Proteomic Identification and High Abundant Proteins Analysis of Human Saliva by Nano-Liquid Chromatography-High Resolution Tandem Mass Spectrometry

In mass spectrometry-based proteomics, one of the most common problem is whether and how to apply the mass spectrum data of qualitative analysis for the relative quantitative analysis, because not only there is interest for making full use of the data but also there is a demand in practical work. In this study, nano flow high performance liquid chromatography-high resolution tandem mass spectrometry (nano-HPLC-Triple TOF 5600) was used to analyze the basic components of the human saliva proteome, furthermore, the relationship between the mass spectrum data and the high abundant proteins in saliva was discussed. A total of 6 044 specific enzyme peptides arising from 521 proteins were identified, in which α-amylase 1, carbonic anhydrase 6, serum albumin, mucin and several kinds of cystatin et al were identified as high abundant proteins. This study provided a basic reference for the component of saliva proteome based on the one-dimensional HPLC-MS/MS method. In addition, the result showed that although the Unused value is the most important parameters to measure the reliability of qualitative analysis protein, only using Unused value to stand for the relative abundance of proteins is not suitable. Fortunately, there is a positive correlation among the combination of the protein rank (Unused value), the number of peptides detected as well as the average intensity of peptides and the relative contents of protein. For example, for those of proteins whose Unused value is low, which only one peptide is detected and the intensity of peptides is also low. Namely, this result indicated that when the relative contents of protein is very different, the chemical properties and ionization efficiency of peptides are not the main parameters to affect the signal intensity. In other words, the low number of peptides detected combined with the low signal intensity indicated the content of protein is low. This result is helpful for evaluating the relatively quantitative composition of human saliva by using Triple TOF 5600 mass spectrometer and for the research on saliva proteome biomarkers.