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Filter a PSM-level summarizedExperiment to remove low quality PSMs

filter_TMT_PSMs.Rd

Filter PSMs from TMT quantification to remove the following:

  1. Missing values (NA) for all tags

  2. Interference/co-isolation above a set value (default=100, e.g no filtering)

  3. Signal:noise ratio below a set value (default=0, e.g no filtering)

  4. SPS-MM below a set value (default=0, e.g no filtering)

  5. Quan.Info is not empty (”)

  6. PSM.Ambiguity is not 'Selected' or 'Unambiguous'

Usage

filter_TMT_PSMs(
  obj,
  inter_thresh = 100,
  sn_thresh = 0,
  spsmm_thresh = 0,
  master_protein_col = "Master.Protein.Accessions",
  inter_col = "Isolation.Interference.in.Percent",
  sn_col = "Average.Reporter.SN",
  spsmm_col = "SPS.Mass.Matches.in.Percent",
  from_PD = TRUE,
  verbose = TRUE
)

Arguments

obj

summarizedExperiment. Should contain PSMs-level TMT quantification

inter_thresh

numeric. Maximum allowed interference/co-isolation

sn_thresh

numeric. Minimum allowed average signal:

spsmm_thresh

numeric. Minimum allowed value for Synchronous precursor selection mass matches (%) - SPS-MM, e.g the percentage of MS3 fragments that can be explicitly traced back to the precursor peptides

master_protein_col

string. Name of column containing master proteins.

inter_col

string. Name of column containing the interference value.

sn_col

string. Name of column containing the signal:noise value.

spsmm_col

string. Name of column containing the SPS-MM value.

from_PD

logical. Input is from ProteomeDiscover. If set, will filter using Quan.Info and PSM.Ambiguity columns. Default is TRUE

verbose

logical. Default is TRUE, use verbose output messages.

Value

Returns an summarizedExperiment with the filtered PSMs.