ms_fit: Match a set of peptides with a Mass Spec

In bioarch-sjh/bacollite: Analysis of MALDI and LC-MS/MS spectral data using sequence data (mainly for collagen)

Match a set of peptides with a Mass Spec

Description

Match a set of peptides with a Mass Spec

Usage

ms_fit(
  peptides,
  sample,
  doplot = T,
  force = F,
  vlevel = 0,
  corlim = 0,
  laglim = 0.6,
  gauss = NA,
  ionlim = NA,
  ignore_warnings = F,
  use_ms_iso = T
)

Arguments

peptides	the set of peptides, in bacollite format
sample	the MS sample data, in bacollite format - three replicates required
doplot	boolean to say if the fit should be plotted
force	boolean to say if *all* fits should be calculated, instead of just the good matches
vlevel	verbose level. 0 means no comments, 3 means full comments
corlim	threshold for correlation scores
laglim	threshold for lag scores
gauss	the level of gaussian smoothing. defaults to NA (no smoothing)
ionlim	the fraction of the highest intensity that is used to calculate the scaling limit for ms_align
ignore_warnings	whether to ignore the check for the input and calculated mass

Value

a dataframe holding the following fields:

hit	Whether a match was found for this peptide
lag1	The lag for sample 1
lag2	The lag for sample 2
lag3	The lag for sample 3
cor1	The correlation coefficient for sample 1
cor2	The correlation coefficient for sample 2
cor3	The correlation coefficient for sample 3
ion1	The proportion of total ions for this peptide in sample 1
ion2	The proportion of total ions for this peptide in sample 2
ion3	The proportion of total ions for this peptide in sample 3

bioarch-sjh/bacollite documentation built on Oct. 7, 2022, 3:34 p.m.