xcms2method: Convenience method to go from XCMS peak tables or diffreports...

In sneumann/MetShot: High throughput prioritized acquisition and processing of tandem mass spectra

Description

This convenience method will create (a set of) Bruker method files from a template, filling it with tandem mass spectrometry target segments for the "interesting" peaks in the peak list

Usage

peaklist2picklist(anyPeaklist, gradientStart = NULL, gradientEnd = NULL,
widthFactor = 1, minWidth = 1, fillGaps=TRUE)

xcms2method(peaklist, methodPrefix = "",
            MSmode = c("positive", "negative"),
            template = "test.m/microTOFQAcquisition.method",
            gradientStart = NULL, gradientEnd = NULL,
            widthFactor = 1, minWidth = 1,
            MSMSManual_ListCollisionEnergy = 15,
            MSMSManual_ListIsolationWidth = 8)

picklist2method(pickList, methodPrefix = "",
                MSmode = c("positive","negative"),
                template = "test.m/microTOFQAcquisition.method",
                MSMSManual_ListCollisionEnergy = 15,
                MSMSManual_ListIsolationWidth = 8,
                instrumentprefix = "qtofacq")

picklists2methods(pickLists, methodPrefix = "", ...)

picklist2Agilent(pickList, filename="TargetedMSMSTable.csv", 
                 delta_ret_time=10,
                 iso_width=c("Narrow (~1.3 m/z)", "Medium (~4 m/z)"),
                 MSMSManual_ListCollisionEnergy = 20)

picklist2waters(pickList,
                methodPrefix="",
                MSmode=c("positive","negative"),
                template=NULL,
                MSMSManual_ListCollisionEnergy=15,
                TOFConeVoltage=NULL,
                lockMassMZ=NULL)

picklists2waters(pickLists, methodPrefix="", ...)

Arguments

peaklist	Eith a peak list with columns rtmin/rt/rtmax and mzmin/mz/mzmax or a diffreport.
anyPeaklist	Eith a peak list with columns rtmin/rt/rtmax and mzmin/mz/mzmax or a diffreport.
pickList	A picklist is XXX.
pickLists	A list of pickLists.
methodPrefix	Outfile prefix for the created method(s)
filename	Outfilename for the created method
MSmode	Polarity of the requested tandem MS measurement
template	A Bruker *.m template file
gradientStart	if present, only use peaks later than this minimum retention time (in seconds)
gradientEnd	if present, only use peaks before this maximum retention time (in seconds)
widthFactor	enlarge the precursor peaks by this factor for the target windows
minWidth	Ensure a minimum retention time window for the target windows
fillGaps	If set to TRUE, then adjacent segments will be enlarged so that they meet "in the middle", otherwise if FALSE then rtmin and rtmax are unchanged
MSMSManual_ListCollisionEnergy	Specify one or more collision energies to use
MSMSManual_ListIsolationWidth	Specify one or more isolation widths to use
iso_width	For Agilent, the requested Isolation width specification.
delta_ret_time	For Agilent.
instrumentprefix	The XML tags inside the Bruker method files depend on the instrument, so for the micrOTOFq use "qtofacq", or for the maXis "qtofmaxacq".
TOFConeVoltage	Specific to Waters
lockMassMZ	Specific to Waters
...	The picklists2something() wrapper methods will pass the ... arguments to the corresponding picklist2something() method.

Details

Prioritizes by what ?

Warning

The created Bruker control files are not guaranteed to work on your setup, and incorrect control files could damage equipment.

Author(s)

Steffen Neumann

See Also

plotMS2windows

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

sneumann/MetShot documentation built on May 30, 2019, 5:05 a.m.