MassHunter integration

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MassHunter integration

Description

This package contains configuration and plugins to import results from MassHunter Quant into SLIMS.

This package works for MassHunter LC/MS and GC/MS setups.

The package contains the following entities:

  • 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
      • By default, the sample sheet export plugin can generate TXT files with the following Columns:
        • Sample ID
        • Method
        • Data File
        • Sample Type
        • Inj Vol
        • Sample Position
        • ExperimentRunStepUid
        • SLIMS Barcode
  • Two tests:
    • Analyte Concentration (SLIMS 6.8 and above)
      • Requires analyte is set to True
      • Value field is type Quantity with default unit mg/ml
    • MassHunter Final Concentration
      • Value field is type Quantity with default unit ng/μl
  • One Grid Template
    • MassHunter
  • One Rule
    • Warning step coming back
      • A rule that will provide a warning when a user clicks “Back” on a Protocol Run Step where the the field from this package Warning coming back is marked true on the corresponding Protocol Step
      • The expectation is that Warning coming back will be marked true on steps where MassHunter Sample Sheets are generated
  • Five custom fields on ExperimentRunStepContent
    • MassHunter method: a field of type Dynamic Choice, with target table Reference Data of type MassHunter Methods.
    • MassHunter data file: a field of type Dynamic Choice, with target table Reference Data of type MassHunter data files.
    • MassHunter sample type: a field of type Dynamic Choice, with target table Reference Data of type MassHunter sample types.

    • MassHunter injection volume (ul): A field of type Decimal number.
    • MassHunter sample position: A field of type Short Text.

  • One custom field on ExperimentStep
    • Warning coming back: A field of type Checkbox. Default value is false
  • One custom field on Result
    • Compound Name: A field of type Short Text.
  • Three Reference Data Types
    • MassHunter methods
    • MassHunter data files
    • MassHunter sample types
  • Three Attachments 
    • SLIMS_map_file.xml: A map file xml that can be used in MassHunter Acquisition to import CSV worklist files generated from SLIMS using the included MassHunter grid template
      • Linked to the Sample Sheet Export plugin
    • 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
      • Linked to the Results import plugin
      • 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
      • Linked to the Results import plugin
      • This report includes rows for compounds with a null final value in Quant

How to use the package

Pre-requisite

  • The results should be exported from MassHunter as a CSV, with one row per imported result and the sample identified on each row.
    • Two example MassHunter report templates which follow this format are included in this package.
  • Units: the package contains the minimum necessary units for the test configuration. However, it is recommended to install the SI Unit package.
  • Lab Settings module: For automatic import, fill out the lab setting “Email templates SMTP URI”

Configuration

Result import plugin

The plugin is configured to have two flows (flowConfigurations):

  • Both flows are for importing a file generated from MassHunter Quant using either of the two included .template.xml attachments. The plugins will get the files by automatically picking them up when they are saved to a watched directory location
    • After installation, you must:
      • Set the file path of the upload directory SLIMS will watch for the files to import using the uploadDirectory parameter
      • Set the uploadNotificationUsers parameter to list the users to be notified if there is a failure to upload a file
      • Set the emailSender parameter to the email address you want emails regarding file upload failures to be sent from
      • Set the emailRecipients parameter to list the email addresses to be notified if there is a failure to upload a file
        • OR
      • Alter the result importer configuration to use a manual upload rather than a watched directory
  • Flow massHunterWatchDir 
    • Creates results with the test “MassHunter Final concentration”
    • Maps the “Compound Name” value from MassHunter to a Short text field on the result
  •  Flow massHunterAnalytesWatchDir
    • Creates results with the test “Analyte concentration”
    • Maps the “Compound Name” value from MassHunter to the result’s Analyte field

With the default configuration of the plugin:

  • The sample is identified by its barcode
  • The protocol run step one step before the step that results will be uploaded to is identified by its unique identifier value

The following parameters are set to the specifics needed for the default export template included with the package:

  • fileHeaders: The list of test properties imported from the file and their mapping to SLIMS fields.

    • Sample Barcode: The barcode of the content record the result will be linked to
    • Final Conc.: The value of the result record to be created
    • RunStep Unique ID: The unique identifier of the protocol run step one step before the run step the results will be linked to
      • It is assumed you will generate the sample sheet in the step before the results step.
    • Compound Name:
      • massHunterWatchDir: a Short Text field for the name of the compound the result is for
      • massHunterAnalytesWatchDir: The analyte field on the result

It is possible to update the configuration of the plugin to:

  • Import more or fewer fields.
  • Change the ignoreTree options.
  • Change the identification of the sample.
    • Replace barcode with custom identifier.
  • Add more custom fields to the test results if you need to import more data from MassHunter.
  • Remove custom fields from the test results.
  • Allow for a manual import rather than import via watched directory
  • Use editor linkResultsToExperimentRunStepImpl instead of linkResultsToNextExperimentRunStepImpl if you want to generate the sample sheet during the same step where you upload the results

