SWATH-MS

SWATH-MS work

Acronym of Sequential Window Acquisition of all Theoretical mass spectrometry (SWATH-MS) / data independent acquisition (DIA)

• swath-ms.R (swath-ms.ini) and swath-ms.sh perform data proceessing and exploratory analysis. From this, we have
  • utils/qctool.sh attempts to extract genotype/sample information into a single .bgen file gives way to qctool.sb for its speed.
  • utils/quicktest.sb is SLURM version of QUICKTEST.
  • utils/quicktest.sh is non-SLURM version of QUICKTEST.
  • utils/plink2.sb is SLURM version of PLINK2.
  • utils/plink2.sh non-SLURM version of PLINK2.
  • utils/check.R attempts to check for consistence with Caprion.
  • utils/affymetrix.sh performs the association analysis on specific protein-variant combinations.
  • utils/pgwas.sh (utils/pgwas.ini) conducts genomewide associations analyses on all proteins. Note that
    • BOLT-LMM took 24hr for one protein from all data (N=43,059) but failed to run on available genotypes and samples (N=196). It also uses 8-bit version of bgen (qctool -bgen-bits 8 and also the master genotype files).
    • PLINK2 is attractive with its speed.
    • QUICKTEST is faster than SNPTEST and takes into account uncertainty, and is therefore more preferable.
    • SNPTEST gives verbose screen output with -printids.
  • utils/sentinels_nold.sh and utils/merge.sh performs sentinel selection.
• swath-ms.ipynb is a Jupyter notebook with some preprocessing done by utils/tensorqtl.sh.

Therefore with the eventual option of pilot samples plut genotypes with an MAF cutoff 0.01, SLURM may or may not be needed.

References

Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R (2018). Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial. Mol Syst Biol 14:e8126, https://doi.org/10.15252/msb.20178126.

OpenSWATH, ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz.