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EpiCypher

Comparison of EpiCypher Peptide Array method with SPOT peptide synthesis method

Comparison of EpiCypher Peptide Array method with SPOT peptide synthesis method

Other histone peptide array manufacturers use a method in which the peptides are synthesisized on a membrane substrate, the SPOT synthesis method. EpiCypher uses the latest in solid-phase peptide synthesis techniques. Each and every peptide is purifiied by HPLC. Peptide identity is validated by MALDI-TOF mass spectrometry and purity measured by analytical HPLC. All the validation data is readily available for our peptides. This level of quality control and peptide validation is not possible with the SPOT method. You have to take the word of the manufacturer that the peptides on the array are of high quality. Any claims made about peptide purity or quality are impossible to substantiate, because each spot on each array represents a unique peptide synthesis reaction.

EpiCypher Method SPOT Synthesis Method

Peptide Purity

HPLC Purified

Can't be readily determined

Peptide Identity

Verified by Mass Spec

Can't be readily determined

Peptide Length

Long peptides (>30 aa) possible

Peptides > 15-20 aa problematic

Full-Length Peptide

Verified by HPLC

Can't be readily determined

Spotting Control

Yes, fluorescent spotting tracer

No

Comparitive Mass Spec Data: SPOT vs EpiCypher Method
SPOT Synthesis Example EpiCypher Method
SPOT synth H3 n-term EpiCyperh peptide synthesis 12-0001

Peptide: H3 1-19, Ac-ARTKQTARKSTGGKAPRKQ
Peak 1:
ARTKQTARKSTGGKAPRKQ Full len., no N-term Ac
Peak 2:
Ac-KQTARKSTGGKAPRKQ N-term missing 3 aa
Peak 3:
Ac-QTARKSTGGKAPRKQ N-term missing 4 aa

Peptide: H3 1-20, ARTKQTARKSTGGKAPRKQK Link
Peak 1:
ARTKQTARKSTGGKAPRKQK Full len. peptide + 1 H+
Peak 2: ARTKKQTARKSTGGKAPRKQ Full len. peptide + 2 H+
Peak 3: ARTKKQTARKSTGGKAPRKQ Full len. peptide + Na+
Peak 4:
Noise due to contamination from solid phase media

For more information on the quality of peptides on SPOT synthesized histone peptide arrays, look at the supplemental data from Bock et al (2011), Epigenetics 6: 256-263. PAPER SUPPLEMENT (pdf)