Description

The package contains a complete workflow for PFAS analysis with SLIMS.

The following entities are present in the package:

  • One Workflow: PFAS analysis, which is build up of four Protocols:
    • Aqueous sample prep: EPA 1633 aqueous sample preparation
    • Solid sample prep: EPA 1633 solid sample preparation
    • Air sample prep: Air sample preparation for PFAS
    • MassHunter GC/MS and LC/MS
  • Two Order types:
    • QC orders
    • Requests and Products Orders
  • One Requestable: PFAS analysis
    • Contains the following tests:
      • Analyte ratio (mg/kg) with analyte group set to PFAS
      • Analyte concentration (µg/l) with analyte group set to PFAS
  • Ten Macros:
    • Create 500 ml HDPE bottle sample
    • Derive filtered extract
    • Create LC/TQ sample
    • Create Formic acid and methanol mix
    • Mix 0.3% ammonium hydroxide in methanol
    • Mix 1% ammonium hydroxide in methanol
    • Take dry weight sample
    • Extract samples
    • Collect Eluate & Filter
    • Take air sample
  • Eight Tests:
    • Analyte ratio (ppm): A test with result datatype quantity and dimension scalar with unit ppm, requires Analyte.
    • Analyte ratio (ppb): A test with result datatype quantity and dimension scalar with unit ppb, requires Analyte.
    • Analyte ratio (mg/g): A test with result datatype quantity and dimension scalar with unit mg/g, requires Analyte.
    • Analyte ratio (ppt): A test with result datatype quantity and dimension scalar with unit ppt, requires Analyte.
    • Analyte ratio (mg/kg): A test with result datatype quantity and dimension scalar with unit mg/kg, requires Analyte.
    • Analyte concentration: A test with result datatype quantity and dimension concentration with standard unit mg/ml and allowed unit variation from µg/l to g/l, requires Analyte.
    • Analyte concentration (µg/l): A test with result datatype quantity and dimension concentration with unit µg/l, requires Analyte.
    • pH: A test with result datatype decimal number.
  • Three Content type categories:
    • Fluid: containing seven Content types
      • Drinking water
      • Wastewater
      • Groundwater
      • Surface water
      • Influent
      • Effluent
      • Leachate
    • Solid: containing three Content types
      • Soil
      • Biosolids
      • Sediment
    • Consumable: containing 28 Content types
      • 0.1M Formic acid
      • 0.1M formic acid/methanol
      • 0.3M formic acid
      • 1% methanolic ammonium hydroxide
      • Acetic acid
      • Analytical Column
      • Autosampler Caps
      • Autosampler Vials
      • Carbon
      • Centrifuge Tubes
      • Glass Wool
      • Methanol
      • Nylon Filters
      • PFC Delay Column
      • SPE Cartridges
      • Syringes
      • UHPLC Guard Column
      • Reagent water
      • Ammonium hydroxide
      • 0.3% methanolic ammonium hydroxide
      • Bond Elut PFAS WAX 150 mg, 6 mL
      • Centrifuge tubes and caps, 50 mL
      • Bond Elut empty SPE cartridges, 60 mL
      • Bond Elut Adapter cap for 1, 3, and 6 mL Bond Elut cartridges
      • Vac Elut SPS 24 manifold with collection rack for 10 × 75 mm test tubes
      • Collection rack and funnel set for 12 or 15 mL conical tubes, for Vac Elut SPS 24 manifold
      • Vac Elut 20 Manifold long valve stopcock
      • InfinityLab PFC-free HPLC Conversion Kit
    • Three Content types are added to the Default category:
      • Sludge
      • Air
      • Soil extract
  • One Reference data submodule:
    • MassHunter: containing three Reference data types:
      • MassHunter data files
      • MassHunter sample types
      • MassHunter methods
  • Four stand-alone Reference data types:
    • Providers
    • Countries
    • Sample location
    • Cold Trap
  • Two Reference Data Records:
    • Material Emissions trap (Markes International, p/n MKI-U-T12ME-2S) – type Cold Trap
    • Agilent Technologies – type Providers
  • Custom Fields for six different modules:
    • Nine fields on Order:
      • Priority : A field of type fixed choice with possible values: 1. High, 2. Medium, 3. Low.
      • Reception date : A field of type date.
      • Due date : A field of type date.
      • Date of analysis : A field of type date.
      • Turn around time: A field of type date difference between “Reception date” and “Date of analysis”.
      • Lab manager : A field of type dynamic choice pointing to records of the User table.
      • Notes : A field of type rich text.
      • Sample location : A field of type dynamic choice pointing to Refence Data Records of the type “Sample Locations”.
      • Collection date : A field of type date and time.
    • Ten fields on Reference Data Record:
      • Provider number : A field of type whole number, restricted to the type Providers.
      • Code : A field of type short text.
      • Contact person : A field of type  short text, restricted to the type Providers.
      • Address : A field of type short text, restricted to the types Providers and Sample location.
      • City : A field of type short text, restricted to the types Providers and Sample location.
      • Zip code : A field of type short text, restricted to the types Providers and Sample location.
      • Country : A field of type dynamic choice pointing to Refence Data Records of the type “Countries”, restricted to the types Providers and Sample location.
      • Website : A field of type URL, restricted to the type Providers.
      • E-mail : A field of type short text, restricted to the type Providers.
      • Phone number : A field of type short text, restricted to the type Providers.
    • Seven fields on Content:
      • Volume : A field of type quantity and dimension volume, with default unit ml and allow choice of unit.
      • Mass : A field of type quantity and dimension mass, with default unit g.
      • Concentration : A field of type quantity and dimension concentration, with default unit mg/ml.
      • Expiry date : A field of type date.
      • Lot number : A field of type short text.
      • Sample location : A field of type dynamic choice to pointing to Refence Data Records of the type “Sample Locations”.
      • Digestion date : A field of type date and time.
    • Two fields on Content type:
      • Vendor : A field of type dynamic choice pointing to Refence Data Records of the type “Providers”.
      • Part number : A field of type short text.
    • 13 fields on Protocol run step:
      • Cold Trap: A field of type dynamic choice pointing to Refence Data Records of the type “Cold Trap”.
      • Flow Path Temperature : A field of type quantity and dimension temperature with default unit °C.
      • Dry Purge : A field of type quantity and dimension time with default unit min.
      • Purge Flow : A field of type quantity and dimension volumetric flow rate with default unit l/min.
      • Desorption Temperature : A field of type quantity and dimension temperature with default unit °C.
      • Desorption Time : A field of type quantity and dimension time with default unit min.
      • Trap in Line (Flow) : A field of type quantity and dimension volumetric flow rate with default unit l/min.
      • Trap Purge : A field of type Short text.
      • Trap Low Temperature : A field of type quantity and dimension temperature with default unit °C.
      • Trap Heating Rate : A field of type Short text.
      • Trap High Temperature : A field of type quantity and dimension temperature with default unit °C.
      • Trap Desorption Time : A field of type quantity and dimension time with default unit min.
      • Outlet Split : A field of type Short text.
    • Five fields on Protocol run step content:
      • MassHunter sample position: A field of type short text.
      • MassHunter injection volume (μl): A field of type decimal number with a lower limit of 0.
      • MassHunter sample type: A field of type dynamic choice on Reference Data Records of type “MassHunter sample types”.
      • MassHunter data file: A field of type dynamic choice on Reference Data Records of type “MassHunter data files”.
      • MassHunter method: A field of type dynamic choice on Reference Data Records of type “MassHunter methods”.
  • Two Plugins:
    • MassHunter result import
      • The result import plugin can by default import Sample results (Concentration of analytes, etc.) from MassHunter.
    • MassHunter sample sheet export
      • A plugin that generates a samples sheet in CSV format based on the data of the grid template MassHunter Sample sheet
  • One Grid Template:
    • MassHunter Sample sheet, a grid template of type block which can be used in simplified protocols
  • One Analyte group called PFAS

