A short script to use the nontarget pattern.match function to print useful information about clusters.
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1.9 KiB

Specifications for the script

Use the Nontarget

  • Clusters should have large enough number of fragments (3+ maybe)

  • nontarget has a pattern match function.

  • Check for chlorinated compounds (has n+2, n+4, ...)

  • GPL License (good)

  • Script to get output for all of the results

  • tabbed-deliminated text file

  • Which clusters contain chlorinated compounds, how many fragments, what other isotopes.

format

  • Readable by R.
  • Manipulatable by Tidyverse
  • Include it in script?

Additional Notes

  • Independent of the ordering (it might get corrupted)

  • Just search for chlorinated/brominated compounds.

  • Use intensity + relative abundances that isos shows.

  • usually, use_charges will be 1

  • Headers to use in script.

  • Packages to do things in parallel (multiple threads)

  • be able to configure the number of cores or threads used.

  • make it a requirement to be tab-deliminated.

  • eliminate clusters with only m/z.

Notes

  • cutint represents high enough intensity.

  • mztol is in terms of ppm.

  • mzfrac is in terms of absolute.

  • PPM = true always

  • First pass - (identify all of the fragments where chlorinated/brominated compounds are found and carbon)

  • If isotopes exist, which ones have chlorines/bromines...

  • return a data frame.

  • No statistical testing required (check if it is chlorine or bromine)

  • Isotopes to check (Carbon, Sulfur, Chlorine, Bromine all have n+2) (check make.isos object)

  • Tweak parameters (but also put them into a slideshow/record, see how good the results are).

  • set all rules to false

Isotopes

  • These isotopes will tend to have different intensities
  • Part of the reasoning can be attributed to differences.
  • Forseeable future, adapt to different isotopes.
  • Capture multiple outputs of different isotopes.

Data Summary

  • Flags for certainty of halogenated compounds

Test Notes

  • mztol seems to have a big impact on chlorine/bromine positives.