
– Enable all macros
Set trusted locations, macros
Setup
• 3 folders, 4 files:
– Backend DB (LM8DATA.mdb)
– Frontend DB (LIMS9 for office 2010.mdb) + Preferences file
– Backup
• Back up Backend DB often!
• Back up Preference files periodically (especially for new
Front end versions)
• Different users can have their own front end and
preferences
• Can install on one computer, network, cloud
• WSU: dropbox; share DB with 7 computers (2 RAID),
multiple smartphones
Projects
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View projects, print reports, and export data to Excel
Import project data from Excel forms
Create new projects
Add new clients
Special Features
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Add new instruments
Add or edit laboratory standards
Backup and customize the database
Design analysis templates
Add or edit media or procedures
Sample Information
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Create sequence files that can be imported into mass spectrometers
Search, view, print and edit specific client samples
Search, view, and edit extractions
Analyses in Progress
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Import IRMS or LAS data
Determine and apply blank corrections and drift corrections
Normalize results to isotope scales
View or edit isotope results
Print or save isotope results to Excel files
Evaluate results and track laboratory QA/QC
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Store final accepted results for reporting
Import project to LIMS
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Manual entry or Excel spreadsheet
Concept of “placeholders”
Adjusting the next “Our Lab ID”
Reference ID’s often set as a low number
Example: References <1000, samples >1000
Keeps all references in one area of the sample table
Enter new clients manually before creating the
first project for that client
Adding a project manually
Date, Name, Media is the
minimum information
needed
More information is better;
i.e. project title and account
are good to reference later
Do not enter duplicate ID’s
and avoid special characters
for sample IDs
Submit to LIMS
• Simple excel templates are available
for modification
• Reduces typographical errors and
valuable time of lab members
• More information is good
• Be unique, but avoid special
characters $/\@#$%^&*!
Sample excel submission form
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Customize to your lab: Letterhead, graphics, captions
Captions must match exactly to what you defined in “special features”
Use different forms for different types of samples
Protect certain cells to reduce customer “tinkering”
Other features
• Track lab extraction procedures
– Make notes about sample prep
– Created primarily for offline procedures
• Create labels for samples
• Use templates to create run sequences of
samples and references
Selling (to) yourself
• Create a “client” entry for your lab tests and
reference material
• We use “reference” and “test”
• All international, commercial, and lab developed
reference material is logged here
• Reference lab ID’s get defined in reference table:
Automatically fit in a normalization
• Test lab ID: treat as a blind sample (Quality Control)
IRMS/software setup
• Machine must use sequential analysis number, with
single letter prefix (ex: A-number)
• Isodat: Configurator > Options > Global settings
• Enter old analyses or those without prefix:
“concatenate” function in excel
• Note analysis number if you ever restore IRMS
software!
Know your media
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KISS IT
More classifications can be useful
Can add more at any time
Tailor specific to your lab
Media
• Media originally designed for 2
isotopes only!
• It is possible to store, edit and
average 4.
• How? Stay tuned
Procedure Codes
Low and High procedure Codes
Running samples
• LIMS ID# “Our lab ID” is most important identifier
to use in sample sequences
• Use LIMS template or design your own in excel
• Template: LIMS automatically designs sample
sequence
Other features: Creating a sample
list/template
Another way to make a run sequence
• Import excel file and generate
LIMS ID’s
• Copy/Paste sample information
into a blank tab of the submission
worksheet
•Insert rows for running standards
and QC’s
• Can customize to instrument
service state, sample types, desired
timing, etc.
Then you run the samples
What Paul
said…
Exporting results and importing to
LIMS
• Must export specific column headings required by LIMS
• Line #, Analysis #, time code, gasconfig, area, peak#, identifier 1,
delta columns, is ref, comment, Rt
• All peaks for reference gas must be marked “Is Ref = 1” or removed
• Perform data preprocessing before importing (i.e. your own
linearity, drift or mass fraction corrections)
Export tips
• Isodat: If a project got created with some special
character, don’t export that column
• Check chromatographs prior to exporting. Is
reprocessing necessary?
• Garbage in garbage out
Importing data
Option to apply linearity
correction at this point
3 point normalization example
Add elemental and blank corrections
Normalize std gasses and data
• Seldom used
• Must import and
properly code ref gasses
• Provides option to
salvage data
Applying an hourly drift correction
Use drift from any single
standard
Override: combination of all
accepted standards, or custom
Apply two drifts: must break up
the sequence into two
corrections
Evaluating/editing samples in progress
Mean, SD and outlier
information
Note: When samples are “in
progress” mean, SD are
available
Some may choose to report at
this point
Rapid tracking of QC/QA
Export full results for samples
Store final results
Stores a single value from all
accepted reps
Marks samples as completed
Provides an extra layer of
protection to data
Necessary to use LIMS report
function
Add stored results to in process
Unlocks samples for editing
Can be done at any time
Store function may be
unnecesary for some users
Storing an additional isotope or other
numeric data
• The “comment” field now averages numeric values and
allows editing
• The high and low comment provide two additional storage
points
• Include data calculated by a different detector, i.e. CNHOS%
• Use with procedures that generate data for more than two
isotopes, i.e. thermal conversion of N2O.
Invoice generation and payment
tracking
Can I use LIMS for GCC-IRMS?
• Yes you can!
• Treat each vial as a project and target compounds are
samples in the project
• Use Rt or component ID feature in LIMS (extraction ID,
Comment, Rt)
• Internal standards should be in each vial
Can I use LIMS for GCC-IRMS?
• Alternative method: Modify file to import
• Sort by component (Rt) and time code
• Assign the same analysis number
• Create unique peak number for every compound
in a sample
Can I use LIMS for Lasers?
• Yes you can!
• See Len Wassenaar’s session on Wednesday
More Advanced
• Open the tables and look in there
• Cut, copy, paste; but watch for linked tables
• Make your own queries
Lab specific queries
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Annual reports, audits and cost evaluations
# days runtime/machine/peripheral/Fiscal year
# samples/machine/peripheral/year
Count of customers by country, state, institution, and
break down by sample type
• # of samples billed by type
• Average turnaround by sample type
• Long term QC/QA
Lab specific queries
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Annual reports, audits and cost evaluations
# days runtime/machine/peripheral/Fiscal year
# samples/machine/peripheral/year
Count of customers by country, state, institution, and
break down by sample type
• # of samples billed by type
• Average turnaround by sample type
• Long term QC/QA
Questions?
What if…
• I need to delete a project
• I entered the wrong media code
• I can’t find my samples in LIMS