Bio-Rad ProteinChip Calibration Standards - Manual (Page 2)

Perform Mass Calibration
1. Open the spectrum obtained using the peptide standard array, and label the 4 peaks indicated in the table below.
Note: Label each peak at its highest point; if not, the mass will be recorded incorrectly, reducing the accuracy of the calibration.
Mass standards included in the ProteinChip peptide standard array. Use the four peaks marked "yes" in the table below.
2. From the toolbar, select Spectra > Calibrate > Internal Calibration (or click the Internal Calibration icon ). The Internal
Calibration dialog opens. The spectrum appears in the bottom half of the window with existing peak labels appearing in red. A table of
calibrants and peaks appears in the top half of the window; the calibrant names are blank.
3. Click the Match Calibrants to Peak icon . Confirm that the peaks are labeled correctly by comparing the peak names to those in the
table.
4. Select 3 parameters from the Calibration type drop-down list and select the Weighted check box. Click the Calibrate icon . The
labels now appear in the spectra.
5. Open the Calibration equation tab. The residual plot displays the error for each calibrant in parts per million (ppm).
6. Select 300 from the Scale (ppm) drop-down list. If the error of a calibrant is greater than ±300 ppm, double-check the peak label or name
to ensure proper labeling. Close the window.
7. Click the Toggle Spectrum Table button to view all the spectrum files within your folder. Note that the Calibration type icon has
changed to green , indicating that the spectrum has been calibrated.
Save the Calibration Equation
1. Select a calibrated spectrum (green icon) from within your Pep Std Array project folder.
2. Save the equation by selecting Spectra > Calibrate > Save Calibration Equation. The Save Calibration Equation dialog opens.
3. Enter a name for the calibration equation. Include the date of creation in the name. Click OK.
Note: A calibration equation can be used to externally calibrate other spectra. For best results, use the calibration equation within 1 day
for mass ranges between 1 kD and 25 kD. For more information on external calibration, refer to the ProteinChip Data Manager Software
Manual.
Ordering Information
C70-00080 ProteinChip OQ Kit, includes 2 detector calibration arrays, 6 detector qualification arrays, 2 peptide standard arrays, CD with
protocols, instructions
C70-00081 ProteinChip System Check Kit, includes 1 detector calibration array, 1 detector qualification array, 1 peptide standard array,
CD with protocols, instruction manual
C50-30013 ProteinChip Cassettes, empty, hold 12 ProteinChip arrays, 5
C10-00001 ProteinChip Protein Calibrant Kit, includes protein MW standards (2 sets of 10 standards)
C10-00002 ProteinChip Peptide Calibrant Kit, includes peptide MW standards (2 sets of 7 standards)
C10-0006 ProteinChip Human Serum Control, 500 µl
C10-0005 ProteinChip All-In-One Peptide Standard, lyophilized, 100 spots
C10-0007 ProteinChip All-In-One Protein Standard II, lyophilized, 100 spots
Legal Notice
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.
The SELDI process is covered by US patents 5,719,060, 6,225,047, 6,579,719, and 6,818,411 and other issued patents and pending applications in the US and other jurisdictions.
Copyright © 2008 by Bio-Rad Laboratories, Inc. All rights reserved.
Label Peak for
Calibration
Peak Name Molecular
Mass (Da)
Yes 1 Arg8-vasopressin 1,084.25
No 2 Somatostatin 1,637.90
Yes 3 Dynorphin A 2,147.50
No 4 ACTH 2,933.50
Yes 5 Beta endorphin 3,465.00
No 6 Arg-insulin 5,963.80
Yes 7 Cytochrome C 12,230.92