Preprocess Proteome Discoverer TMT exports

Converts a Proteome Discoverer protein export (wide TSV format, with Abundance: <Condition>_<Replicate> columns) into the same output structure as preprocess_spectronaut(): three data.frames (metadata, protein_id, protein_quant) ready for the downstream pipeline (process_proteomics() and the associated modules).

The global PD identification metrics (# PSMs, # Peptides, # Unique Peptides, Coverage [%]) are replicated into per-channel columns to fit the wide Spectronaut contract.

Usage

preprocess_tmt(
  file_path,
  condition_order,
  annot_path = NULL,
  export_dir = NULL,
  timestamp_suffix = TRUE,
  verbose = TRUE
)

Arguments

file_path

Path to the TSV exported from Proteome Discoverer.

condition_order

Character vector with the order of the experimental conditions (e.g. c("A","B","D","IS")). Only the channels whose condition is in this vector are kept – handy for excluding Internal Standards by omitting "IS". Conditions listed but absent from the report are dropped, with a warning, so that no empty factor level reaches the metadata.

annot_path

Path to a sample sheet with columns Column and Condition, for reports whose channels are not named <Condition>_<Replicate> – an export left with the TMT tags, 126, 127N and so on. Column holds the text after Abundance: . If NULL (default), the design comes from the suffixes. Any other column in the sheet is ignored – batch structure belongs in covariate_df of process_proteomics(), see vignette("batch-correction").

export_dir

Directory to export the TSV files to. If NULL (default), no files are exported.

timestamp_suffix

Logical. If TRUE (default), appends a timestamp to the names of the exported files.

verbose

Logical. If TRUE (default), shows progress messages.

Value

A list with class c("tmt_data", "proteomics_data", "list") containing:

metadata

Data frame with one record per channel/sample

protein_id

Data frame with the identification metrics per protein (wide format, global metrics replicated per channel)

protein_quant

Data frame with the quantification metrics per protein (includes PG.Quantity_<Coding>)

The call that produced the object and a fingerprint of the file it was read from (path, size, modification time and MD5) travel with it as the attributes nadia_call and nadia_source. They are attributes rather than list elements so that the three-element structure above is unchanged; write_nadia() records them as the provenance of an analysis.

Examples

# A trimmed Proteome Discoverer TMTpro report ships with the package: three
# conditions of eight replicates, split across two TMT mixes (replicates 1-4
# are the first mix, 5-8 the second) and bridged by four "IS" channels.
report <- system.file("extdata", "nadia_tmt_report.tsv.gz", package = "NADIA")

# condition_order is required, and doubles as a filter: the report also holds
# an "IS" channel (internal standards) that is left out by not listing it
tmt <- preprocess_tmt(report,
                      condition_order = c("A", "B", "D"),
                      verbose = FALSE)
tmt
#> Preprocessed TMT (Proteome Discoverer) data
#> ------------------------------------------
#> Channels (metadata): 24 
#> Proteins (ID): 2000 
#> Proteins (QUANT): 2000 
#> 
#> Conditions: A, B, D 
table(tmt$metadata$R.Condition)
#> 
#> A B D 
#> 8 8 8