Is there life after LIMS?

LIMS for Light Stable IsotopesCreated by T.B. Coplen, USGS Reston

Benjamin Harlow, Stable Isotope Core Facility at Washington State University

No, but thankfully there is beer.

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

View projects, print reports, and export data to Excel Import project data from Excel forms Create new projects Add new clients

Special Features

Add new instruments Add or edit laboratory standards Backup and customize the database Design analysis templates Add or edit media or procedures

Sample Information

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

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

Store final accepted results for reporting

Import project to LIMS

• 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

• 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

• KISS IT• More classifications can be useful• Can add more at any time• Tailor specific to your lab

• Media originally designed for 2 isotopes only!

• It is possible to store, edit and average 4.

• How? Stay tuned

Media

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

• 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 GCC-IRMS?

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

• 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

• 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