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.
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).
Technical Considerations n If your sample has salt or urea contamination, proceed directly to Protocol 2. Otherwise, perform Protocol 1 first. If there is insufficient signal after reading the arrays, a cleanup step is recommended: Add 5 µl of 0.1% trifluoroacetic acid (TFA) to the spot; do not agitate; remove the 0.1% TFA droplet after 30 sec; and add 5 µl 25% acetonitrile (ACN) and 0.1% TFA to the spot.
Chemical Noise Because ProteinChip alpha-cyano-4-hydroxycinnamic acid (CHCA) matrix is integral to the array surface, chemical noise from matrix peaks are significantly reduced with the ProteinChip SEND ID array when compared to standard MALDI or SELDI analysis.
Protocol 1 The following method can be used to apply a sample directly to the ProteinChip SEND ID array for peptide analysis. 1. Mix your sample 1:1 (v/v) with 50% ACN (v/v) and 0.2% TFA in deionized (DI) water. 2. Add 1–2 µl of sample to each spot on the ProteinChip SEND ID array. 3. Allow the spots to air-dry. 4. Read the arrays in the ProteinChip SELDI reader. Protocol 2 The following method can be used to clean up a sample on the ProteinChip array to remove salt and urea contamination (see Figure 4).
Relative intensity ProteinChip SEND ID array 30 1,859.01 20 2,482.0 2,230.97 1,060.46 10 0 1,000 2,000 Relative intensity ProteinChip NP20 array with CHCA matrix 60 40 20 0 1,000 m/z 2,000 Fig. 4. Clearly visible peptide peaks with the ProteinChip SEND ID array.
The SELDI process is covered by U.S. patents 5,719,060, 6,225,047, 6,579,719, 6,818,411, and other issued patents and pending applications in the U.S. and other jurisdictions. Bio-Rad Laboratories, Inc. Web site www.bio-rad.