How to use the package

It is recommended to install the SI Unit package. Several unit packages are available that contain more units in the dimension of each respective quantity field.

Configuration

Fields

Fields can be further configured in the Fields module.

It is possible to filter the Lab manager field to users with a specific role or roles by using the filter value table option on the field in the Fields module.

Reference Data

Providers should be created in the Reference Data module to use the field Vendor.

Sample locations should be created in the Reference Data module to use in the fields that are available for Orders and Content to track where samples where collected.

Cold trap systems can be created in the Reference Data module to use in the air sample preparation protocol.

Products & Specifications

The included order types require products with specifications to exist in SLIMS and send related content to the workflow.

MassHunter integration

Reference data

The methods, data files etc. need to be added as reference data records in the correct reference data type.

Sample sheet

Additional information can be outputted to the sample sheet field by creating the additional fields and adding them to the grid template. This would require updating the mapping that came from the supplied mapping file.

This flow can be reused for exporting other grid template blocks as csv files, renaming the plugin is suggested for this.

Automatic import

The automatic import needs to have the following filled to work:

  • In the Lab settings module, the email smtp needs to be set
  • In the plugin configuration
    • The folder were the results files will be located and to which SLIMS gate has access
    • The email addresses that send and receive the emails regarding the import
    • The usernames which should receive the notifications

The automatic import is only available for on-premises installations as it requires access to the folder directory that contains the result files.

The automatic import can only work if the experiment run step identifier is passed trough the MassHunter from import to export.

MassHunter Quant templates

Upon request three different files can be obtained from Agilent to import into MassHunter Quant:

  • SLIMS_map_file.xml: A map file xml that can be used in MassHunter Acquisition to import CSV worklist files generated from SLIMS
  • SLIMS_Export_exclude_not_found_compounds.template.xml: A report template XML that can be used in MassHunter Quant to generate a report to be imported to SLIMS
    • This report does not include rows for compounds with a null final value in Quant
  • SLIMS_Export.template.xml: A report template XML that can be used in MassHunter Quant to generate a report to be imported to SLIMS
    • This report includes rows for compounds with a null final value in Quant

Complimentary packages

  • PFAS Analytes Package
  • US PFAS Regulatory limits
  • Records for the Countries reference data type can be imported with the Countries package from the SLIMS Store.

Where to Look Next

These references have further information on how to configure or use the package contents after the initial installation and integration.

SLIMS Administration Manual:

  • Content Management > Content types
  • Content Management > Reference Data
  • Experiments and Workflows > Order Types
  • Experiments and Workflows > Tests
  • Experiments and Workflows > Requestables
  • Experiments and Workflows > Protocols
  • Experiments and Workflows > Workflow Management
  • Experiments and Workflows > Workflow Module
  • Experiments and Workflows > Analytical Workflows
  • Automations > Fields
  • Automations > Macro

This package uses entities from several other Store packages. For more in-depth information, please refer to the following documentation:

  • Environmental Basics Package Guide
  • EPA 1633 Aqueous Sample Preparation Package Guide
  • EPA 1633 Solid Sample Preparation Package Guide
  • Air Sample Preparation for PFAS Package Guide
  • MassHunter simplified Protocol Package Guide