Poster Presentation 23rd Annual Lorne Proteomics Symposium 2018

SWATH-MS spectral reference library species conversion with the R package ‘dialects’ (#132)

Madeleine J Otway 1 , Peter G Hains 1 , Phillip J Robinson 1
  1. Children's Medical Research Institute, Westmead, NSW, Australia

SWATH-MS is a mass spectrometry (MS) approach that measures all theoretical peptide fragments. The resulting file is extremely complex and identification of peptides generally relies on an independently generated spectral reference library (SRL). The SRL comprises a table of transitions, defined though a series of data-dependent acquisition (DDA)-MS runs. The SWATH-MS data are searched with the SRL for the presence of the predefined peptides and associated fragments. Creation of an SRL is a lengthy process with large computational requirements. Additional searching of DDA-MS files with species other than the original sample is often avoided. This approach can preclude using large well characterised SRLs designed in one species from the use with alternate species. To overcome this, we developed an R package named ‘dialects’ (data independent acquisition library editing to convert the species) for SRL conversion between species. This package contains five core functions: 1. import a UniProt protein sequence database (fasta file); 2. import a PeakView/OneOmics or OpenSWATH SRL; 3. perform an in silico tryptic digestion on UniProt proteins; 4. convert the species of the SRL to that of the digested UniProt database, only for full sequence identity peptides; 5. export the new SRL in either PeakView/OneOmics or OpenSWATH format. This R package aids the creation of comprehensive SRLs, without the need for repeated MS runs and/or reprocessing of MS searches. This reduces the time to convert between species of an SRL and expands the utility of large, well characterised SRLs.