Sample Sheet Export Plugin

The included Grid Template and map file attachment (SLIMS_map_file.xml) map the following SLIMS fields to the following MassHunter columns:

Input Column (from CSV) = GridTemplate “Title”
MassHunter Quant column (Map Column)
Column Type
SLIMS Field
Sample ID Sample ID System cntn_id
Sample Position Sample Position System xrsc_cf_masshunterSamplePosition
Method Method System xrsc_cf_masshunterMethod
Data File Data File System xrsc_cf_masshunterDataFile
Sample Type Sample Type System xrsc_cf_masshunterSampleType
Inj Vol (µl) Inj Vol (µl) System xrsc_cf_masshunterInjectionVolume
ExperimentRunStepUid User Defined 9 User Defined xprs_uniqueIdentifier
SLIMS Barcode User Defined 8 User Defined cntn_barCode

With the default configuration of this plugin:

  • You will have a flow that can be added to Protocol Steps: MassHunter worklist CSV
    • This flow will export the above columns for the samples in the step when used
  • The name of the exported file will be “masshunter-csv-sample-sheet-yyyy-MM-ddHH-mm-ss.SSS.csv”
    • The yyyy-MM-dd and the HH-mm-ss,SSS will be replaced by the date and time of export
  • Using SLIMS_map_file.xml as the template file, this generated file can be used to import a worklist to MassHunter Acquisition

This SLIMS GATE flow can be used in a protocol step in your workflow proceeding the result step or in the same step as the result import.

  • The following ExperimentRunStepContent fields will need to be filled out by the user or by a custom groovy script during the step where you do the export
    • MassHunter method: a field of type Dynamic Choice, with target table Reference Data of type MassHunter Methods.
    • MassHunter data file: a field of type Dynamic Choice, with target table Reference Data of type MassHunter data files.
    • MassHunter sample type: a field of type Dynamic Choice, with target table Reference Data of type MassHunter sample types.

    • MassHunter injection volume (ul): A field of type Decimal number.
    • MassHunter sample position: A field of type Short Text.

Attachments for MassHunter

To include other data in either the import to MassHunter or the export from the program, the files need to be adjusted or new ones created.

Please contact your local MassHunter support team in case assistance with this is required.

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:
    • Miscellaneous > Plugins Module
    • Miscellaneous > Fields > Custom Fields
    • Electronic Lab Notebook > Tests and Test groups
    • Reporting and Grids > Grid templates
    • Workflows

Description

Description

This package contains configuration and plugins to import results from MassHunter Quant into SLIMS.

This package works for MassHunter LC/MS and GC/MS setups.

The package contains the following entities:

  • 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
      • By default, the sample sheet export plugin can generate TXT files with the following Columns:
        • Sample ID
        • Method
        • Data File
        • Sample Type
        • Inj Vol
        • Sample Position
        • ExperimentRunStepUid
        • SLIMS Barcode
  • Two tests:
    • Analyte Concentration (SLIMS 6.8 and above)
      • Requires analyte is set to True
      • Value field is type Quantity with default unit mg/ml
    • MassHunter Final Concentration
      • Value field is type Quantity with default unit ng/μl
  • One Grid Template
    • MassHunter
  • One Rule
    • Warning step coming back
      • A rule that will provide a warning when a user clicks “Back” on a Protocol Run Step where the the field from this package Warning coming back is marked true on the corresponding Protocol Step
      • The expectation is that Warning coming back will be marked true on steps where MassHunter Sample Sheets are generated
  • Five custom fields on ExperimentRunStepContent
    • MassHunter method: a field of type Dynamic Choice, with target table Reference Data of type MassHunter Methods.
    • MassHunter data file: a field of type Dynamic Choice, with target table Reference Data of type MassHunter data files.
    • MassHunter sample type: a field of type Dynamic Choice, with target table Reference Data of type MassHunter sample types.

    • MassHunter injection volume (ul): A field of type Decimal number.
    • MassHunter sample position: A field of type Short Text.

  • One custom field on ExperimentStep
    • Warning coming back: A field of type Checkbox. Default value is false
  • One custom field on Result
    • Compound Name: A field of type Short Text.
  • Three Reference Data Types
    • MassHunter methods
    • MassHunter data files
    • MassHunter sample types
  • Three Attachments 
    • SLIMS_map_file.xml: A map file xml that can be used in MassHunter Acquisition to import CSV worklist files generated from SLIMS using the included MassHunter grid template
      • Linked to the Sample Sheet Export plugin
    • 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
      • Linked to the Results import plugin
      • 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
      • Linked to the Results import plugin
      • This report includes rows for compounds with a null final value in Quant

How to use the package

Pre-requisite

  • The results should be exported from MassHunter as a CSV, with one row per imported result and the sample identified on each row.
    • Two example MassHunter report templates which follow this format are included in this package.
  • Units: the package contains the minimum necessary units for the test configuration. However, it is recommended to install the SI Unit package.
  • Lab Settings module: For automatic import, fill out the lab setting “Email templates SMTP URI”

