Mass spectrometry (MS) is a technique that is used for biological studies. It consists in associating a spectrum to a biological sample. A spectrum consists of couples of values (intensity, m/z), where intensity measures the abundance of biomolecules (as proteins) with a mass-to-charge ratio (m/z) present in the originating sample. In proteomics experiments, MS spectra are used to identify pattern expressions in clinical samples that may be responsible of diseases. Recently, to improve the identification of peptides/proteins related to patterns, MS/MS process is used, consisting in performing cascade of mass spectrometric analysis on selected peaks. Latter technique has been demonstrated to improve the identification and quantification of proteins/peptide in samples. Nevertheless, MS analysis deals with a huge amount of data, often affected by noises, thus requiring automatic data management systems. Tools have been developed and most of the time furnished with the instruments allowing: (i) spectra analysis and visualization, (ii) pattern recognition, (iii) protein databases querying, (iv) peptides/proteins quantification and identification. Currently most of the tools supporting such phases need to be optimized to improve the protein (and their functionalities) identification processes. In this article we survey on applications supporting spectrometrists and biologists in obtaining information from biological samples, analyzing available software for different phases. We consider different mass spectrometry techniques, and thus different requirements. We focus on tools for (i) data preprocessing, allowing to prepare results obtained from spectrometers to be analyzed, (ii) spectra analysis, representation and mining, aimed to identify common and/or hidden patterns in spectra sets or in classifying data, (iii) databases querying to identify peptides, and (iv) improving and boosting the identification and quantification of selected peaks. We trace some open problems and report on requirements that represent new challenges for bioinformatics.