make_every_XIC_MS2_single: make_every_XIC_MS2_single

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

Description

make_every_XIC_MS2_single

Usage

make_every_XIC_MS2_single(
  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` = 0.9889, `14N` = 0.99636),
  fragment_charges = c(1:50),
  fragment_types = c("b", "y"),
  fragment_mz_range = c(300, 2000),
  fragment_pos_cutoff = c(1, 50),
  abund_cutoff = 5,
  XIC_tol_MS2 = 10,
  XIC_cutoff = 1e-09,
  use_IAA = FALSE,
  include_PTMs = TRUE,
  scoreMFAcutoff = 0.3,
  cosinesimcutoff = 0.975,
  SN_cutoff = 20,
  resPowerMS2 = 150000,
  isotopologue_window_multiplier = 6,
  mz_window = 5,
  rawrrTemp = tempdir(),
  save_spec_object = FALSE
)

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.
isoAbund	Named numeric vector specifying abundances of isotopes to be used for generating theoretical isotopic distributions. See data(isotopes, package = 'enviPat') for isotope names.
fragment_charges	Numeric vector. Range of charges used to generate fragment libraries. Argument passed to MSnbase::calculateFragments.
fragment_types	Character vector. Types of fragments to be included in generation of fragment libraries. Argument passed to MSnbase::calculateFragments.
fragment_mz_range	Numeric vector, length 2. Range of m/z values to use for filtering fragment libraries. Fragments whose theoretical m/z values are outside of this range will be removed before analysis.
fragment_pos_cutoff	Numeric vector, length 2. Range of fragment positions, or lengths, to be used for generating fragment libraries.
abund_cutoff	Numeric vector, length 1. Controls the minimum relative abundance (compared to the theoretical highest abundance isotopologue) a fragment isotopologue peak must have to be included in the search. Defaults to 5.
XIC_tol_MS2	Numeric vector, length 1. Tolerance (in ppm) used to generate extracted ion chromatograms from theoretical isotopic distributions. Defaults to 5.
XIC_cutoff	Numeric vector, length 1.
use_IAA	Boolean value. Controls whether fragments 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 for fragments. If false, ONLY the bare fragment sequence is considered. Defaults to TRUE.
scoreMFAcutoff	Numeric vector, length 1. Minimum value of ScoreMFA for comparison of theoretical and observed isotopic distributions to be considered valid.
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.
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.
resPowerMS2	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 resPowerMS2 at a particular m/z value, it is multiplied by this number to determine width of the isotopologue window.
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 fragments.
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 MS2 spectra is saved to the outputdir. Defaults to FALSE.

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