Analyzing plexDIA data


This section organizes libraries, tutorials and links to software and pipelines for searching, optimizing and analyzing plexDIA data.


Searching plexDIA data

Libraries for searching plexDIA data

These libraries are for searching spectra from mTRAQ-labeled peptides. All libraries and FASTAs below include canonical and isoform protein sequences from Swissprot.

Predicted libraries output from DIA-NN:

  1. Human, Yeast, E. coli & corresponding Human, Yeast, E. coli FASTA (source: Derks et al, 2022)

  2. Human & corresponding Human FASTA (source: Derks et al, 2022)

Empirical, curated libraries:

  1. Human, 100 cells of PDAC, melanoma, and monocytes from Q-Exactive & corresponding Human FASTA (source: Derks et al, 2022)
  2. Human, THP-1 macrophages from timsTOF SCP & corresponding Human FASTA (source: manuscript in preparation Derks et al, 2023)


Tutorial on searching plexDIA data

Searching plexDIA data with DIA-NN is described in this tutorial. The tutorial is for DIA-NN v1.8.1 and searching with later versions of DIA-NN has some changes.

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These detailed methods are from: Derks, J., Leduc, A., Wallmann, G. et al. Increasing the throughput of sensitive proteomics by plexDIA. Nat Biotechnol (2022). 10.1038/s41587-022-01389-w, Preprint, Nature Research Briefing


Data pipelines for optimizing and processing plexDIA data

A pipeline for analyzing plexDIA data and reproducing the analysis by Derks et al are available at the plexDIA GitHub repository.