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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
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