General

Epitope mapping – peptide microarrays are in situ synthesized peptide microarrays that utilize the µParaflo® microfluidics technology for on-chip synthesis of peptides. Each microarray consists of thousands of peptides that act as epitopes. We have array designs of both 4K and 30K defined amino acid sequences. The sequences can be completely customer defined or we have a LC Sciences’ standard designs as well.

These microarrays are a quick and efficient method for performing thousands of binding assays in parallel. Typical applications include: immunological studies, drug discovery research, vaccine development, biosensor development and other applications.

Microarray Design

These are not spotted arrays! Our peptide microarray synthesis is based on a proprietary µParaflo® microfluidic chip technology developed in house. This flexible technology enables fast, on chip synthesis of microarrays when ordered. (vs. an off-the-shelf spotted array) Please see our µParaflo® technology bulletin or the following references 1-2 for further information.

1. Pellois, J. P., Zhou, X., Srivannavit, O., Zhou, T., Gulari, E., and Gao, X. (2002) “Individually addressable parallel peptide synthesis on microchips“. Nat. Biotechnol. 20, 922-926.

2. Gao, X., Pellois, J. P., Kim, K., Na, Y. , Gulari, E., and Zhou, X. (2004) “High density peptide microarrays. In situ synthesis and applications”. Molecular Diversity. 8, 177-187.

The microarray is composed of thousands of microfluidic PicoArray reactors and is made from silicon using standard microelectronic fabrication procedures. Each PicoArray reactor contains three topographical features: pico-reaction chambers, fluid microchannels, and inlet/outlet through holes. The microarray is sealed with a glass coverslip.

Each peptide sequence is synthesized from C-to N-terminus, thus the peptide will be linked to the support via the C-terminus. We use a linker molecule to space the target peptide sequence away from the support (~30 amino acids in length) to achieve reaction kinetics that mimic “in-solution” conditions.

Yes, by default the peptides are acetylated as this makes them more stable to degradation and better represent a part of a protein.

These are completely custom microarrays so you decide what goes on the array. This service gives you total freedom for the choice of probes, up to thousands of sequences. Please talk to our customer support about your requirements.

Yes, the sequences are completely customizable, however, you are not required to add any controls of your own. We typically include multiple controls on each microarray that we synthesize, both to check the quality of the array synthesis and also to monitor the performance of the assay.

No, the peptide sequences are produced in situ or “on chip”. We have a unique synthesis chemistry which allows us to synthesize the peptide sequences directly on a microchip, similar to the method for synthesizing oligo arrays.

No, we make every array to order. You can create a totally custom array and order just one.

Custom Sequences

Yes, these are completely custom microarrays.  All the sequences come from you.

Typically 8 mers are sufficient to represent binding epitopes, however longer (and shorter) peptide sequences are possible. Maximum length we offer are 12 mers.

If any of your sequences are longer than 8 residues, there will be a fee for each additional residue. Cost depends on the chip type and are subject to change. Currently, there is a $195 charge each for residue for the smaller 4k chip, and a $295 charge each for residue for the larger 30k chip. Maximum length we offer are 12 mers.

We recommend triplicates although this will reduce the total number of sequences you can add to the array. If there is space left we will fill up the chip with additional replicates.

Yes, our synthesis chemistry is based on standard t-boc peptide synthesis chemistry. Any amino acid building block, analog, or modification that is commercially available in t-boc protected format can be incorporated into the peptide sequences.

Sample Preparation

The required sample amount varies and will be determined by binding affinity and the objective of the chip assay. Typically, each assay requires about 150 µL (250 µL for 30k chip) of the sample at µM concentration. This is about 0.25 nmol or 25 µg of a protein (Mw 100 kDa). The binding of Kd ~ 1 µM can be detected under this condition. Proteins of higher binding affinities will require less than the amount given and of lower binding affinities will require more than the amount given.

We prefer to receive a higher concentrated stock solution so that we can dilute the sample to the final concentration here. This allows us to re-run the chip at a higher concentration, should there be no binding during the initial run.

Sample Submission

Please complete a sample submission form and email to us prior to sending your sample to us.

We cannot begin work on your array without a PO Number or Credit Card Number.

See our sample submission page for further information.

Please transfer your sample to a 1.5ml microcentrifuge tube for shipment (0.5 ml or smaller PCR tubes can crack when frozen).

If you want to seal the tubes or hold them in a rack, please don’t use tape (it will crack when frozen), use parafilm.

Pack the sample with dry ice in a thermal insulated shipping box. Ship by overnight carrier for delivery the next day.

Note: Do not ship samples on Friday as they will sit over the week-end and deteriorate. Wait until the following Monday to ship the package for Tuesday delivery.

Mail your package to:
Attn: Peptide Microarray Sample
LC Sciences
2575 West Bellfort Street, Ste 270
Houston, TX 77054

Yes, we have no problems with shipments coming from overseas.

Binding Assays

We use fluorescence for detection of antibody bound to the peptide target.  There are a two scenarios possible for fluorescence detection:

  • Direct detection of a dye labeled antibody. In this scenario, the customer will supply the dye labeled protein.
  • A non-labeled sample(antibody) is used in combination with a dye labeled secondary antibody.This is the most frequently used option.

Our microarrays are adapted to fit into standard 1″ x 3″ compatible microarray scanners.  We use a Molecular Devices GenePix scanner. With each order , you will receive an image of the scanned microarray along with the array layout file we used.

Currently the array chips are not available for separate purchase without the service. Our technology utilizes a microfluidics chip that requires additional liquid handling equipment not available outside our lab. In the future we hope to be providing this equipment so that users may perform their own experiments.  Please inquire if you are interested in obtaining a microfluidics station.

We have a very well-trained and knowledgeable staff of scientists here at LC Sciences. If there is some specific experimental work you need done, we would be more than happy to put together custom service package designed specifically for your research needs.

No, we do not recommend re-using the arrays with a different protein sample.  However, we can run multiple assay reactions with varying (increasing) concentrations of your single protein to measure reaction kinetics and perform Kd calculations for thousands of peptide sequences.

We synthesize all sequences in a minimum of triplicate on the chip and our intra chip variability is very low. For single species arrays, more replicates can be added upon your request. Further, because our chips are based on the µParaflo® technology, the spot uniformity is excellent both within the chip and from chip to chip. The decision of how many replicate chips to run is up to you. Generally, for epitope mapping, customers will run a single chip per sample.

Array Results

Turn around time depends on peptide length, number of samples. We can generally have data back to you within about 4 weeks from the date we receive your protein/antibody sample and sequence information for the peptides.

For each array, you will receive the original and processed microarray scan images, an array layout file, a raw intensity data file in Excel, and a fully processed data file in Excel.

Additionally, for each batch of samples, you will receive a Data Summary containing a catalog of data files, images of representative regions of corresponding arrays, and descriptions of specific features of the arrays.

The above files will be stored on a CD and will be delivered to you by express mail.

When plotting the binding intensities of the peptides you will look for regions that show an almost Gaussian bell curve shape. A good epitope will show such characteristics.

Our control peptides on the chip will reveal unspecific binding to particular amino acid residues. Take this into account when looking at the data.

Data Analysis

We perform the data processing and provide background subtracted intensity data.

You will receive the background subtracted intensity data indicating the antibody binding for each peptide. Sample data are available for download here.

Yes, the data package that we send to you contains the raw data and array layout information for you to carry out you own data analysis.

Additional Questions

For other questions please send us an email at service@lcsciences.com or call us at 1-888-528-8818.