Bio-Rad ProteinChip Calibration Standards - Manual

General Recommendations
• Store the array in the original packaging and do not open the packaging until ready to use
• Prepared arrays can be used multiple times, though the peak features will degrade over time. After opening, store arrays in a dry and dark
location and their original packaging. Record the usage dates
• The ProteinChip premade array supplied with this kit has been prepared with a mixture of peptides and matrix. Avoid exposing these arrays to
vibration, moisture, or light
• ProteinChip array spots contain chemically treated surfaces. Avoid contamination of these surfaces: always handle ProteinChip arrays by
their edges, and never touch the spots
• When running single ProteinChip arrays on the ProteinChip instrument, Enterprise Edition, always fill empty locations in the cassette with
blank, expired, or used arrays.
• To ensure best results, evaluate the performance of the ProteinChip system using the ProteinChip system check kit (catalog #C70-00081) or
ProteinChip OQ kit (catalog #C70-00080), or as included in service contracts
Introduction
Mass calibration is the process by which the time-of flight data obtained by mass spectrometry are converted to molecular mass data. Data collected
using standards (known peptides or proteins) are used to derive a calibration equation, which is then applied to the spectra of experimental samples.
In the following protocol, you use the spectra obtained from the ProteinChip ® peptide standard array to perform the mass calibration procedure.
The procedures for importing protocols and performing mass calibration are illustrated in a tutorial video included on the ProteinChip Peptide Mass
Calibraiton Kit CD. The tutorial video is also available online at www.bio-rad.com/proteinchip/starterkit.
Import the Pep Std Array Protocol
The ProteinChip reader uses data collection protocols to collect data from arrays. The protocol used with this kit is provided with the CD. Import the
protocol into the Protocols folder of the ProteinChip data manager software.
1. Ensure that the ProteinChip reader is turned on and connected to the computer. (This is usually done during installation.)
2. Insert the ProteinChip Peptide Mass Calibration Kit CD and launch the ProteinChip data manager software.
3. In the Explorer pane, select the Protocols folder. In the toolbar, select Protocols>Import Protocol. The Choose File(s) to Import
dialog opens.
4. Select the file named Pep Std Array.ptx and click import. Click OK at the prompt.
Read the Peptide Standard Array
1. Insert the ProteinChip peptide standard array into the instrument. If you are using an Enterprise Edition instrument, place the array
into a cassette, fill the remaining slots in the cassette with blank or used arrays, and place the cassette into the instrument.
2. In ProteinChip data manager software, click Start and open the Protocol Mode tab.
3. Select Instrument > Preferences. In the Preferences dialog, click "…". The Select Folder dialog opens.
4. Select New Folder, name the new folder Peptide Mass Calibration and click OK.
5. Optimize the laser intensity. Run protocol Pep Std Array on any partition ("n") of 10 on spot A. Adjust the laser energy until the
height of the insulin peak at 5.96 kD is 100–200 µA.
6. Run protocol Pep Std Array. Run on partition 1 of 4 on spot A of chip. Record usage on the label provided on the package. Each
spot on the array may be read up to 5 times on each of 4 partitions (1 of 4, 2 of 4, 3 of 4 and 4 of 4).
ProteinChip
®
Peptide Mass Calibration Kit
Catalog #C70-00070