The former head of the unit, Dr Holger Wenschuh, is expected to head up the business, which is to trade under the name JPT Peptide Technologies (JPT).
JPT provides peptide-based products and services whereas Jerini will focus on drug discovery and development.
Berndt Modig, chief financial officer at Jerini, said: "While the business is profitable at strong growth rates, the peptide technologies business is a different business from the drug discovery and development business of Jerini, with different cash flows."
"It is not the intention to invest any of the funds raised in the recent financing round into the peptide technologies business. We believe that the increased financial transparency will benefit both business areas."
JPT Peptide Technologies GmbH has taken over all employees, production facilities, intellectual property, and contractual obligations related to the former business unit.
Holger Wenschuh, managing director of JPT said: "The foundation of an independent company facilitates our strategic development towards an outsourcing partner for pharmaceutical companies."
"Our main efforts will be related to the further development and provision of high-content peptide tools for signal transduction research, immunology and high-throughput screening."
Modig added that the strict focus of the new entity to the fee-for-service business would ease and accelerate outsourcing negotiations with a number of companies which already indicated potential interest.
JPT Peptide Technologies product lines will continue to include peptide macro and micro arrays, ready-to-use peptide tools and custom peptide services with the main fields of applications include signal transduction (kinase-, phosphatase-protease research), immunology (T-cell stimulation, immune monitoring) and high-throughput screening.