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LIMS for Light Stable Isotopes Created by T.B. Coplen, USGS Reston Benjamin Harlow, Stable Isotope Core Facility at Washington State University No, but.

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Presentation on theme: "LIMS for Light Stable Isotopes Created by T.B. Coplen, USGS Reston Benjamin Harlow, Stable Isotope Core Facility at Washington State University No, but."— Presentation transcript:

1 LIMS for Light Stable Isotopes Created by T.B. Coplen, USGS Reston Benjamin Harlow, Stable Isotope Core Facility at Washington State University No, but thankfully there is beer.

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4 Thankfully there is beer.

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6 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

7 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

8 Set trusted locations, macros

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12 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 Keeps all references in one area of the sample table

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14 Enter new clients manually before creating the first project for that client

15 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

16 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 $/\

17 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”

18 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

19 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)

20 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!

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

22 Media originally designed for 2 isotopes only! It is possible to store, edit and average 4. How? Stay tuned Media

23 Procedure Codes

24 Low and High procedure Codes

25 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

26 Other features: Creating a sample list/template

27 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.

28 Then you run the samples What Paul said…

29 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)

30 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

31 Importing data Option to apply linearity correction at this point

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33 3 point normalization example

34 Add elemental and blank corrections

35 Normalize std gasses and data Seldom used Must import and properly code ref gasses Provides option to salvage data

36 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

37 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

38 Rapid tracking of QC/QA

39 Export full results for samples

40 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

41 Add stored results to in process Unlocks samples for editing Can be done at any time Store function may be unnecesary for some users

42 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.

43 Invoice generation and payment tracking

44 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

45 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?

46 Can I use LIMS for Lasers? Yes you can! See Len Wassenaar’s session on Wednesday

47 More Advanced Open the tables and look in there Cut, copy, paste; but watch for linked tables Make your own queries

48 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

49 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

50 Questions?

51 What if… I need to delete a project I entered the wrong media code I can’t find my samples in LIMS

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