20220721 Visualizing Proteoform Spectrum Matches in ProSight Lite and ClipsMS

Visualizing a proteoform-spectrum match is an essential skill for every top-down proteomics researcher. "Fragment Maps" represent our most common strategy for illustrating the evidence for a proteoform's identification. This tutorial demonstrates the use of two different tools for this purpose, ProSight Lite (http://prosightlite.northwestern.edu/) and ClipsMS (https://github.com/loolab2020/ClipsMS). We use this file from PXD032724 as a demonstrator: 20140210_F_EV_Hpylori_dilby10_r120-4usc-2e5_top2int-ETD5-r60-2e5-15usc_grad40-80.raw, examining scan 794, which matches this sequence: MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEIYEEFADMFDDLAERIAQLGHHPLVTLSEALKLTRVKEETKTSFHSKDIFKEILGDYKHLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHLA

Our flow follows these steps:
1 Deconvolve the original MS/MS in FreeStyle, using the Xtract algorithm.
2 Clean the mass and intensity list in NotePad Plus Plus (https://notepad-plus-plus.org/).
3 Enter information in ProSight Lite, but removing incorrectly handled intensity information. Save document as pcML and export figures.
4 Prepare CSV of mass and intensity list for use in ClipsMS.
5 Enter information in ClipsMS (hopefully avoiding the unprintable characters I encountered). Save visualizations and tables.

I would like to thank Julia Chamot-Rooke of Institut Pasteur and EPIC-XS for supporting the development of these videos.