get_xic: Get the Extracted Ion Chromatogram object "xic"

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

Get the Extracted Ion Chromatogram object "xic"

Description

Pulls the intensity and retention times for each isotope and adjacent charge state.

Usage

get_xic(
  ScanMetadata,
  MZ,
  RTRange,
  IsotopeNumber = c(0:5),
  Charges = c(1:3),
  XICTol = 1000,
  Messages = TRUE
)

Arguments

ScanMetadata	Object of the scan_metadata class from get_scan_metadata. Required.
MZ	The mz value to extract the ion chromatogram. Required.
RTRange	The retention time range to pull isotope and charge values from. It should be a vector of length two with the min and max RT in minutes. Required.
IsotopeNumber	A vector of isotopes to plot. 1 indicates M+1, etc. The max isotopes is 5, ranging from 0 to 5 where 0 is the non-isotope peak. Default is 0:5.
Charges	A vector indicating which charges to plot. There is a max of 3, ranging from 1-3. Default is 1:3.
XICTol	The tolerance for XIC, used only with raw data.
Messages	Should progress messages be printed? Default is TRUE.

Details

The data.table outputted by this function contains 16 main columns of data from both the MS and ID file.

Charge	The charge (Z) state for each trace of the XIC.
Isotope	Written as "M+n", the n is indicative of each successive isotope after the fragment, where the fragment is M+0 or 0.
Intensity	The intensity at the given m/z and retention time range.
RT	The retention time

Examples

## Not run: 

# Test with bottom up data
xictest1 <- get_xic(ScanMetadata = BU_ScanMetadata, MZ = 659.8596, RTRange = c(58, 60))

# Test with top down raw data
xictest2 <- get_xic(ScanMetadata = RAW_ScanMetadata, MZ = 669.8381, RTRange = c(0, 1))


## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.