findEIC

msRaw

The mass or mass range to extract the EIC for: either a single mass
(with the range specified by <code>limit</code> below) or a mass range
in the form of <code>c(min, max)</code>.

If a single mass was given for <code>mz</code>: the mass window to extract.
A limit of 0.001 means that the EIC will be returned for <code>[mz - 0.001, mz + 0.001]</code>.

limit

If given, the retention time limits in form <code>c(rtmin, rtmax)</code> in seconds.

rtLimit

If present, the complete <code>mzR::header(msRaw)</code>. Passing
this value is useful if spectra for multiple compounds should be 
extracted from the same mzML file, since it avoids getting the data
freshly from <code>msRaw</code> for every compound.

headerCache

A fitting function that <code>predict()</code>s a mass shift based on the retention time. Can be used
if a lockmass calibration is known (however you have to build the calibration yourself.)

floatingRecalibration

If present, the complete output of <code>mzR::peaks(msRaw)</code>. This speeds up the lookup
if multiple compounds should be searched in the same file.

peaksCache


Extract EICs from raw data for a determined mass window.


Workflow to process tandem MS files and build MassBank records.
Functions include automated extraction of tandem MS spectra, formula
assignment to tandem MS fragments, recalibration of tandem MS spectra with
assigned fragments, spectrum cleanup, automated retrieval of compound
information from Internet databases, and export to MassBank records.

RMassBank at Eawag

RMassBank

Workflow to process tandem MS files and build MassBank records

findEIC function

The mass or mass range to extract the EIC for: either a single mass
(with the range specified by <code>limit</code> below) or a mass range
in the form of <code>c(min, max)</code>.

If a single mass was given for <code>mz</code>: the mass window to extract.
A limit of 0.001 means that the EIC will be returned for <code>[mz - 0.001, mz + 0.001]</code>.

If present, the complete <code>mzR::header(msRaw)</code>. Passing
this value is useful if spectra for multiple compounds should be 
extracted from the same mzML file, since it avoids getting the data
freshly from <code>msRaw</code> for every compound.

A fitting function that <code>predict()</code>s a mass shift based on the retention time. Can be used
if a lockmass calibration is known (however you have to build the calibration yourself.)

If present, the complete output of <code>mzR::peaks(msRaw)</code>. This speeds up the lookup
if multiple compounds should be searched in the same file.

Extract EICs from raw data for a determined mass window.

findEIC: Extract EICs

Description

Usage

Arguments

Value

See Also