Bio-Rad Matrix-Prepared Surfaces User Manual

ProteinChip®
SEND ID Array

Instruction Manual

Catalog #C57-30081

For Technical Support, contact your
local Bio-Rad office, or in the U.S.,
call 1-800-4BIORAD (1-800-424-6723).

Use

n

Peptide analysis

Introduction

Fundamental to most applications of laser desorption/ionization
mass spectrometry (LDI-MS) is the addition of matrix to the
analyte. Matrix signals interfere in the low molecular weight (MW)
range of the spectra, rendering matrix-assisted laser desorption/
ionization (MALDI)-MS and surface-enhanced laser desorption/
ionization (SELDI)-MS techniques problematic for peptide
analysis. Surface-enhanced neat desorption (SEND) technology
is unique in that the matrix is integral to the ProteinChip array
surface. The chemical noise in the spectra from the matrix is
significantly reduced when compared to addition of matrix
on-spot (particularly in the region 600 to 1,500 Da). This allows
the use of SELDI for lower MW species analysis with a reduced
amount of interfering peaks in the spectra.

The ProteinChip SEND ID array has C-18 as a functional group,
allowing the use of the array for on-chip cleanup, removing salt
and denaturant (such as urea) prior to analysis by SELDI.

The primary application of the ProteinChip SEND ID array is
peptide analysis. Successful mass determination of molecules
lower than 600 Da will be determined by how well these
molecules are ionized, desorbed, and detected by the mass
spectrometer. If laser intensity has to be increased above a
certain level to detect the molecule, the background peaks below
the 600 Da range may interfere with detection of analyte peaks.

1 © 2007 Bio-Rad Laboratories, Inc.

Storage and Packaging

Store ProteinChip SEND ID arrays at room temperature. They
should be stored in the foil pouch in which they are supplied to
limit their exposure to light.

ProteinChip SEND ID arrays are packaged in a 12-array
ProteinChip cassette. A bioprocessor reservoir is included in the
package to protect the arrays during shipment (see Figure 1).
The spare ProteinChip cassette included to separate the
reservoirs from the arrays should be removed before use in
the ProteinChip cassette-compatible bioprocessor (catalog
#C50-30011). As the recommended protocols are rarely done
with more than a few microliters of sample, this reservoir is not
needed and should be discarded.

The arrays can be used in the cassette, or individual arrays can be
removed for processing. Take care to avoid touching the arrays.
A pair of ProteinChip array forceps (catalog #C20-10002) helps to
remove the arrays from the cassette (see Figure 2).

Fig. 1. ProteinChip cassette
and reservoir.

2 © 2007 Bio-Rad Laboratories, Inc.

Fig. 2. Removal of ProteinChip
arrays from the cassette using
array forceps.