make_every_XIC_MS1: make_every_XIC_MS1

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

Description

make_every_XIC_MS1

Usage

make_every_XIC_MS1(
  rawFileDir = NULL,
  rawFileName = NULL,
  targetSeqData = NULL,
  outputDir = getwd(),
  target_col_name = "UNIPROTKB",
  target_sequence_col_name = "ProteoformSequence",
  PTMname_col_name = "PTMname",
  PTMformula_col_name1 = "FormulaToAdd",
  PTMformula_col_name2 = "FormulaToSubtract",
  isoAbund = c(`12C` = 0.9893, `14N` = 0.99636),
  target_charges = c(1:50),
  mass_range = c(0, 1e+05),
  mz_range = c(600, 2000),
  abund_cutoff = 5,
  sample_n_pforms = NULL,
  XIC_tol = 5,
  use_IAA = FALSE,
  include_PTMs = TRUE,
  save_output = TRUE,
  scoreMFAcutoff = 0.3,
  cosinesimcutoff = 0.9,
  SN_cutoff = 20,
  resPowerMS1 = 3e+05,
  isotopologue_window_multiplier = 8,
  mz_window = 3,
  return_timers = TRUE,
  rawrrTemp = tempdir(),
  save_spec_object = TRUE
)

Arguments

rawFileDir	Directory containing target raw file.
rawFileName	Target raw file name.
targetSeqData	Path to target sequences data. Should be a .csv file.
outputDir	Path to output directory.
target_col_name	Name of column in target sequences data which contains unique identifiers for proteoforms to be identified.Defaults to "UNIPROTKB".
target_sequence_col_name	Name of column in target sequences data which contains the amino acid sequences of target proteoforms.Defaults to "ProteoformSequence".
PTMname_col_name	Name of column in target sequences data which contains names and positions of PTMs. Defaults to "PTMname".
PTMformula_col_name1	Name of column in target sequences data which contains chemical formulas for PTMs to be added to the formula of the bare proteoform sequence. Defaults to "FormulaToAdd".
PTMformula_col_name2	Name of column in target sequences data which contains chemical formulas for PTMs to be subtracted from the formula of the bare proteoform sequence. Defaults to "FormulaToSubtract".
isoAbund	Named numeric vector specifying abundances of isotopes to be used for generating theoretical isotopic distributions. See data(isotopes, package = 'enviPat') for isotope names. Defaults to c("12C" = 0.9893, "14N" = 0.99636).
target_charges	Numeric vector, length 2. Range of charges used to generate theoretical isotopic distributions.
mass_range	Numeric vector, length 2. Mass range used to filter the target sequences data on the basis of monoisotopic mass. Defaults to c(0, 100000) - effectively no filter.
mz_range	Numeric vector, length 2. m/z range used to filter putative theoretical isotopic distributions, i.e. only theoretical peaks in this m/z range will be considered. Defaults to c(600,2000).
abund_cutoff	Numeric vector, length 1. Controls the minimum relative abundance (compared to the theoretical highest abundance isotopologue) an isotopologue peak must have to be included in the search. Defaults to 5.
sample_n_pforms	Numeric vector, length 1. Number of proteoforms to randomly sample from the the target sequences data. Defaults to NULL.
XIC_tol	Numeric vector, length 1. Tolerance (in ppm) used to generate extracted ion chromatograms from theoretical isotopic distributions. Defaults to 5.
use_IAA	Boolean value. Controls whether proteoform sequences should be considered to be alkylated with iodoacetamide at all cysteine residues. Argument is passed to OrgMassSpecR::ConvertPeptide.
include_PTMs	Boolean value. Controls whether PTM chemical formulas are added when generating theoretical isotopic distributions. If false, ONLY the bare sequence is considered. Defaults to TRUE.
save_output	Boolean value. Controls whether output is saved to outputDir. Defaults to TRUE.
scoreMFAcutoff	Numeric vector, length 1. Minimum value of ScoreMFA for comparison of theoretical and observed isotopic distributions to be considered valid. Defaults to 0.3.
cosinesimcutoff	Numeric vector, length 1. Minimum value of cosine similarity (AKA dot product) for comparison of theoretical and observed isotopic distributions to be considered valid. Defaults to 0.9.
SN_cutoff	Numeric vector, length 1. Minimum allowed value for the estimated S/N of the observed isotopologue peak corresponding to the theoretical highest abundance isotopologue. Defaults to 20.
resPowerMS1	Numeric vector, length 1. Resolving power to be used with isotopologue_window_multiplier to determine size of the isotopologue window. USe resolving power at 400 m/z for best results.
isotopologue_window_multiplier	Numeric vector, length 1. After the width at half-max is estimated from resPowerMS1 at a particular m/z value, it is multiplied by this number to determine width of the isotopologue window. Defaults to 8.
mz_window	Numeric vector, length 1. Controls the width of the window used for the "specZoom" output which focuses on isotopic distributions of single charge states of single proteoforms. Defaults to 3.
return_timers	Boolean value. Controls whether the function returns a dataframe of timers (TRUE) or an R object containing the zoomed MS2 spectra (FALSE). Defaults to TRUE.
rawrrTemp	Path to temporary directory to be used by the rawrr package. Defaults to tempdir().
save_spec_object	Boolean value. Controls whether an R object containing the zoomed MS1 spectra is saved to the outputdir. Defaults to TRUE.

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