0010681A.qxp 8/17/2007 11:22 AM Page FC1 ® ProteinChip System Check Kit Instruction Manual Catalog #C70-00081 For use with the ProteinChip SELDI system, Personal or Enterprise Edition, with embedded system processor (ESP) version 1.1.
10010681A.qxp 8/17/2007 11:22 AM Page FC4 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.
10010681A.qxp 8/17/2007 11:22 AM Page i Table of Contents Chapter 1 1.1 1.2 Chapter 2 2.1 2.2 2.3 2.4 Introduction ..........................................................1 Product and Protocol Description ..................................1 Storage and Handling ....................................................3 Use of the ProteinChip® System Check Kit ......4 Overview ........................................................................4 File and Protocol Setup .............................
10010681A.qxp 8/17/2007 11:22 AM Page 1 Chapter 1 Introduction 1.1 Product and Protocol Description The ProteinChip system check kit provides tools for performing two maintenance procedures (detector calibration and high voltage conditioning) as well as prepared ProteinChip arrays for testing detector sensitivity, resolution, and mass drift.
10010681A.qxp 8/17/2007 11:22 AM Page 2 Table 1. Summary of procedures and tests. Title Initial Setup File and protocol setup Maintenance Procedure 1 High voltage (HV) conditioning Maintenance Procedure 2 Test 1 Consumable Used Estimated Time Required Description 20 min Complete this procedure the first time you use the ProteinChip system check kit. This procedure creates the file structure necessary for storing the protocols and creates the routines for high voltage conditioning.
10010681A.qxp 8/17/2007 11:22 AM Page 3 Table 1. Summary of procedures and tests (continued). Test Test 2 Mass drift and resolution at 5.96 kD Consumable Used Estimated Time Required ProteinChip peptide standard array 20 min to 1 hr Description This test uses the ProteinChip peptide standard array to measure the mass drift and resolution of insulin. These measurements are compared to a specification, and a pass/fail disposition is obtained. 1.
10010681A.qxp 8/17/2007 11:22 AM Page 4 Chapter 2 Use of the ProteinChip System Check Kit 2.1 Overview This chapter outlines the protocols used to perform the procedures and tests that comprise the ProteinChip system check kit.
10010681A.qxp • 8/17/2007 11:22 AM Page 5 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 use the ProteinChip system check kit.
10010681A.qxp 8/17/2007 11:22 AM Page 6 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.
010681A.qxp 8/17/2007 11:22 AM Page 7 2.3 System Check Maintenance Procedures 2.3.1 Maintenance Procedure 1 –– High Voltage (HV) Conditioning This procedure helps to decontaminate the surfaces of the ProteinChip instrument and is essential for obtaining correct test results. Run this procedure weekly using any blank ProteinChip array (or an array that has already been used). The procedure takes 1–2 hr to complete.
10010681A.qxp 8/17/2007 11:22 AM Page 8 Note: The detector calibration procedure is intended to standardize instrument performance over time. First-time use may alter system response and is not recommended within a series of experiments. It is, however, possible to manually set the voltage back to its original state through the instrument’s web page. 1. Insert the ProteinChip detector calibration array into the instrument.
10010681A.qxp 8/17/2007 11:22 AM Page 9 5. If this is the first calibration performed on the instrument, or if the last calibration was performed more than two weeks ago, select two previously unused spots. If this is a routine, weekly calibration, select one unused spot. 6. Click Start. 7. The time required to complete this procedure is variable, and it may require up to several hours as the instrument continually collects data of a specific intensity.
10010681A.qxp 8/17/2007 11:22 AM Page 10 2.4 System Check Tests 2.4.1 Test 1 –– Detector Sensitivity This test uses the ProteinChip detector qualification array to measure the signal-to-noise 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. Array Type ProteinChip Detector qualification array Usage Information Use once and discard; do not open until ready to use.
10010681A.qxp 8/17/2007 11:22 AM Page 11 6. Plot the peaks with noise set to 12,000 Da: a. Select all 8 spectra. b. Click on the data analysis icon dialog opens. c. Open the Noise tab and set Start Measuring Noise From to 12,000 Da. Click OK. 11 .
10010681A.qxp 8/17/2007 11:22 AM Page 12 7. Plot all 8 spectra and select the IgG peak using the peak selection tool. Note: Spots with high concentrations (spots A, C, E, and G) alternate with those with low concentrations (spots B, D, F, and H). Due to the different concentrations on different spots, it is critical to export the peak data with the spots in alphabetical order from A to H. 8.
10010681A.qxp 8/17/2007 11:22 AM Page 13 2.4.2 Test 2 — Mass Drift and Resolution 5.96 kD This test uses the ProteinChip peptide standard array to measure the mass drift and resolution of insulin. These measurements are compared to a specification, and a pass/fail disposition is obtained. Array Type ProteinChip peptide standard array Usage Information Each test uses 1 partition on all 8 spots on the array. The array can be used up to 20 times (5 times on each of 4 partitions).
10010681A.qxp 8/17/2007 11:22 AM Page 14 6. Run the same protocol on partition “n” of 4 for all 8 spots. Record the partition number on the usage chart provided with the product packaging. 7. Make sure that a peak intensity of 50–500 µA is visible on each spot. If peak intensities appear out of this range, change the laser energy and run the test again.
10010681A.qxp 8/17/2007 11:22 AM Page 15 8. Plot the peaks with the filtering option turned off: a. Select all 8 spectra. (Do not select the first laser optimization spectrum.) b. Click the analysis settings icon. The Analysis Settings dialog opens. c. Open the Filtering tab and deselect the On checkbox. d. Click OK.
10010681A.qxp 8/17/2007 11:22 AM Page 16 9. Plot all 8 spectra. Using the peak selection tool, select the insulin peak (5.963 kD) in all spectra. 10. Export the data according to the instructions in Appendix A and selecting the parameters for export in the following order: • • • • • • Array bar code Spot name Substance mass Intensity Resolution S/N 11. Paste the data into the ProteinChip SELDI system check form, data sheet “Test 2 Mass Drift and Resolution”. 12.
10010681A.qxp 8/17/2007 11:22 AM Page 17 Appendix A Data Export Procedure Use this procedure to export the data obtained during testing to the Microsoft Excel spreadsheet provided with the kit (ProteinChip SELDI system check form). Following export, open the resulting .csv file using the Excel program and copy and paste the contents into a COPY of the spreadsheet provided. Retain this copy for your records. 1. In the Explorer pane, open the Projects folder and select the spectra to be exported.
10010681A.qxp 8/17/2007 11:22 AM Page BC1 Bio-Rad Laboratories, Inc. Web site www.bio-rad.
