Input parameters

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

spectra.to.compare.folder is the path that contains spectra in the comparison data set (currently supporting mgf files)

output.folder is the path where output text file is stored.

Calculation parameters

is.charged.based 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. (is.charged.based=true on, is.charged.based=false off)

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 precursor.tolerance=0, precursor tolerance option is ignored, and any spectrum is compared.

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

calculate.only5 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, and separated by “_”. The index of the slice number of the mgf file must be given on slice.index. For example, ni_hq_Goat_taenia_hydatigena_rt_1.mgf shows that the mgf comes from the slice number 1 and the slice index is 6, note that indexing starts from 0 (calculate.only5=true on, calculate.only5=false off).

##Preprocessing parameters

transformation enables intensity transformation of peaks. Currently, there are three options avaliable: transformation=0: none, transformation=1: log2 or transformation=2: square root transformation of peak intensities. Must be one of these three integer values!

noise.filtering enables noise filtering, by removing peaks. Currently, there are three options avaliable: noise.filtering=0: none, noise.filtering=1: pride-asap-adaptive noise filtering, noise.filtering=2: topN intense peak selection and noise.filtering=3: discarding peaks with less than x% of the precursor intensity. Must be one of these four integer values!

topN is required for noise.filtering=2. A number of peaks with top intensity to keep in a spectrum. Must be an integer value!

percent is required for noise.filtering=3. The percentage value of precursor intensity in order to keep any peaks with bigger than this percentaged value. Must be a double value between 0-100!

precursor.peak.removal enables removing peaks derived from the precursor peak (precursor.peak.removal=true on, precursor.peak.removal=false off).

isNFTR enables the order for preprocesing. Either noise filtering follows to a peak transformation (isNFTR=true) or peak transformation follows to noise filtering (isNFTR=false).

Other

thread.numbers is required for multi-threaded spectrum comparison. Shows the number of threads.