PFAS Workflow

Description

The package is based on EPA 1633 guidelines and it 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 three Protocols:
  • Aqueous sample prep: EPA 1633 aqueous sample preparation
  • Solid sample prep: EPA 1633 solid sample preparation
  • MassHunter LC/MS

• Two Order types:
  • QC orders
  • Requests and Products Orders
• One Requestable: PFAS analysis
  • Containing the following tests:
    • Analyte ratio (mg/kg) with analyte group set to PFAS
    • Analyte concentration (µg/l) with analyte group set to PFAS
• Nine 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
• 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. This test is restricted to contents types of category solid and content types ‘sludge’ and ‘soil’ of category default.
  • 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. This test is restricted to contents types of category solid and content types ‘sludge’ and ‘soil’ of category default.
  • Masshunter analyte concentration: A test with result datatype quantity and dimension concentration with standard unit ng/ml and it requires Analyte.
  • Analyte concentration (µg/l): A test with result datatype quantity and dimension concentration with unit µg/l, requires Analyte. This test is restricted to content types of category ‘fluid’.
  • pH: A test with result datatype decimal number.
• Five 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: For this category the field “Can be inventoried ” is set to true on the category itself and the fields Expires after, Vendor, Part number and Webshop is set to the provided for the whole category. 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
  • Default: Two Content types are added:
    • Sludge
    • Soil extract
  • Standard: For this category the field “Can be inventoried ” is set to true on the category itself and the fields Expires after, Vendor, Part number and Webshop is set to the provided for the whole category. Seven Content types are added:
    • 537.1 Analyte Primary Dilution Standard
    • 537.1 Internal Primary Dilution Standard
    • 537.1 Surrogate Primary Dilution Standard
    • Perfluoro octane sulfonic acid (PFOS)
    • Perfluorooctanoic acid (PFOA)
    • PFCs calibration standard
    • PFOA and PFOS standard
• One Reference data submodule:
  • MassHunter: containing five Reference data types:
    • MassHunter data files
    • MassHunter sample types
    • MassHunter methods
    • MassHunter Sequence Templates
    • MassHunter analysis programs
• Three stand-alone Reference data types:
  • Providers
  • Countries
  • Sample location
• Four Reference Data Records:
  • Agilent Technologies – type Providers
  • Sample – type MassHunter sample types
  • pfas.m – type MassHunter methods
  • pfas LC/MS template – type MassHunter Sequence Templates
• 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 Reference Data Records of the type “Sample Locations”.
    • Collection date : A field of type date and time.
  • Eleven 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 Reference 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.
    • Sequence template definition: A field of type text box.
  • Ten 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 Reference Data Records of the type “Sample Locations”.
    • Digestion date : A field of type date and time.
    • Opening date:  A field of type date.
    • Temperature at arrival: A field of type quantity and dimension temperature, with default unit °C.
    • Holding period end date: A field of type date.
  • Five fields on Content type:
    • Can be inventoried : A field of type checkbox. This field is used to identify the content type as consumables which can be inventoried.
    • Vendor : A field of type dynamic choice pointing to Reference Data Records of the type “Providers”. Only shown if “Can be inventoried” field is checked.
    • Part number : A field of type short text. Only shown if “Can be inventoried” field is checked.
    • Expires after: A field of type quantity and dimension time, with default unit month. Only shown if “Can be inventoried” field is checked.
    • Webshop: A field of type URL. Only shown if “Can be inventoried” field is checked.
  • One field on Protocol:
    • MassHunter Sequence Template: A field of type dynamic choice pointing to the Reference data records of type “Masshunter Sequence templates”.
  • Ten 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”.
    • MassHunter Sample Name: A field of type short text.
    • MassHunter Level: A field of type short text.
    • Dilution: A field of type decimal number.
    • MassHunter Wt/Vol: A field of type decimal number.
    • Comment: A field of type text box.
  • Five fields on Result:
    • Acquisition time: A field of type date and Time. restricted to test “Masshunter analyte concentration”.
    • Comment: A field of type text box, restricted to test “Masshunter analyte concentration”.
    • Area: A field of type quantity, dimension scalar. This field is restricted to test “Masshunter analyte concentration”.
    • Accuracy: A field of type quantity and dimension scalar with unit ‘%’. this field is restricted to test “Masshunter analyte concentration”.
    • Retention time: A field of type quantity and dimension time with unit ‘min’. This field is restricted to test “Masshunter analyte concentration”.
• Two Rules:
  • Pfas sample temperature rule: A rule of type conditional value expression on the content table for the field “Temperature at arrival”.
  • Pfas pH rule: A rule of type conditional value expression on the result table for the test pH and restricted to two protocols EPA 1633 Aqueous sample preparation and EPA 1633 Solid sample preparation.
• Two Plugins:
  • MassHunter result import
    • The result import plugin can by default import Sample results (Concentration of analytes, etc.) from MassHunter.
  • MassHunter worklist sequence templating
    • A plugin that generates a sample sheet in CSV format based on the data of the grid template MassHunter LC/MS Sample sheet
• One Grid Template:
  • MassHunter LC/MS 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.

