TOFsPRO toolbox

Signal processing for time-of-flight mass spectra over the broad m/z range (1-200 kDa)

Description

This tool enhances signal detection for broad-mass TOF spectra by accounting for changing peak width and providing peak-shape-dependent filtering capabilities. A set of input TOF spectra is processed to produce aligned peak list and array of corresponding signal intensities. Signal processing includes model-based baseline subtraction (MBS), integrative down sampling (IDS), target filtering (TF), pedestal removal (PR), peak detection with automated SNR threshold (PD-SNR) and alignment to the average peak list (APL). Corresponding algorithms are described in [Malyarenko et al: Clin Chem 2005, and RCMS 2006] and [Bunai et al: JPR 2007].

The input data is an array of TOF spectra with corresponding m/z calibration axis. The resulting output data matrix may be used for downstream statistical analysis, e.g., in comparative proteomics.

• Required Products: Signal Processing Toolbox
• MATLAB release: MATLAB 7.2 (R2006a)

[Wolfgang Schellenberger]

Its a bit complicated to use the spOptions module. Is there a script for parameter selection?

[Dariya Malyarenko]

There are several aux-functions to help select parameters, described next to the corresponding field in spOptions. Best is to follow instructions in spOptions for a certain parameter selection, and plot the output for an average spectrum to view. No automated "global" para-optimization is available yet.