Sorting the Muck from the Brass: Analysis of Protein Complexes and Cell Lysates

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Abstract

Reliable determination of protein complex composition or changes to protein levels in whole cells is challenging. Despite the multitude of methods now available for labeling, analysis, and the statistical processing of data, this large variety is of itself an issue: Which approach is most appropriate, where do you set cutoffs, and what is the most cost-effective strategy? One size does not fit all for such work, but some guidelines can help in terms of reducing cost, improving data quality, and ultimately advancing investigations. Here we describe two protocols and algorithms for facile sample preparation for mass spectrometric analysis, robust data processing, and considerations of how to interpret large proteomic datasets in a productive and robust manner.

Original languageEnglish
Title of host publicationTrypanosomatids
Subtitle of host publicationMethods and Protocols
EditorsPaul A. M. Michels, Michael L. Ginger, Dan Zilberstein
Place of PublicationNew York
PublisherHumana Press
Pages645-653
Number of pages9
Volume2116
ISBN (Electronic)9781071602942
ISBN (Print)9781071602935
DOIs
Publication statusPublished - 2020

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

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Keywords

  • Data presentation
  • MaxQuant
  • Proteomics
  • SDS-PAGE
  • Sample preparation
  • Trypanosoma

Cite this

Zoltner, M., Del Pino, R. C., & Field, M. C. (2020). Sorting the Muck from the Brass: Analysis of Protein Complexes and Cell Lysates. In P. A. M. Michels, M. L. Ginger, & D. Zilberstein (Eds.), Trypanosomatids: Methods and Protocols (Vol. 2116, pp. 645-653). (Methods in Molecular Biology). Humana Press. https://doi.org/10.1007/978-1-0716-0294-2_38