LIPID MAPS mass spectrometry combinatorial expansion package

NAME

GP_expand.php - Generate a combinatorial dataset for Glycerophospholipids (GP)

SYNOPSIS

php GP_expand.php [none|chains] [ion type] [Minimum carbons in chain] [Maximum carbons in chain] [Maximum ratio of carbons in chain to double bonds]

DESCRIPTION

Generate a tabular output of glycerophospholipid species containing the species abbreviation, nominal mass, exact mass (or m/z if charged), molecular formula, ion type (if specified) by a combinatorial expansion of a user-specified range of chain lengths and chain-length-to-double-bond restrictions. The output is printed to standard output (screen) but may conveniently be saved to a tab-delimited file (e.g. "php GP_expand.php > GP_output.txt")

Headgroups

Glycerophospholipids with the following headgroups are enumerated: PA, PC, PS, PE, PI, PIP (phosphatidylinositol phosphate), PG.

OPTIONS

There are 5 optional command-line arguments:

1st argument: Display individual chains
Options: none | chains
Default:none

Specifying "chains" outputs the species abbreviation in a format showing each chain (e.g. PA(16:0/18:1) and additional columns for each chain (e.g 16:0 and 18:1)

Examples:

php GP_expand.php none > GP_output.txt
outputs data in the format:
674 674.4887 PA(34:1) 34 1 C37H71O8P A
Nominal m/z<tab>exact m/z<tab>abbreviation<tab>chain carbons<tab>chain double-bonds<tab>formula<tab>type(A:acyl;O:ether;P:plasmalogen)

php GP_expand.php chains > GP_output.txt
outputs data in the format:
674 674.4887 PA(16:0/18:1) 34 1 16:0 18:1 C37H71O8P A
Nominal m/z<tab>exact m/z<tab>abbreviation<tab>chain carbons<tab>chain double-bonds<tab>sn1 chain<tab>sn2 chain<tab>formula<tab> type(A:acyl;O:ether;P:plasmalogen)

2nd argument: Specify ion type
Options: neutral | M. | M+H | M+2H | M+3H | M+4H | M-H | M-2H | M-3H | M-4H | M+NH4 | M+Ag | M+Na | M+2Na | M+K | M+2K | M+Li | M+2Li | M.Cl | M.OAc | M-DFPU+NH4 | M-diDFPU+NH4
Default:neutral (uncharged)

Specifying an ion-type (other than neutral) adjusts the nominal m/z, exact m/z and molecular formula for each species.

Examples:

php GP_expand.php none neutral > GP_output.txt
outputs data in the format:
689 689.4996 PE(32:1) 32 1 C37H72NO8P A

php GP_expand.php none M-H > GP_output.txt
outputs data in the format:
688 688.4923 PE(32:1) 32 1 C37H71NO8P A [M-H]-

php GP_expand.php none M-2H > GP_output.txt
outputs data in the format:
343 343.7425 PE(32:1) 32 1 C37H70NO8P A [M-2H]2-

3rd and 4th arguments: Acyl chain length range
Options: Lower limit >=2, upper limit >lower limit (high values for upper limit will have a large impact on computation time and size of output)
Default:10 (lower), 34 (upper)
Note:The following alky-ether and vinyl-ether (plasmenyl) chains are also included independently:O-16:0, O-18:0, O-20:0, P-16:0, P-18:0, P-20:0. This list may be edited in the GP_expand.php script.

Examples:

php GP_expand.php none neutral 16 24 > GP_output.txt
outputs species composed of chains from C16 to C24:

php GP_expand.php none neutral 16 > GP_output.txt
outputs species composed of chains from C16 to C34 (upper default limit)

5th argument: Minimum ratio of chain carbons to double bonds allowed
Options: A positive number
Default:3.5

Values of 3.5 and above will preclude the presence of species with unrealistically large numbers of double bonds from a biosynthetic standpoint.

Example:

php GP_expand.php none neutral 16 24 3 > GP_output.txt
outputs species composed of chains from C16 to C24 with a minimum chain-length to double-bond ratio of 3

AUTHOR

Eoin Fahy

SEE ALSO

GL_expand.php, SP_expand.php, CL_expand.php

COPYRIGHT

Copyright (C) 2006-2014. The Regents of the University of California. All Rights Reserved.