Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling

Isotope labeling combined with LC-MS/MS provides a robust platform for quantitative proteomics. Protein quantitation based on mass spectral data falls into two categories: one determined by MS/MS scans, e.g., iTRAQ-labeling quantitation, and the other by MS scans, e.g., quantitation using SILAC, ICAT, or ¹⁸ O labeling. In large-scale LC-MS proteomic experiments, tens of thousands of MS and MS/MS spectra are generated and need to be analyzed. Data noise further complicates the data analysis. In this chapter, we present two automated tools, called Multi-Q and MaXIC-Q, for MS/MS- and MS-based quantitation analysis. They are designed as generic platforms that can accommodate search results from SEQUEST and Mascot, as well as mzXML files converted from raw files produced by various mass spectrometers. Toward accurate quantitation analysis, Multi-Q determines detection limits of the user’s instrument to filter out outliers and MaXIC-Q adopts stringent validation on our constructed projected ion mass spectra to ensure correct data for quantitation.