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
  - Predicted libraries output from DIA-NN:
  - Empirical, curated libraries:
Tutorial on searching plexDIA data
Data pipelines for optimizing and processing 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:

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

Empirical, curated libraries:

Human, 100 cells of PDAC, melanoma, and monocytes from Q-Exactive & corresponding Human FASTA (source: Derks et al, 2022)
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.

Download Slides

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.