README.md

In davidsbutcher/meXICan-spectrum: Generate XICs and MS for a set of search sequences

GEX

Generate XICs and mass spectra for theoretical charge states of target protein sequences with or without isotopic depletion or carbamidomethylation.

Installation

Install from GitHub:

remotes::install_github("davidsbutcher/GEX")

Usage

The main functionality of the package is split into two functions, make_every_XIC and make_every_spectrum. The output of make_every_XIC must be used for make_every_spectrum.

Arguments to make_every_XIC

Mandatory

• rawFileDir Character vector, length 1. Directory containing the raw file to be searched. Can be any level above the raw file in the directory structure.

• rawFileName Character vector, length 1. Full name of the raw file to be searched including extension.

• targetSeqData Character vector, length 1. Full or relative path to the csv file containing the target sequences. The csv must have columns specifying name, proteoform sequence, PTM name, PTM formula to add and PTM formula to subtract. See input/example_sequences.csv for an example. Column names should be UNIPROTKB, ProteoformSequence, PTMname, FormulaToAdd, and FormulaToSubtract unless specified otherwise using optional arguments.

Optional

• outputDir Character vector, length 1. Directory to place output results. A new directory will be created in outputDir providing the date and time of the analysis, raw file name, number of sequences searched, and whether depleted isotopes were used.

• mz_range Numeric vector, length 2. Range of m/z values to use for filtering theoretical isotopic distributions. Should most likely be set to m/z range of MS1 scans in raw file. Defaults to 600 - 2000.

• use_depleted_isotopes Boolean value (TRUE or FALSE). Determines whether depleted isotopic abundances are used to generate theoretical isotopic distributions. Defaults to FALSE.

• mass_range Numeric vector, length 2. Mass range of proteoforms from input csv to include in search. This range is compared to monoisotopic masses calculated from the proteoform sequence. Defaults to 0 - 100,000.

• abund_cutoff Numeric vector, length 1. Percentage cutoff for relative abundance of theoretical isotopologues - all theoretical isotopologues with relative abundance (compared to most abundant isotopologue at 100%) lower than this value are truncated prior to XIC generation. Defaults to 5.

• XIC_tol Numeric vector, length 1. Tolerance (in ppm) to use for generation of XICs from theoretical isotopic distributions. Defaults to 2. Can be set higher for non-complex samples.

• use_IAA Boolean value (TRUE or FALSE). Determines whether cysteines in target sequences should be considered carbamidomethylated when generating chemical formulas prior to calculating theoretical isotopologue m/z values. Note that this is an all-or-nothing parameter, with no option for partial carbamidomethylation. Defaults to FALSE.

• target_charges Numeric vector, length 2. Specified what range of charge states to use for calculation of theoretical isotopic distributions. Defaults to 1 - 50.

• target_col_name Character vector, length 1. Allows the name of the target sequences name column from the input csv to be specified. Defaults to UNIPROTKB.

• target_sequence_col_name Character vector, length 1. Allows the name of the target sequences proteoform sequence column from the input csv to be specified. Defaults to ProteoformSequence.

• PTMname_col_name Character vector, length 1. Allows the name of the target sequences PTM name column from the input csv to be specified. Defaults to PTMname.

• PTMformula_col_name1 Character vector, length 1. Allows the name of the target sequences PTM formula to add column from the input csv to be specified. Defaults to FormulaToAdd.

• PTMformula_col_name2 Character vector, length 1. Allows the name of the target sequences PTM formula to subtract column from the input csv to be specified. Defaults to FormulaToSubtract.

Arguments to make_every_spectrum

The only mandatory argument to make_every_spectrum is the output from make_every_XIC, which should be the first argument (see example below).

Optional

• mz_window Numeric vector, length 1. Size of m/z window to use in generation of zoomed mass spectra. Defaults to 3.

Example run with minimal arguments

library(GEX)

XIC_output <-
   make_every_XIC(
      rawFileDir = "C:/Users/dbutcher/Documents/raw_files",
      rawFileName = "example_file.raw",
      targetSeqData = "input/example_sequences.csv",
      outputDir = "C:/Users/dbutcher/Documents/GEX_output"
   )

GEX_timer <-
   make_every_spectrum(
      XIC_output
   )

davidsbutcher/meXICan-spectrum documentation built on Sept. 1, 2021, 1:35 p.m.