MSMS extraction - adelabriere/SLAW GitHub Wiki

MS-MS spectra extraction

SLAW extracts representative MS-MS spectra of the aligned features when available in any samples. However, for some samples, notably in DDA with a lot of fragmentation events, the numbers of points on each chromatographic peak across MS1 scans can be way lower, making peak picking performs poorly on these samples. In this case, SLAW allows the extraction of MS-MS spectra without peak picking. MS2 only files need to be tagged as MS2 into the summary.csv, by putting their 'type' label as 'MS2'. For every other file, MS2 spectra will also be extracted, as well as MS1 features.

As the MS-MS spectra extraction is performed at the same time as peak picking, the related parameters are stored in the peak picking step parameters:

• peakpicking/peaks_deconvolution/ms2_mz_tol: (Float). The tolerance in Dalton to map an MS2 precursor to a peak.
• peakpicking/peaks_deconvolution/ms2_rt_tol: (Float). The tolerance in minutes to map an MS2 precursor to a peak.
• peakpicking/noise_level_ms2:: (Float). A cut-off threshold in intensity. All points below this threshold will be discarded.

These spectra are then fused and will be placed into the fused_mgf folder in a single MGF, which can be processed using any other software.

The individual MS-MS files (.mgf) are also extracted into individuals .mgf files which can be found under the PEAKPICKING/msms subfolder.