add_isotope_features: Extend IceR features by expected +1-isotopic features

In mathiaskalxdorf/IceR: Requantification of label-free DDA proteomics data pre-analyzed by MaxQuant.

Extend IceR features by expected +1-isotopic features

Description

Extend IceR features by expected +1-isotopic features

Usage

add_isotope_features(
  path_to_features,
  feature_table_file_name = "Features_aligned_merged_IceR_analysis.txt",
  min_observations = 0
)

Arguments

path_to_features	Path to folder where results of align_features() are stored.
feature_table_file_name	File name which contains align_features() results. By default is set to Features_aligned_merged_IceR_analysis.txt.
min_observations	Specifying how many MaxQuant features had to be previously detected for monoisotopic IceR features to be extended by +1-isotopic features. By default set to 0 indicating that all for all monoisotopic IceR features a +1-isotopic feature is added.

Details

Optional step of the IceR workflow appending the list of IceR features by respective expected +1-isotopic features. Isotopic features are expected to show an m/z shift by +1.002 Da/z relative to the monoisotopic IceR feature. Only IceR features with at least min_observations and with mean Andromeda score > 25

Value

Extended list ist stored in the specified feature_table_file_name.

mathiaskalxdorf/IceR documentation built on Aug. 1, 2022, 8:03 a.m.