FAQ: Peptide Microarrays

Please refer to the corresponding frequently asked questions (FAQs) below.
If you can not find the question you are looking for, please contact our customer support team:

What kind of hardware do I need to read-out my peptide microarrays?

You need a microarray scanner with the following specifications:
For low densitiy peptide microarrays (up to 3 x 384 Peptides/Microarray):
- Minimum scanning-resolution: 50 um / Pixel - Focusing should be possible - Intensity should be adjustable
- Size of slide: 1 x 3 inch
- Size of scanned area should be at least 63 x 21mm
- Extinction/emission filters depending on the fluophores used
For high densitiy peptide microarrays (more than 3 x 384 Peptides/Microarray):
- Minimum scanning resolution: 10 um / Pixel
- Focusing should be possible - Intensity should be adjustable - Size of slide: 1 x 3 inch
- Size of scanned area should be at least 63 x 21mm
- Extinction/emission filters depending on the fluophores used
- Software capable of reading and analyzing .gal-files.
JPT is working with a Genepix Axon 4000B, Genepix 4200 and a Genepix 4300 Scanner system. The resulting image should be an 8- or 16-bit format to be compatible with most microarray processing softwares.

Do you have specific protocols for peptide microarrays?

JPT Peptide Technologies provides a detailed protocol together with every peptide microarray.
These can also be downloaded from our website.

How does JPT QC the production of peptide microarrays?

With each synthesis batch we run well selected control peptides that are analyzed by HPLC-MS and need to pass quality control.
These control peptides include sequences that are difficult to synthesize.
After printing each microarray slide is scanned using our high throughput-scanning device and the immobilized peptide array is checked for completeness and uniformity.

How are the peptides immobilized onto the microarrays?

Peptides are covalently linked to the microarray surface chemoselectively via the N-terminus.
A flexible linker is inserted between peptide and microarray surface ensuring availablity of the binding sites within the peptide.
By capping steps during synthesis we achieve that only full length peptides carry the N-terminal coupling moiety, thus enabling a high-throughput purification of all peptides during immobilization.

Do you recommend substitution of cystein residues by serine residues?

Yes, as cysteine containing peptides are very sensitive to oxidation and cyclization, substitution of Cys by Ser increases peptide stability.
Additionally, unspecific interactions between cysteine residues and antibodies/proteins sometimes occur and give false-positive results.
Finally, Cysteine is very scarcely an essential residue in antibody epitopes.

How are incubation results evaluated?

JPT recommends using fluorescence readout-systems in combination with dye-labeled antibodies.
Since the glass surface is optimized for low background in fluorescence scanner systems, high S/N ratios can be achieved using high resolution laser scanners.

What is the concentration of each peptide on the microarrays?

The amount of peptide immobilized in one spot (100µm diameter) depends on the surface loading of the peptide microarray.
Experiments showed a loading capacity of 4pmol/mm³.
Therefore, the amount of peptide immobilized in one spot is approx 30 fmol/ peptide.

What is the size of a peptide microarray?

JPT´s peptide microarrays are compatible with most scanner system accepting microarrays of 1 x 3 inches (or 2.5 x 7.5 cm).

What is the size of the peptide spots on the peptide microarray?

The diameter of the individual spots is approx 80-140µm.
The size mainly depends on the physicochemical properties of the peptide solution spotted and is very hard to predict.

What is the layout of JPT´s microarrays?

All our microarrays display each peptide in several copies to ensure verifiable results.
The exact layout for each microarray is noted in the product description.

What is the chemical stability of JPT´s peptide microarrays?

The bond between peptides and microarray surface is stable in a range of pH 4 -10.
Higher or lower pH values might lead to signal loss due to degradation.

What are the appropriate storage conditions for the microarrays?

Peptide microarrays should be stored at 4°C.
JPT recommends NOT to freeze the microarrays since the effects of freeze thaw cycles on the glass surface are unclear.
Properly stored, our peptide microarrays are stable for 18 months.

Is it possible to regenerate a peptide microarray?

JPT does not recommend regeneration of peptide microarrays by stripping bound proteins or antibodies from the surface because the surface can be damaged and also very low remainders of protein or antibody can cause a very high background.

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