Bio-Rad ProteinChip Qualification and Calibration Kits User Manual

ProteinChip®OQ Kit

Instruction Manual and Documentation

Catalog #C70-00080

For technical support call your local Bio-Rad office, or in the US, call 1-800-4BIORAD (1-800-424-6723)

For use with the ProteinChip SELDI system, Personal or Enterprise Edition, with embedded system processor (ESP) version 1.1.15 or higher

Notices

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage or retrieval system, without permission in writing from Bio-Rad.

Bio-Rad reserves the right to modify its products and services at any time. This user guide is subject to change without notice.

Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or for any damages resulting from the application or use of this information.

ProteinChip is a trademark of Bio-Rad Laboratories. Microsoft and Excel are trademarks of Microsoft Corporation.

The SELDI process is covered by U.S. patents 5,719,060, 6,225,047, 6,579,719, and 6,818,411 and other issued patents and pending applications in the U.S. and other jurisdictions.

Table of Contents

Chapter 1 Introduction ............................................................................................1

1.1 Product and Protocol Description........................................................................1

1.2 Storage and Handling..........................................................................................2

Chapter 2 Use of the ProteinChip®OQ Kit ............................................................4

2.1 Overview..............................................................................................................4

2.2 File and Protocol Setup .......................................................................................5

2.3 OQ Maintenance Procedures..............................................................................9

2.3.1 Maintenance Procedure 1 — High Voltage (HV) Conditioning ..............9

2.3.2 Maintenance Procedure 2 — Detector Calibration ................................9

2.4 OQ Tests............................................................................................................12

2.4.1 Test 1 — Detector Sensitivity ...............................................................12

2.4.2 Test 2 — Mass Drift and Resolution at 5.96 kD...................................15

2.4.3 Test 3 — Mass Resolution at 1 kD.......................................................19

2.4.4 Test 4 — Mass Accuracy .....................................................................22

Appendix A Installation Qualification (IQ) Certificate ...........................................29

Appendix B Protocol Acceptance Form .................................................................30

Appendix C Data Export Procedure........................................................................31

Chapter 1 Introduction

Qualification of analytical instruments is a formal process of documenting that an instrument is fit for its intended use and that it is maintained and calibrated.

• Installation qualification (IQ) checks that the correct system or instrument was received and that it was properly installed. IQ is performed by a Bio-Rad service engineer following installation of the ProteinChip®SELDI system. The engineer will provide an IQ certificate upon completion (see Appendix A for an example of this certificate. If you do not have a copy of this certificate, contact technical support). IQ should also be performed by a service engineer when the ProteinChip SELDI system is moved to a new location and when the software is upgraded.

• Operational qualification (OQ) demonstrates that the ProteinChip SELDI system operates in accordance with Bio-Rad’s requirements. The ProteinChip SELDI OQ kit is used to qualify the installation and operation of the ProteinChip SELDI system, Personal or Enterprise Edition. Bio-Rad recommends that the OQ protocols be performed in total upon installation (following IQ), on a regular basis to confirm that the system is performing to specifications, and whenever it is suspected that the instrument is not performing to specifications.

For audit review, maintain records of IQ and OQ of the ProteinChip SELDI system in a single notebook or folder.

1.1 Product and Protocol Description

The ProteinChip OQ kit contains all the ProteinChip arrays and instrument protocols required to perform OQ on a ProteinChip SELDI system, Personal or Enterprise Edition. The kit is designed to qualify the operating specifications of the ProteinChip instrument and is a valuable tool that allows discrimination between assay and instrumentation problems.

The components of each ProteinChip OQ kit support maintenance and testing for a three month period. Each kit contains the following:

1 CD containing the OQ instrument protocols and the ProteinChip SELDI OQ form

2 ProteinChip detector calibration arrays

6 ProteinChip detector qualification arrays

2 ProteinChip peptide standard arrays

1 ProteinChip OQ kit instruction manual

The OQ protocol involves two maintenance procedures (detector calibration and high voltage conditioning) followed by a series of four tests of instrument resolution, mass accuracy and drift, and sensitivity (Table 1).

Completion of each maintenance procedure and test is tracked using the ProteinChip SELDI OQ form, a Microsoft Excel spreadsheet supplied on the CD. Test data are exported to the ProteinChip SELDI OQ form, which then calculates whether the test passed or failed.

