Project | Plate layout

Introduction | Create kit plate layout

• Before measuring a kit, a plate layout is designed in WebIDQ.
• Each kit uses a plate layout with blank, zero, calibration standard (Cal), quality control (QC), and study samples (unknowns).
• Well position and injection replicates of samples can be defined.
• A kit plate layout is created under a project, submission, and worklist.
• Kit plate layout is available for download for
  the kit preparation in the laboratory (plate report), and
  to analyze a kit with the LC-MS system (worklist for MS).
• To create a plate layout for kit run, follow the instructions below.

• Use one submission and worklist per kit.
• Use each WebIDQ sequence export only once.
• If a kit was run but the corresponding plate run is missing in WebIDQ, refer to section Import plate run(s).

Procedure | Create kit plate layout

1. Select a project and submission
2. Generate a worklist
3. Select an OP
4. Select samples
5. Download worklist for kit preparation and run

Default kit plate layout

1. Select a project and submission

Step 1: select a project to which a kit plate is added.

For example: project "biocrates kit", submission "YYYY-MM-DD - kit plate ##"

ⓘ To create a project → Create a project

Step 2: select a submission to which a kit plate is added.

For example: project "biocrates kit", submission "YYYY-MM-DD - kit plate ##"

ⓘ To create a submission → Create a submissions

2. Generate worklist

1. To define a kit plate layout, click on Generate worklist.
   
2. The "worklist generation" wizard is opened.
   

3. Select OP(s)

In the "worklist generation" wizard, under Select OPs select the kit specific OP(s) for the used kit and LC-MS instrument.

Quant 500 XL | Quant 500 | p400 HR | p180

Select kit specific OPs of all kit parts.

Kit part	Quant 500 XL	Quant 500	p400 HR	p180
LC	MxP500L-0-####	MxP500L-0-####	KIT2-0-1##1 (KIT2-0-1##2)	KIT2-0-####
FIA	MxP500F-0-####	MxP500F-0-####	KIT3-0-1##1 KIT3-0-1##2	KIT3-0-####
FIA XL	MxP500X-0-####

Click Next.

Quant 1000 | MxQuant

Select one kit specific OP of one kit part.

Generate separate worklists for each kit part, NPH and PITC.

NPH part	PITC part
Q1000NPH-0-###1	Q1000PITC-0-###1

Click Next.

LxQuant | SMartIDQ alpha | Bile Acids

Select the kit specific OP.

LxQuant	SMartIDQ alpha	Bile Acids
Q1000Lipid-0-###1	SMalpha-0-####	BA02-0-####

Click Next.

WebIDQ's operating procedures (OPs) are kit and LC-MS instrument specific.

Example

Kit:            Quant 500 (XL)

MS system: SCIEX 5500

LC system:  UHPLC

Matrix:       0 = universal

Kit	LC part	Matrix	MS system	LC system	OP version
MXP500	L	0	55	1	3

→ OP name = MXP500L-0-5513

4. Select samples

Define the pipetting orientation, vertical (A1, A2, A3, ...) or horizonal (A1, B1, C1, ...).

Step by step, select the samples to be analyzed with a kit.

ⓘ Details → Generate worklist | How to select samples

Step	Sample type	Used for	Number of sample(s)
	Blank, predefined	Check LC-MS cleanliness and purity of solvents	1
1	Zeros	LOD calculation	3
2	Calibration standards	Calibration curves and calculation of concentrations	7
3	QCs , 3 levels	Kit performance check and results normalization	6 = 1x QC1, 4x QC2, 1x QC3
	Custom QCs	Optional, e.g. study pool sample	User-defined
5	Unknowns	Study samples, to be analyzed with a kit ⓘ Details → Find samples using metadata	79

To sort samples click on the table's header.

Samples are added to the plate in the same order as shown in the list during worklist generation.

• Values in column Number of samples are recommendations.
  Sample replicates may be defined → Sample replicates
• Custom QCs are optional.
• A plate preview is shown.
  

Step 1 | Zeros

Use a zero sample suitable for the matrix of the analyzed unknowns.

For plasma or serum samples use PBS.

For other matrices, follow the recommendations in the corresponding SOP or the biocrates recommendations.

If analyzing samples from different matrices with one kit plate, register matrix specific Zero samples for each sample matrix.

Example

PBS for sample matrix plasma.

Isopropanol for sample matrix tissue extracts.

Step 2 | Cal Stds

1. Open the vial box of the kit.
2. Take out the calibration standard vials and note the barcodes for WebIDQ on the vials.
   
3. In the worklist generation wizard, select calibration standards with barcodes as printed on the corresponding vials.
   

Step 3 | QCs

1. Open the vial box of the kit.
2. Take out the QC vials and note the barcodes for WebIDQ on the vials.
   
3. In the worklist generation wizard, select QCs with barcodes as printed on the corresponding vials.
   
4. Define QC2 replicates, according to kit user manual.
   Default: 4 replicates.

   

Step 4 | Unknowns

Select unknown samples.

Mind the number of available wells on the kit plate.

• 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 (→ Plate preview).

When finished with defining the worklist layout, click OK.

5. Download worklist for kit preparation and MS software

• Check the plate layout.
• To download a plate layout for the kit preparation and MS software, click Export worklist to MS.
  
• Define the export options, like MS type, autosampler, and Plate position.
  For details → Export options and Exported files
• In the window "Export worklist to MS" click Export.
  

Exported files

A ZIP file is downloaded containing

• the plate layout for the kit preparation in the laboratory, and
• the sequence for running the kit with the MS software.

One sequence file is generated for each kit plate run, to be imported into the MS software before starting the LC-MS run.

For processing the kit, refer to the kit user manual.