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511. CYCPEP: Sequence Determination of Cyclic Peptides
by A. A. Tuinman, CSIR, National Chemical Research Laboratory, Pretoria, South Africa Given a cyclic peptide of known amino acid composition but unknown sequence, the sequence may often be derived from correct interpretation of the high-resolution electron impact mass spectrum (HR-EIMS) of the peptide. Because of the numerous possibilities of fragmentation of such molecules, manual evaluation of the data is fraught with the danger of misinterpretation. The program CYCPEP is designed to help avoid such misinterpretation. CYCPEP accepts as input a set of amino acid residues known to comprise a cyclic peptide or a cyclodepsipeptide. CertainIE-fragmentation characteristics of these residues are incorporated into the input. Execution of the program is divided into three parts: PART I. CYCPEP checks the input for errors and inconsistencies, then commences the calculation of all possible fragments which might arise from any residue sequence. Each such fragment is assigned a calculated accurate mass and stored in coded form on a direct access file ( =DAF). Up to 10,000 such possible fragments may be stored. The calculation of these possible fragments is governed by the published rules of cyclopeptide fragmentation and by the "subunit loss input" described in the documentation for the program. PART II. If instructed to do so, CYCPEP reads a list of empirical masses generated from an EIMS of the cyclic peptide. Each of these masses is associated with a tolerance ( = window of uncertainty). Each mass is compared with the list on DAF, and fragments which could have generated the MS-peak are printed in the output. PART III. If instructed to do so, CYCPEP will generate all possible sequence permutations of the cyclic peptide and compare each of these with the output of PART II. FORTRAN 77 (CDC) Lines of Code: 4450 |