Original title: FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe
Authors: Edgar Manriquez-Sandoval,Joy Brewer,Gabriela Lule,Samanta Lopez,Stephen D. Fried
In this article, the authors introduce a new tool called FLiPPR, which stands for FragPipe LiP (limited proteolysis) Processor. FLiPPR is designed to make it easier to analyze data from limited proteolysis mass spectrometry (LiP-MS) experiments, a method used to gain information about protein structure. LiP-MS has become popular in biological and biophysical research, but analyzing the resulting data can be slow and challenging. To address this, the authors use the fast and accurate algorithms in FragPipe for search and quantification, and then process the output in FLiPPR. FLiPPR includes a data imputation heuristic that utilizes missing data in LiP-MS experiments to highlight significant structural changes. It also introduces a new data merging scheme and a multiple hypothesis correction scheme to enhance the robustness of processed LiP-MS datasets. Additionally, FLiPPR allows for the collection of structural metadata to identify correlations between experiments and structural features. By providing a standardized and streamlined approach to LiP-MS data analysis, FLiPPR aims to encourage more researchers to adopt this method and facilitate the integration of LiP-MS data on a larger scale.
Original article: https://www.biorxiv.org/content/10.1101/2023.12.04.569947v1