Products & Specifications

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

Macros

Macros can be adjusted for volume and location . This helps to process multiple samples at once which have the same values for volume and location.

Volume can be adjusted in macros namely,

• Create 500 ml HDPE bottle sample
• Derive filtered extract

Location can be adjusted in macros namely,

• Take dry weight sample
• Extract samples
• Derive filtered extract
• Create LC/TQ sample
• Create 500 ml HDPE bottle sample
• Collect Eluate & Filter

Consumable and Standard Category

• Content Category of type Consumables are defined as Inventory by checking the field ‘can be inventoried’. The following fields are linked to ‘can be inventoried’ field which helps in tracking the expiration and reordering,
  • Expires after: Fields are updated with a value according to the Agilent EPA 1633 guidelines
  • Vendor and Part number: If the vendor is Agilent, the part number field is updated according to the Agilent EPA 1633 guidelines
  • Webshop:  This is updated with the url to the part number at Agilent site.
• Content Category of type Standard are defined as Inventory by checking the field ‘can be inventoried’. And the fields like Part number and Webshop are updated according to Agilent EPA 1633 guidelines.  The description field in the content types are filled in with the list of solutions in the standard.

For tracking the consumables and standards that are not ordered from Agilent, the fields expire after, vendor, part number and webshop in the content types can be filled.

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

A new PFAS masshunter (LC/MS) specific sample sheet creation plugin called ‘MassHunter worklist sequence templating’ is available. This plugin generates a sample sheet in CSV format based on the data of the grid template MassHunter LC/MS sample sheet. This slims generated ‘Masshunter csv sample sheet’ can be directly imported into Masshunter, no longer requiring the mapping files needed in the past.

Data import

If automatic import is needed instead of manual via the UI button, the following is needed:

• In the Lab settings module, the email smtp needs to be set
• In the plugin configuration
  • The folder where 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 through the MassHunter from import to export.

Masshunter standard output ‘report.results.xml’ contains all data including standard, samples and blank. When the access of its folder directory is updated in the plugin, the Masshunter output file ‘report.results.xml’ is automatically imported into Slims. Once the result import is successful, the results from Masshunter expressed in ng/mL is automatically converted into the respective tests units namely mg/kg and µg/l. The result values for the respective test and  result file uploaded can be seen in the grid below the macro ‘Masshunter import results’.

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.
• Location types package
• Hidden default fields package (without product field import)

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
• Experiments and Workflows > Analytes and Analyte groups
• Automations > Fields
• Automations > Macro
• Automations > Rules > Conditional value expressions
• Audit Tools and Quality control > Grid Templates
• Automations > Plugins module

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
• MassHunter simplified Protocol Package Guide