LIPID MAPS mass spectrometry combinatorial expansion package

NAME

CL_expand.php - Generate a combinatorial dataset for Cardiolipins (GP)

SYNOPSIS

php CL_expand.php [none|chains] [ion type]

DESCRIPTION

Generate a tabular output of cardiolipin 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 CL_expand.php > CL_output.txt")

List of chains

The list of chains used to enumerate the cardiolipin species is as follows:10:0, 12:0, 14:0, 14:1, 16:0, 16:1, 18:0, 18:1, 18:1, 18:2, 18:3, 18:4, 20:0, 20:1, 20:2, 20:3, 20:4, 20:5, 22:0, 22:1, 22:2, 22:4, 22:5, 22:6, 24:0, 24:1, 24:2, 24:3, 24:4, 24:5, 24:6, 26:0, 26:1, 26:2, 26:3, 26:4, 26:5, 26:6, 28:0, 30:0, 32:0, 34:0, 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 CL_expand.php to alter the set of enumerated cardiolipin species. In contrast to the glycerophospholipid and glycerolipid scripts which compute all possible acyl chains over a a defined length range (e.g. C10 to C34) and with a carbon-chain to double-bond ratio exceeding a defined limit (e.g 3.5), the cardiolipin script uses a much smaller set of chains to avoid creating unsuitably large sets of species due to the fact that these structures contain 4 chains and 4ⁿ permuations from a list of n input chains.

OPTIONS

There are 2 optional command-line arguments:

[none|chains]: Default:none
[ion type]: Default:neutral (uncharged)

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

Specifying "chains" outputs the species abbreviation in a format showing each chain (e.g. CL(16:0/18:1/18:0/20:0) and additional columns for each chain (e.g 16:0,18:1,18:0,20:0)

Examples:

php CL_expand.php none > CL_output.txt
outputs data in the format:
1260 1260.8157 CL(58:4) 58 4 C67H122O17P2 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 CL_expand.php chains > CL_output.txt
outputs data in the format:
1260 1260.8157 58 4 CL(16:0/20:4/10:0/12:0) 16:0 20:4 10:0 12:0 C67H122O17P2 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 CL_expand.php none neutral > CL_output.txt
outputs data in the format:
1260 1260.8157 CL(58:4) 58 4 C67H122O17P2 A

php CL_expand.php none M-H > CL_output.txt
outputs data in the format:
1259 1259.8084 CL(58:4) 58 4 C67H121O17P2 A [M-H]-

AUTHOR

Eoin Fahy