Experimental Input
File type
Plain text. (Save Excel files as ‘Tab Delimited Text’.)
Identifier Line (M/z input)
The first line should consist of the following tab-separated items:
mode_charNo. base:expt name1 name2 name3 (etc.)
where:
mode_char = ‘P’, ‘N’, or ‘U’ for positive, negative or neutral mode.
No. = number of conditions in the experiment
base = condition number of base of comparison (100%)
expt = condition number for change to be flagged in colour
name1 etc = names of conditions (for labelling bar charts)
N.B. It is unwise to try to insert this line in Excel as it will mangle the term with the colon.
Identifier Line (Kegg ID input)
The first line should consist of the following tab-separated items:
CNo. base:expt name1 name2 name3 (etc.)
where:
CNo. = Upper-case C followed by number of conditions (e.g. C3)
Everything else is exactly as for M/z input.
Identifier Line (MetaCyc UID input)
The first line should consist of the following tab-separated items:
MNo. base:expt name1 name2 name3 (etc.)
where:
MNo. = Upper-case M followed by number of conditions (e.g. M3)
Everything else is exactly as for M/z input.
Data Lines (M/z input)
Each data line should be tab-separated and of the form:
Mz cond1 cond2 cond3 SE1 SE2 SE3
where:
Mz is the M/z value.
cond1 etc = are the peak intensity values for the experimental conditions
SE1 etc = are the standard errors for the experimental conditions
N.B. As a minimum, two conditions are required, but there is no maximum. Data lacking Standard Errors will still be analysed: the program will insert SE values of 0.
Data Lines (Kegg ID input)
Each data line should be tab-separated and of the form:
ID cond1 cond2 cond3 SE1 SE2 SE3
where:
ID is the Kegg ID assigned by the user.
Everything else is exactly as for M/z input.
Data Lines (MetaCyc UID input)
Each data line should be tab-separated and of the form:
UID cond1 cond2 cond3 SE1 SE2 SE3
where:
UID is the MetaCyc UID assigned by the user.
Everything else is exactly as for M/z input.
Example
An example file for M/z input, ‘exptmz.txt’ can be found in the folder of examples (in ‘Downloads’). The first few lines are as follows:
U2 1:2 wt mutant 115.0632802 1450 175000 1560 26000 228.1108135 1720 7770 1550 2190 307.0834627 25000 92600 13600 45200 188.1159052 400000 1430000 133000 348000 147.0530695 508000 1510000 165000 330000 129.0424718 17000 28200 8130 13600
The identifier line indicates that the data have been converted to neutral mode, and that there are two conditions, the first (wt) being the base and the second (mutant) being the experimental one of interest.