Project | Features

Import plate run(s)

If a kit was run but the corresponding plate run is missing in WebIDQ use this feature, e.g. a plate run was accidentally deleted. The plate run is created based on the MS data of the measured kit.

1. Select an existing submission or create a new one, e.g. "TQ-XS example kit".
   
2. Click Import plate run(s).
   
3. Drop the MS data of a plat run, e.g. WIFF or RAW files.
   
4. Select the pipetting mode, the way how the kit was pipetted in the laboratory. Default is "Vertical".
   
5. To create the plate run, click Import.
   

Example | Recreate kit plate layout with “Import plate run(s)”

If kit MS data was acquired with WebIDQ but the corresponding plate run(s) are not available in WebIDQ, as they were for example accidentally deleted, plate run(s) can be recreated by using the feature Import plate runs(s). For this procedure, MS data from the corresponding kit run is used.

1. Select a submission, e.g. “YYYY-MM-DD_Quant 500 kit”.

   

2. Click Import plate runs(s).

3. Navigate to the MS data of the corresponding kit run(s) using the Windows File Explorer. Select MS data in the File Explorer and drop the files in WebIDQ into the field “Drop files here”. Folders containing MS data may be dropped.

   
   MS data of multiple plate runs may be uploaded and imported together.

4. Select the pipetting mode used for kit plate preparation, “vertical” or “horizontal”, and click Import.

5. Corresponding plate run(s) to the uploaded MS data was(were) created. Please find an example below.

   
   To move plate runs between submissions, us the feature Move plate.

6. Study samples (unknowns) were imported without sample information. Adding sample information is is described in section , refer to the next section Add information to study samples (unknowns).

Kit data quantification is described in section Quantification.

Create worklist features

This section describes features for generating a worklist.

Create a project

Click New project or +, if another project was selected.

In the pop up box, define a Project code and Project name.

Optionally, enter a description, define contacts, and access rights (project team).

Option	Description
Project code	Prefix project's name
Project name	Suffic of project's name
Description	Additional information
Contacts	To link one or muliple contacts, Click +. To remove a contact, click x.
Project team	Define users with access to a project. To grant access to all users, leaving this field blank.

Click Save.

Project team | project access restrictions

A user or user group can be granted with exclusive access to a specific project.

1. Select a project,
2. In the field Project team and select a user, e.g. biocrates Customer Support.

No user linked (field is empty): all users have access to a project.

Users are linked: these users have access to a project, e.g. biocrates Customer Support.

Users with the WebIDQ role "admin" have access to all projects.

User roles are managed in mybiocrates, see section Edit users.

Create a submission

Create one submission per kit.

With a project selected create a submission by clicking New submission.

Define the submission's name and click Save.

The submission is created in the selected project.

How to select samples

ⓘ Associated section → Create kit plate layout > 4. Select samples

1. Click Zeros and select a zero sample, from the top pane.

   • Add three zero sample replicates, as shown below.
   • For serum and plasma samples, select "PBS".
   • To add a sample, click Select samples.
     

   

2. Click Cal Stds and select Calibration Standards of the kit.

   E.g. for Quant 500 (XL) kit "Q500(XL)_Cal1" - "Q500(XL)_Cal7".

   To select the multiple samples, keep Ctrl or Shift key pressed.

   

3. Click QCs and select Quality Controls of the kit.

   E.g. for Quant 500 (XL) kit "Q500(XL)_QC1" - "Q500(XL)_QC3".

Define QC replicates, according to kit user manual.

1. Click Unknowns and select study samples to be analyzed with a kit, e.g. samples "2022-01" - "2022-12".

   ⓘ To sort samples, click on the table's header. Samples are added to the plate in the same order as shown in the list.

   

• The number of samples linked with a plate is shown in brackets next to "All", e.g. 96.
• To remove samples, press Del.
• Calibration standards are not included in FIA plates.
• Reorder samples by dragging them to a new position in the selected samples list.
  

Find samples using metadata

ⓘ Associated section → Create kit plate layout > 4. Select samples

Example: Category "Gender" with groups "female" and "male" linked with samples, see Groups and variables

1. Select the category "Gender" and a group, e.g. "female".
   Multiple filter options can be defined.
   
   Click Search.
2. Samples matching the defined filter options are shown.
   

Sample replicates

ⓘ Associated section → Create kit plate layout > 4. Select samples

Sample replicates can be defined during worklist generation.

Distribute replicates: select a sample and define the number of replicates distributed across a kit plate

Multiple injections per well: select a sample and define the number of injection replicates from a well

No replicates: Apply the default values.

Plate preview

During worklist creation, a preview of all plate runs is shown.

Calibration standards are not included in FIA plates.

Export options

In the popup window, select the MS type and autosampler according to your instrument configuration.

Option	Description
MS Type	Output file format for importing into MS vendor software
Autosampler	Defines well position format according to autosampler configuration
Order by	Default settings are defined in OP
Randomize sample injection order	Randomizes the injection order of "unknowns" in the worklist
Export worklist / plate report PDF	Creats PDF document of worklist / plate report
Plate positions	Sequences are created for selected plate runs. Define rack position in the autosampler.