Upon completion of the OQ procedure, save, print, sign, date, and place copies of the following documentation into a notebook or folder for audit review:

• Protocol acceptance page (Appendix B)

• ProteinChip SELDI OQ form summary

Table 1. Summary of procedures and tests.

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TTiittllee FFrreeqquueennccyy UUsseedd RReeqquuiirreedd DDeessccrriippttiioonn

File and protocol

IInniittiiaall SSeettuupp

setup 20 min Complete this procedure the

first time you use the ProteinChip OQ kit. This procedure creates the file structure necessary for storing the protocols and creates the routines for high voltage conditioning and mass calibration.

MMaaiinntteennaannccee

High voltage Weekly N/A 1–2 hr HV conditioning helps to

PPrroocceedduurree 11

(HV) depending on decontaminate the surfaces conditioning instrument in the instrument.

MMaaiinntteennaannccee

Detector Weekly ProteinChip 45 min to 4 hr This procedure uses the

PPrroocceedduurree 22

calibration detector depending on ProteinChip detector

calibration instrument calibration array to adjust array the detector voltage. These

adjustments are based on a rolling average that stabilizes the gain, improving spectral reproducibility over the lifetime of the detector.

TTeesstt 11

Detector Biweekly ProteinChip 30 min to 1 hr This test uses the ProteinChip sensitivity detector detector calibration array to

qualification measure the signal-to-noise array ratio (S/N) of immunoglobubulin

(IgG) at two different concentrations (10 fmol and 140 fmol). Measurements are compared to a specification, and a pass/fail disposition is obtained.

Table 1. Summary of procedures and tests (

continued).

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TTeesstt 22

Mass drift and Weekly ProteinChip 20 min to 1 hr This test uses the ProteinChip resolution at peptide peptide standard array to

5.96 kD standard array measure the mass drift and resolution of insulin. These measurements are compared to a specification, and a pass/fail disposition is obtained.

TTeesstt 33

Resolution at Weekly ProteinChip 20 min to 1 hr This test uses the ProteinChip 1 kD peptide peptide standard array to

standard array measure the resolution of

Arg-vasopressin. These measurements are compared to a specification, and a pass/fail disposition is obtained. The test is run in higher-resolution (lower source voltage) mode.

TTeesstt 44

Mass Weekly ProteinChip 30 min to 1 hr This test evaluates the mass accuracy peptide accuracy when compared to

standard internal and external array calibrations. These measurements

are compared to a specification, and a pass/fail disposition is obtained.

1.2 Storage and Handling

Store the arrays supplied in the kit in the original packaging at room temperature and in a dry and dark location. Each array is individually wrapped. Do not open the array packaging until ready to use. Take care when handling the ProteinChip arrays to avoid contaminating or disturbing the matrix crystals on the surface of the arrays.

Chapter 2 Use of the ProteinChip OQ Kit

2.1 Overview

This chapter outlines the protocols used to perform the procedures and tests that comprise the ProteinChip OQ kit. Please note the following:

• Export data acquired during testing to the ProteinChip SELDI OQ form using the export instructions described in Appendix C

• Protocol transfer from the CD to ProteinChip data manager software needs only to occur once; however, new files must be created each time a test is run

• Neither spreadsheets nor protocols are write-protected. Overwriting may result in erroneous results and calculations

• Always perform the two maintenance procedures before running any of the tests

• Maintenance procedure 2 (detector calibration) is designed to standardize and stabilize detector performance over time, by resetting any drift in the response due to natural component aging. First or delayed use of this procedure may alter system response after calibration. Do not run this procedure within a series of related experiments if it has been more than two weeks since the last detector calibration

• All tests require peak measurements that are compared to specification. Incorrect peak selection may lead to erroneous results. While selecting peaks for measurement, zoom in on them so that they resemble the peaks in the examples provided

• When running single ProteinChip arrays on the ProteinChip instrument, Enterprise Edition, always fill empty locations in the cassette with blank, expired, or used arrays. Blank arrays are available as components of the ProteinChip cassette-compatible bioprocessor (catalog #C50-30011)

• The ProteinChip detector calibration array and ProteinChip peptide standard array can be used multiple times. After opening, store these arrays in a dry and dark place and in their original packaging

• When running protocols, you specify how many sections (partitions) the spot is divided into for sampling. You also specify which of these partitions should be used. For spectra intended for analysis, no more than four ("of 4") partitions should be used, with 10 shots/pixel

2.2 File and Protocol Setup

Complete this procedure the first time you run the ProteinChip OQ kit. This procedure sets up the file structure necessary for storing the protocols and creates the routines for high voltage conditioning (procedure 1) and mass accuracy (test 4).

