Inputs - adelabriere/SLAW GitHub Wiki

All the inputs of SLAW should be given in a single input folder.

SLAW recommended inputs format is mzML. SLAW input files may be split across 4 different classes:

• QC: QC samples scattered in your experiment, these samples are theorytically identical the QC sample are used at different steps of the processing, to extract reference peaks for alignment and to detect isotopes and adducts. They can also be used to filter QCs.
• blank: Blanks are empty samples which only contains solvent and chemical noise, they will be discarded from the final peaktable.
• MS2: Samples which includes MS2 spectra but on which MS1 peakpicking should not be performed. These MS2 spectra will be mapped to the feature after alignment. This is useful if you do an heavy DDA on a specific file or if you do targeted DIA, as these can drastically reducing the number of scans for each LC-MS peaks.
• samples: All the other samples, if they include MS2 spectra these spectra will also be extracted. While all the samples can have different concentration of samples, they should potentially

The recommended way to provide these input to SLAW is by supplying a summary.csv table which should include 2 columns, path, and types. Only the basename to the sample will be considered, eg if ou part is (C:/some/path/to/sample1.mzML) only the sample1.mzML part will be matched against the filename.