How to use open-pFind in deep proteomics data analysis?—A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data

摘要

High-throughput proteomics based on mass spectrometry（MS） analysis has permeated biomedical science and propelled numerous research projects. p Find 3 is a database search engine for high-speed and in-depth proteomics data analysis. p Find 3 features a swift open search workflow that is adept at uncovering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline. In this protocol, we provide step-by-step instructions to help users mastering various types of data analysis using p Find 3 in conjunction with p Parse for data pre-processing and if needed, p Quant for quantitation. This streamlined p Parse-p Findp Quant workflow offers exceptional sensitivity, precision, and speed. It can be easily implemented in any laboratory in need of identifying peptides, proteins, or post-translational modifications, or of quantitation based on 15N-labeling, SILAC-labeling, or TMT/i TRAQ labeling.