Mass spectrometry instrumentation has continued to develop rapidly in the last two decades, enabled in part by advances in microelectronic hardware controllers and computerized control and data acquisition systems. The wealth and complexity of data produced by a modern instrument is such that the data can no longer be analyzed manually. Computerized data analysis has become de rigueur and the bioinformatics field has expanded to provide software applications for all aspects of the data analysis needed by LC-MS/MS. The bioinformatics field is evolving rapidly and software applications are continually being improved or replaced for existing applications as well as developed to support new types of experiments and analysis enabled by modern instrumentation. Entire books have been written on MS data analysis in proteomics but this review will be necessarily brief. In this chapter we will review the bioinformatics software applications available for different LC-MS/MS analysis tasks.