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peptide spectral library
A peptide spectral library is a curated, annotated and non-redundant collection/database of LC-MS/MS peptide spectra. One essential utility of a peptide spectral library is to serve as consensus templates supporting the identification of peptide/proteins based on the correlation between the templates with experimental spectra. The process of peptide/protein identification is called spectral library searching. Compared to the traditional peptide spectra identification approach, sequence database searching, spectral library searching offers many unique benefits.
Spectral libraries have been used in the small molecules mass spectra identification since the 1980s.〔Domokos, L., Hennberg, D., and Weimann, B. 1984. Computer-aided identification of compounds by comparison of mass spectra. Anal. Chim. Acta 165:61-74.〕 In the early years of shotgun proteomics, pioneer investigations suggested that a similar approach might be applicable in shotgun proteomics for peptide/protein identification.〔Yates, J.R., 3rd, Morgan, S.F., Gatlin, C.L., Griffin, P.R., and Eng, J.K. 1998. Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractvie analysis. Anal. Chem., 70:3557-3565.〕 But until recent years, with the availability of millions of confidently identified MS/MS spectra, the implementation of peptide spectral libraries shows practical value.
==Shotgun proteomics==
Modern tandem MS instruments combine features of fast duty cycle, exquisite sensitivity, and unprecedented mass accuracy. Tandem mass spectrometry, which is an ideal match for the large-scale protein identification and quantification in complex biological systems. In a shotgun proteomics approach, proteins in a complex mixture are digested by proteolytic enzymes such as trypsin. Subsequently, one or more chromatographic separations are applied to resolve resulting peptides, which are then ionized and analyzed in a mass spectrometer. To acquire tandem mass spectra, a particular peptide precursor is isolated, and fragmented in a mass spectrometer; the mass spectra corresponding to the fragments of peptide precursor is recorded. Tandem mass spectra contains specific information regarding the sequence of the peptide precursor, which can aid the identification of peptide/protein.
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