Table 4.

Types of input to the DIA reanalysis pipeline implemented in Nextflow.

Analysis pipeline inputs

An iRT file in OpenSWATH conformant .TraML format

A collection of .wiff/.scan files (alternatively pre-processed .osw files)

Target library file in OpenSWATH conformant.tsv format (alternatively a prepared .pqp file)

Study design annotation in MSstats conformant format and SDRF format (.txt/.sdrf)

Parameter .yaml file (in case the defaults need to be changed)

Output upstream Nextflow

FDR filtered alignment results of transition quantifications (.tsv)

QC records for each MS run (.json)

Output downstream Nextflow

MSstats analysis object (.rda)

Dataset analysis report (.pdf)

Prefiltered Expression Atlas upload input (.tsv)