Task

Step 1

Import Protocols

From CD

Step 2

Create the File

Structure

Note: Create new folders each

time the OQ tests are run. The instructions in this manual assume you are following the convention described here. However, any file structure and naming convention may be used.

Import the protocols supplied on the CD into the Protocols folder of ProteinChip data manager software:

1. Insert the CD into the computer and launch ProteinChip data manager software.

2. Select Protocols > Protocols > Import Protocols.

3. Use the Import Protocols dialog to import all protocols (files with a .ptx extension) from the CD to the Protocols folder.

Note: The protocols are NOT write-protected. Do not alter them.

Create a new folder for each test (1–4) to be run:

1. In the Explorer pane of ProteinChip data manager software, open the Projects folder and select File > New > Folder.

2. Create a folder,

OQ_####,

where

####

is the serial number of the instrument.

3. Click on this folder and select File > New > Folder. Create a separate folder for the date of the test.

4. Click on the folder created in step 3 and select File > New > Folder. Create a separate folder for each of the following tests:

• Test 1 Detector sensitivity

• Test 2 Mass drift and resolution 5.96 kD

• Test 3 Resolution 1 kD

• Test 4 Mass accuracy

Step 3

Set Up the

High Voltage (HV)

Conditioning Routine

1. Insert a blank ProteinChip array into the reader. If blank arrays are not available, use expired arrays or arrays that have already been used.

a. For the Enterprise Edition instrument: place a cassette filled with

12 blank or used arrays into the instrument.

b. For the Personal Edition instrument: insert a blank ProteinChip

array.

2. In ProteinChip data manager software, select the instrument and click Start.

3. In the Protocol Mode tab, select Instrument > Quick Run.

4. Select all 8 spots, then set up a Quick Run protocol as shown below:

a. For the Enterprise Edition instrument:

RC3 HV pos 15 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 20 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 25 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 30 kV conditioning, partition 1 of 8, all 8 spots RC3 HV neg 15 kV conditioning, partition 1 of 8, all 8 spots RC3 HV neg 20 kV conditioning, partition 1 of 8, all 8 spots RC3 HV neg 25 kV conditioning, partition 1 of 8, all 8 spots RC3 HV neg 30 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 15 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 20 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 25 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 30 kV conditioning, partition 1 of 8, all 8 spots RC3 HV pos 25 kV conditioning, partition 1 of 8, all 8 spots

b. For the Personal Edition instrument:

5. Click Save in the Quick Run dialog, and save the protocol as

SoftHV

in the Quick Run directory (C:\\XXXXXXX). The Quick Run directory location is defined by the user. The default location, "My Documents", will work as well as any other location that is easy to remember.

Step 4

Create a Standard

Mass Calibration

Routine

6. In the Explorer pane of ProteinChip data manager software, select Projects and click on any spectrum file (for example, the spectrum obtained during installation).

1. Select Spectra > Calibrate > Internal Calibration.

2. Select Create calibration protocol.

3. In the Calibration protocol name field, enter

OQ Mass Cal.

4. Select [Arg8]-Vasopressin (1084.247) from the drop-down list, and click Add (keep the default values of 3% of expected peaks and minimum signal/noise of 5).

5. Select Dynorphin A (2147.5) from the drop-down list, and click Add (keep the default value of 3% of expected peaks and signal/noise of 5).

6. Select Beta-endorphin (3465.0) from the drop-down list, and click Add (keep the default value at 3% of expected peaks and signal/noise of 5).

7. Select Arg-insulin (5963.8) from the drop-down list, and click Add (keep the default value at 3% of expected peaks and signal/noise of 5).

8. Select Fit all 3 coefficients. Click OK.

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