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Shubham Gupta edited this page Jul 17, 2023 · 6 revisions

Welcome to the DIAlignR wiki!

Please consult our vignette.

The tool is designed for aligning Targeted Proteomics / SWATH-MS data processed with OpenSWATH + pyProphet. For runs processed with other software, some formatting should be done. The workflow outputs two files: 1) feature file (osw), 2) chromatogram file (sqMass) for each run.

Follwing datasets were analyzed with DIAlignR in the paper:

  1. Streptococcus Pyogenes cell lysate: The data containing 16 runs was analyzed with library having xxx peptides. Resulting osw files were of only 300 MB, hence, we merged all 16 osw files. The merged file was scored with pyProphet and also used for alignment.

  2. Multispecies data: This data included Yeast, Ecoli and human cell lysate in a known quantity to understand the quantitative error-rate.

  3. Multisite HEK293 cell lysate: Total 229 runs of HEK293 cell lysate were acquired in 11 different labs. The data was analyzed with pan-human library. Since merging of osw file would result into a file that can't fit in the memory, we scored it using subsampling. For alignment, chromtograms belonging to 1% peptide FDR were kept to reduce the size of sqMass files.

  4. Prediabetic plasma cohort: We analyzed 949 plasma samples with a plasma library. Similar to multisite data, the subsampling method was used for scoring and a subset of chromatograms were kept for signal alignment.

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