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EICExtractor

Extracts EICs from an MS experiment, in order to quantify analytes at a given position

pot. predecessor tools $ \longrightarrow $ EICExtractor $ \longrightarrow $ pot. successor tools
FileConverter statistical tools, e.g., Excel, R, ...

Use this instead of FeatureFinder, if you have bad features which are not recognized (much noise etc) or if you want to quantify non-peptides.

The EDTA file will specify where to search for signal. Retention time is in seconds [s]. 'int' and 'charge' are ignored but need to be present. However, you MUST specify a 'rank' column. Rows with equal rank are summed up in intensity (e.g. useful if you have charge variants you want to sum up to enhance quantitation robustness). Each rank represents a so called Master Compound, which constists of one or more sub compounds. If you do not require ranks, give each row a unique number, e.g. start numbering from 1 to n.

The intensity reported is the MAXIMUM intensity of all peaks each within the given tolerances for this row's position.

Example:

RT	m/z	int	charge	rank
19.2	431.8599024	0	0	1
21	678.7729237	0	0	2
25	660.7629237	0	0	2
59.2	431.8599024	0	0	3

Here, rows 2 and 3 will be summed up, as they have the same rank.

As output, two files in text format are given. The detail file gives RT and m/z deltas from expected to identified signal position etc, the sum file represents the master compounds.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 1.11.1 Documentation generated on Sun Sep 7 2014 06:42:38 using doxygen 1.8.8