The Search Engine for Multi‐Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes

Owen S. Skinner1, Luis F. Schachner1, Neil L. Kelleher2

1 Department of Chemistry, Northwestern University, Evanston, Illinois, 2 Department of Molecular Biosciences, Northwestern University, Evanston, Illinois
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.30
DOI:  10.1002/cpbi.16
Online Posting Date:  December, 2016
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Abstract

Recent advances in top‐down mass spectrometry using native electrospray now enable the analysis of intact protein complexes with relatively small sample amounts in an untargeted mode. Here, we describe how to characterize both homo‐ and heteropolymeric complexes with high molecular specificity using input data produced by tandem mass spectrometry of whole protein assemblies. The tool described is a “search engine for multi‐proteoform complexes,” (SEMPC) and is available for free online. The output is a list of candidate multi‐proteoform complexes and scoring metrics, which are used to define a distinct set of one or more unique protein subunits, their overall stoichiometry in the intact complex, and their pre‐ and post‐translational modifications. Thus, we present an approach for the identification and characterization of intact protein complexes from native mass spectrometry data. © 2016 by John Wiley & Sons, Inc.

Keywords: protein complexes; multi‐proteoform complexes; top‐down proteomics; native mass spectrometry

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Characterizing a Multi‐Proteoform Complex with SEMPC
  • Alternate Protocol 1: Targeted Characterization of a Protein Complex not Present in the Corum Database
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Literature Cited

Literature Cited
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