Mass Spectrometry Label-free Quantitative Approach For Complex Proteomes And Its Application

Complex proteomes are widely applied in biomarkers discovery, signaling pathway and drug discovery. In terms of molecular biology, the evolvement of diseases is expressed by the changes of protein abundance. In this regard, quantitative analysis for complex proteomes is an important way to investigate the mechanism of disease. Meanwhile, complex proteomes, featured with tremendous proteins and functions, pose a challenge for quantitative proteomics. Label-free quantitative approach based on spectral count gains popularity because its ability to quantify large-scale proteomes. However, the method expresses obvious shortages in complex proteomes analysis.Thus, building a method combining other MS abundance features to lower variances between replicate MS measurements is really urgent. On the other hand, complex proteomes have multifarious functions. Combining functional analysis and quantification is meaningful to deeply explore the functions and interactions in a large-scale manner.To systematically overcome this challenge, this paper builds a mass-spectrometry label-free quantitative approach for complex proteomes. The detail works are as follows:·Building an optimized algorithm with shared peptide based on NSAF to overcome inaccurate and overestimated results for low-abundant proteins.· Building a method combining spectral count and total ions to lower variances between replicate MS measurements to improve accuracy.· Large-scale functional annotations for complex proteomes which are extracted by g:Profiler can thoroughly comprehend functions and relationships.· Selecting mitochondria for analysis to validate the above-mentioned methods.· Building a software tool based on label-free approach for complex proteomes to combine quantification and qualification.The results show that the methods combining quantification and qualification can improve accuracy with broader dynamic range and low variance.