Skip to contents

Filter MaxQuant DDA output

filter_features_mq_dda.Rd

This function filters the output .txt files (peptide groups or PSMs) from Proteome Discoverer for DDA, based on various criteria:

  1. Remove features without a master protein

  2. Remove features without a unique master protein (i.e. Number.of.Protein.Groups == 1)

  3. Remove features matching a contaminant protein

  4. Remove features matching any protein associated with a contaminant protein (see below)

  5. Remove features without quantification values

Usage

filter_features_mq_dda(
  obj,
  master_protein_col = "Leading.razor.protein",
  protein_col = "Proteins",
  unique_master = TRUE,
  filter_contaminant = TRUE,
  contaminant_proteins = NULL,
  filter_associated_contaminant = TRUE,
  remove_no_quant = TRUE
)

Arguments

obj

SummarisedExperiment containing output from MaxQuant. Use readQFeatures to read in .txt file

master_protein_col

string. Name of column containing master proteins.

protein_col

string. Name of column containing all protein matches.

unique_master

logical. Filter out features without a unique master protein.

filter_contaminant

logical. Filter out features which match a contaminant protein.

contaminant_proteins

character vector. The protein IDs form the contaminant proteins

filter_associated_contaminant

logical. Filter out features which match a contaminant associated protein.

remove_no_quant

logical. Remove features with no quantification

Value

Returns a SummarisedExperiment with the filtered MaxQuant output.

Details

Associated contaminant proteins are proteins which have at least one feature shared with a contaminant protein. It has been observed that the contaminant fasta files often do not contain all possible contaminant proteins e.g. some features can be assigned to a keratin which is not in the provided contaminant database.

In the example below, using filter_associated_contaminant = TRUE will filter out f2 and f3 in addition to f1, regardless of the value in the Leading.razor.protein column.

feature  Proteins                          Leading.razor.protein
f1       protein1, protein2, contaminant,  protein1
f2       protein1, protein3                protein3
f3       protein2                          protein2