Peak extraction from raw data is the first step in LC-MS data analysis. The quality of this procedure can have dramatic effects on the quality and accuracy of all subsequent data analysis steps such as database searches and peak quantitation. The most important and most accurately measured physical entity provided by mass spectrometers is m/z. Peak processing algorithms must extract m/z values unaffected from overlapping peaks to avoid confusing downstream algorithms. The aim of this chapter is to provide a discussion of peak processing methods and furthermore discuss some of the yet unresolved or neglected issues. The chapter mainly discusses possible software developed in R for spectra processing and free software to generate Mascot generic files (mgf-see Chapter 1 ).
Keywords: Decharging; Deisotoping; Noise filtering; Peak extraction.