Input & Output

Select the spectra directory is the path that contains spectra (currently supporting mgf files).

Select the comparison spectra directory is the path that contains spectra in the comparison data set (currently supporting mgf files).

Select the output directory is the path where output text file is stored.

Pipeline parameters

Compare spectra regarding to precursor charge enables the comparison of spectra with the same precursor charge. If this option is not checked, a spectrum is compared to another one ignoring the precursor charge.

Precursor tolerance enables the comparison of spectra within this precursor tolerance (in ppm) against a spectrum of the comparison data set. If this value is set to 0.0, the precursor tolerance option is ignored, and any spectrum is compared.

Fragment tolerance enables the matching peaks of both spectra within this given fragment tolerance (in Da).

Consider only the 5 neighbour slice enables the comparison of the spectra coming from the closer slices on gel runs. The slice name must be part of the file name of a given mgf spectra, separated by “_”. the index of the slice number of the mgf file must be given on File name slice index. For example, ni_hq_Goat_taenia_hydatigena_rt_1.mgf shows that the mgf comes from slice number 1 and the slice index is 6, note that indexing starts from 0.

Precursor charge (Max in both data set) is the maximum precursor charge of any spectrum on both data sets. This is required only during the comparison of the spectra regarding to precursor charge. In other words, this option sets the maximum precursor charge to compare when Compare spectra regarding to precursor charge is selected.

Preprocessing

Preprocessing order enables to change the order for preprocesing. Either noise filtering follows to a peak transformation or peak transformation follows to noise filtering.

Transformation enables intensity transformation of peaks. Currently, there are three options avaliable: none, log2 or square root transformation of peak intensities.

Noise filter enables noise filtering by removing peaks. Currently, there are three options avaliable: none, pride-asap-adaptive noise filtering, topN intense peak selection and discarding peaks with less than x% of precursor intensity

Number of peaks cutoff is required for topN intense peak selection a number of peaks with top intensity to keep in a spectrum.

Peak intensity cutoff (%) is required for discarding peaks with less than x% of the precursor intensity: the percentage value of the precursor intensity in order to keep any peak larger than this percentaged value.

Remove precursor ion peak enables removing peaks derived from the precursor peak.

Other

Number of threads is required for multi-threaded spectrum comparison.