Select Export. A ZIP file is created.

"Rack type" for SCIEX OS and autosampler model "Agilent Infinity II"

Autosampler model	Rack type
Agilent Infinity II - 1	Multisampler 2H 2H 2B 2B 5Ref
Agilent Infinity II - 2	Multisampler 2H 2H 2H 2B 5Ref
Agilent Infinity II - 3	Multisampler 2H 2H 2H 2H 5Ref
Agilent Infinity II - 4	Multisampler 2H 2B 2B 2B 5Ref
Agilent Infinity II - 5	Multisampler 2B 2B 2B 2B 5Ref

Exported files

The ZIP file contains the sequence for running the kit at the LC-MS system. Extract the contents onto the LC-MS operating PC. txt/csv files are generated for each kit plate run to be imported into the MS software before starting the LC-MS run.

Instrument	Format
Analyst®	.csv
SCIEX OS	.csv
MassHunter	.csv
MassLynx™	.txt
Xcalibur™	.csv

View and edit worklist

A worklist can be selected underneath the submission on the righthand sidebar.

Plate and worklist view

Select the plate run to view or edit the worklist:

Available features

• To show additional information, mouse over samples in the plate view.

  

• To select multiple samples, control or shift click well positions on the plate view or rows in the sample list.

• To copy, cut, delete, or select all, right click on a sample or multiple selected samples.

• To insert additional samples or paste a copied or cut sample, right click on empty wells. Inserted samples will fill in order using available empty well positions.

• To update sample volume pipetted to the kit plate or change the number of injection replicates, select a sample or multiple samples from the sample list.

The size and level of detail of the shown plate layout is adjustable.

small size

sample IDs shown

sample barcodes shown

large size

Measure a plate run again

To measure a plate run again, either

- create a second plate run (recommended) by clicking Clone plate run, or

- make a copy of a plate run by clicking Copy plate run.

Clone plate run

1. To create a new plate run, click Clone plate run.
2. Export the new sequence, using Export worklist to MS.
3. Use this sequence to measure a plate run again.

Use each WebIDQ sequence export only once, received from Export worklist to MS.

Otherwise the corresponding MS data will not be compatible with WebIDQ.

A plate run is cloned by right clicking on the first plate run and selecting Clone plate run.

Cloned plate runs keep the plate barcode and receive a new run number.

Define the new run number, e.g. 2.

Click Create.

Copy plate run

Select the new plate run and change the OP to the FIA OP according to the respective kit user manual, e.g. to "MXP500F-0-5813".

All kits require several plate runs, except the Bile Acids kits. Example for Quant 500 XL kit & SCIEX 5500+:

• plate run 1: LC part, e.g. OP MXP500L-0-5813
• plate run 2: FIA part, e.g. OP MXP500F-0-5813
• plate run 3: XL part, e.g. OP MXP500X-0-5813

Quantify plate run with new OP

Data linked with a plate run can be processed with another OP.

1. Selct a plate run which contains quantified data, e.g. 1052001288-1.
   Click Clone plate run.
   
2. Click Delete measurements and change the OP, e.g. from "MXP500L-0-8313" to "MXP500L-0-8413".
   
3. Quantify the cloned plate run, e.g. 1052001288-2.
   
   Perform
   Integration,
   Calibration (LC part only), and
   Validation.

Run a worklist again | Copy worklist

A worklist can be copied, consisting of multiple plate runs.

Example: Quant 500 kit, LC part and FIA part.

1. Select a worklist.
   
2. Click Copy worklist.
   
3. Select a submission, where this worklist is copied to.
   Click Copy worklist.
   
4. The worklist was copied. All plate runs have received new plate run numbers.
   

Merge plate runs | Move plate

Plate runs can be moved to one worklist.

1. In LIMS > Projects select a plate run and right-click.
2. From the drop-down menu, select Move plate.
3. Define the worklist, where the selected plate run should be moved to.

If e.g. the LC and FIA plate runs of one kit were created in separate worklists, e.g. by Import plate run(s), use this feature to merge them.

Remove content

Delete projects, submissions, and worklists

With one of the following selected in the project tree: Project, Submission, or Worklist, click the trashcan icon next to the searchbar and follow the on-screen prompts to delete:

Note that anything inside the selected item will also be removed, i.e. deleting a Submission will also remove, the worklists and plate runs inside.

Delete plate run

To delete an individual plate run, select it in the worklist, right click, and "Delete plate run".

Delete measurements

Measurements, which include validation status and results (calculated concentrations), may be cleared by selecting "Delete measurements"

Note that this only removes results and validation status. Imported raw data files are still stored in the database.

Delete raw data files

After completing an experiment or project, raw data files stored in the WebIDQ database can be removed to free up storage space (See: Storage space | WebIDQ cloud)

Right click the plate run and select "Delete converted raw data files"

Note that deleting raw data files does not delete measurements or results. These can still be accessed in Quantification and Results sections, respectively. However, in order to reprocess data (Integration and calibration), raw data files would need to be re-imported into WebIDQ.