Configuration

Result import plugin

The plugin is configured to have two flows (flowConfigurations):

  • Both flows are for importing a file generated from MassHunter Quant using either of the two included .template.xml attachments. The plugins will get the files by automatically picking them up when they are saved to a watched directory location
    • After installation, you must:
      • Set the file path of the upload directory SLIMS will watch for the files to import using the uploadDirectory parameter
      • Set the uploadNotificationUsers parameter to list the users to be notified if there is a failure to upload a file
      • Set the emailSender parameter to the email address you want emails regarding file upload failures to be sent from
      • Set the emailRecipients parameter to list the email addresses to be notified if there is a failure to upload a file
        • OR
      • Alter the result importer configuration to use a manual upload rather than a watched directory
  • Flow massHunterWatchDir 
    • Creates results with the test “MassHunter Final concentration”
    • Maps the “Compound Name” value from MassHunter to a Short text field on the result
  •  Flow massHunterAnalytesWatchDir
    • Creates results with the test “Analyte concentration”
    • Maps the “Compound Name” value from MassHunter to the result’s Analyte field

With the default configuration of the plugin:

  • The sample is identified by its barcode
  • The protocol run step one step before the step that results will be uploaded to is identified by its unique identifier value

The following parameters are set to the specifics needed for the default export template included with the package:

  • fileHeaders: The list of test properties imported from the file and their mapping to SLIMS fields.

    • Sample Barcode: The barcode of the content record the result will be linked to
    • Final Conc.: The value of the result record to be created
    • RunStep Unique ID: The unique identifier of the protocol run step one step before the run step the results will be linked to
      • It is assumed you will generate the sample sheet in the step before the results step.
    • Compound Name:
      • massHunterWatchDir: a Short Text field for the name of the compound the result is for
      • massHunterAnalytesWatchDir: The analyte field on the result

It is possible to update the configuration of the plugin to:

  • Import more or fewer fields.
  • Change the ignoreTree options.
  • Change the identification of the sample.
    • Replace barcode with custom identifier.
  • Add more custom fields to the test results if you need to import more data from MassHunter.
  • Remove custom fields from the test results.
  • Allow for a manual import rather than import via watched directory
  • Use editor linkResultsToExperimentRunStepImpl instead of linkResultsToNextExperimentRunStepImpl if you want to generate the sample sheet during the same step where you upload the results

Sample Sheet Export Plugin

The included Grid Template and map file attachment (SLIMS_map_file.xml) map the following SLIMS fields to the following MassHunter columns:

Input Column (from CSV) = GridTemplate “Title”
MassHunter Quant column (Map Column)
Column Type
SLIMS Field
Sample ID Sample ID System cntn_id
Sample Position Sample Position System xrsc_cf_masshunterSamplePosition
Method Method System xrsc_cf_masshunterMethod
Data File Data File System xrsc_cf_masshunterDataFile
Sample Type Sample Type System xrsc_cf_masshunterSampleType
Inj Vol (µl) Inj Vol (µl) System xrsc_cf_masshunterInjectionVolume
ExperimentRunStepUid User Defined 9 User Defined xprs_uniqueIdentifier
SLIMS Barcode User Defined 8 User Defined cntn_barCode

With the default configuration of this plugin:

  • You will have a flow that can be added to Protocol Steps: MassHunter worklist CSV
    • This flow will export the above columns for the samples in the step when used
  • The name of the exported file will be “masshunter-csv-sample-sheet-yyyy-MM-ddHH-mm-ss.SSS.csv”
    • The yyyy-MM-dd and the HH-mm-ss,SSS will be replaced by the date and time of export
  • Using SLIMS_map_file.xml as the template file, this generated file can be used to import a worklist to MassHunter Acquisition

This SLIMS GATE flow can be used in a protocol step in your workflow proceeding the result step or in the same step as the result import.

  • The following ExperimentRunStepContent fields will need to be filled out by the user or by a custom groovy script during the step where you do the export
    • MassHunter method: a field of type Dynamic Choice, with target table Reference Data of type MassHunter Methods.
    • MassHunter data file: a field of type Dynamic Choice, with target table Reference Data of type MassHunter data files.
    • MassHunter sample type: a field of type Dynamic Choice, with target table Reference Data of type MassHunter sample types.

    • MassHunter injection volume (ul): A field of type Decimal number.
    • MassHunter sample position: A field of type Short Text.

Attachments for MassHunter

To include other data in either the import to MassHunter or the export from the program, the files need to be adjusted or new ones created.

Please contact your local MassHunter support team in case assistance with this is required.

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:
    • Miscellaneous > Plugins Module
    • Miscellaneous > Fields > Custom Fields
    • Electronic Lab Notebook > Tests and Test groups
    • Reporting and Grids > Grid templates
    • Workflows

Additional information

packages

VERSION_6_7:631, VERSION_6_8:632

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