Spectra-comp is an Ms/Ms spectra comparison tool. It used to compare between reference spectra and test spectra using dot product method. The reference spectra could be loaded from:

• Proline project (you should have proline software installed and a proline account as well https://github.com/profiproteomics).
• Peaklist file (.mgf or .pkl).

The tested spectra could be loaded from :

• Proline project (you should have proline software installed and a proline account as well https://github.com/profiproteomics).
• Peaklist file (.mgf or .pkl).

The spectra are compared using a dot product method. The user could set up the comaprison spectra parameters from the graphical interface or from the paremeters JSON file (default-params.json). The parameters of comparison are :

• Precursor delta Moz: the delta (+- Moz), it will be used for the precursor moz.
• Fragment delta Moz: the delta (+- Moz), it will be used for the fragment moz.
• Delta retention time: the delta retention time (-+ in secondes).
• Number of minimum peaks: the minimum number of peaks that matched between the reference spectrum and the tested spectrum.
• Number of peaks: the number of peaks that matched: for the tested spectra if a value is present for the same peak of reference spectra, we keep the most intense value of intensity.
• Minimum theta: this value is computed as Math.cos(Math.toRadians(thetaMin))

Cos theta = ∑NB_PEAKS(√RS.peak * √TS.peak)/(√(∑NB_PEAKS(RS.peak))*√(∑NB_PEAKS(TS.peak)))

TS.peak = intensity of peaks TS(tested spectra)
RS.peak = intensity of peaks RS(reference spectra)

Usage

Spectra-comp has been developped in Java and can be used on Windows and Linux.
Spectra-comp requires Java 8 at least.
The latest release can be downloaded from here: https://github.com/LSMBO/spectra-comp/releases
To run Spectra-comp, you can double-click on the script start_spectra_comp.bat(Windows) or start_spectra_comp.sh(Unix)