LIPID MAPS mass spectrometry combinatorial expansion package

NAME

SP_expand.php - Generate a combinatorial dataset for sphingolipids (SP)

SYNOPSIS

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

DESCRIPTION

Generate a tabular output of sphingolipid 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 SP_expand.php > SP_output.txt")

Headgroups

Sphingolipids with the following headgroups are enumerated: Cer, SM, CerP, HexCer.

List of chains

The list of long-chain bases and N-acyl chains used to enumerate the sphingolipid species is as follows:
Long-chain bases:m14:0, m14:1, d14:1, d14:0, d14:2, t14:0, t14:1, m15:0, m15:1, d15:1, d15:0, d15:2, t15:0, t15:1, m16:0, m16:1, d16:1, d16:0, d16:2, t16:0, t16:1, m17:0, m17:1, d17:1, d17:0, d17:2, t17:0, t17:1, m18:0, m18:1, d18:1, d18:0, d18:2, t18:0, t18:1, m19:0, m19:1, d19:1, d19:0, d19:2, t19:0, t19:1, m20:0, m20:1, d20:1, d20:0, d20:2, t20:0, t20:1, m21:0, m21:1, d21:1, d21:0, d21:2, t21:0, t21:1, m22:0, m22:1, d22:1, d22:0, d22:2, t22:0, t22:1.
N-acyl chains:12:0, 13:0, 14:0, 14:0h, 15:0, 15:0h, 16:0, 16:1, 16:0h, 16:1h, 17:0, 17:0h, 18:0, 18:1, 18:0h, 18:1h, 19:0, 19:0h, 20:0, 20:1, 20:0h, 20:1h, 21:0, 21:0h, 22:0, 22:1, 22:0h, 22:1h, 23:0, 23:0h, 24:0, 24:1, 24:0h, 24:1h, 25:0, 25:0h, 26:0, 26:1, 26:0h, 26:1h, 27:0, 27:0h, 28:0, 28:0h, 29:0, 29:0h, 30:0, 30:0h, 31:0, 31:0h, 32:0, 32:0h, 33:0, 33:0h, 34:0, 34:0h.
Syntax of LCB abbreviations: [number of hydroxyl groups][number of carbons]:[number of double bonds] e.g d18:1 = sphingosine (2 hydroxyl groups and 1 double bond); m18:0 = 1-deoxy sphiganine; t18:1 = phytosphingosine.
Syntax of N-acyl abbreviations: [number of carbons]:[number of double bonds][hydroxyl group in chain] e.g 26:0h = saturated C26 chain containing a hydroxyl group.
This list may be edited in the SP_expand.php to alter the set of enumerated sphingolipid species.

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. Cer(d18:1/18:0))

Examples:

php SP_expand.php none > SP_output.txt
outputs data in the format:
565 565.5434 Cer(d36:1) Cer 36 1 C36H71NO3
Nominal m/z<tab>exact m/z<tab>abbreviation<tab>headgroup<tab>chain carbons<tab>chain double-bonds<tab>hydroxyl group in chain(h)<tab>formula

php SP_expand.php chains > SP_output.txt
outputs data in the format:
565 565.5434 Cer(d18:1/18:0) Cer 36 1 C36H71NO3
Nominal m/z<tab>exact m/z<tab>abbreviation<tab>headgroup<tab>chain carbons<tab>chain double-bonds<tab>hydroxyl group in chain(h)<tab>formula

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 SP_expand.php none neutral > SP_output.txt
outputs data in the format:
565 565.5434 Cer(d36:1) Cer 36 1 C36H71NO3

php SP_expand.php none M+H > SP_output.txt
outputs data in the format:
566 566.5507 Cer(d36:1) Cer 36 1 C36H72NO3 [M+H]+

AUTHOR

Eoin Fahy