Strategies of peptide identification using tandem Mass Spectrometry

Proteomics has made a massive advance and reached enough fullness previously reserved only for genomics. Therefore, it generates a flood of data that represents significant challenges for their interpretation. With the technological advances of mass spectrometers that allow the study of proteins in a large-scale, the analysis of complex protein samples becomes possible. The capacity to identify reliably all proteins present in a sample is a requirement to provide the suitable biologically interpretation. Mainly, two basic strategies are used for protein identification: Database searching strategy and De novo sequencing strategy. These two strategies differ in term of their ability and performance to control the false discovery rate (FDR). Here we review the achivements of mass spectrometry-based proteomics. We are shedding light on strategies of peptide/protein identification and the challenge of sensitivity and specificity, as they are the key factor to control the growth of false positive.