Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down to 50000 Cells as Starting Material

Qi Guo, Simone Sidoli, Benjamin A. Garcia, Xiaolu Zhao

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Histone post-translational modifications (PTMs) are fundamental players of chromatin regulation, as they contribute to editing histone chemical properties and recruiting proteins for gene transcription and DNA repair. Mass spectrometry (MS)-based proteomics is currently the most widely adopted strategy for high-throughput quantification of hundreds of histone PTMs. Samples such as primary tissues, complex model systems, and biofluids are hard to retrieve in large quantities. Because of this, it is critical to know whether the amount of sample available would lead to an exhaustive analysis if subjected to MS. In this work, we assessed the reproducibility in quantification of histone PTMs using a wide range of starting material, that is, from 5000000 to 50000 cells. We performed the experiment using four different cell lines, that is, HeLa, 293T, human embryonic stem cells (hESCs), and myoblasts, and we quantified a list of 205 histone peptides using ion trap MS and our in-house software. Results highlighted that the relative abundance of some histone PTMs deviated as little as just 4% when comparing high starting material with histone samples extracted from 50000 cells, for example, H3K9me2 (40% average abundance). Low abundance PTMs such as H3K4me2 (<3% average abundance) showed higher variability, but still ∼34%. This indicates that most PTMs, and especially abundant ones, are quantified with high precision starting from low cell counts. This study will help scientists to decide whether specific experiments are feasible and to plan how much sample should be reserved for histone analysis using MS.

Original languageEnglish (US)
Pages (from-to)234-242
Number of pages9
JournalJournal of Proteome Research
Volume17
Issue number1
DOIs
StatePublished - Jan 5 2018
Externally publishedYes

Fingerprint

Post Translational Protein Processing
Histones
Ions
Mass spectrometry
Mass Spectrometry
Myoblasts
Transcription
Stem cells
DNA Repair
Proteomics
Chemical properties
Chromatin
Repair
Software
Cell Count
Experiments
Cells
Throughput
Tissue
Cell Line

Keywords

  • bottom-up
  • data-independent acquisition
  • histones
  • mass spectrometry
  • post-translational modifications

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down to 50000 Cells as Starting Material. / Guo, Qi; Sidoli, Simone; Garcia, Benjamin A.; Zhao, Xiaolu.

In: Journal of Proteome Research, Vol. 17, No. 1, 05.01.2018, p. 234-242.

Research output: Contribution to journalArticle

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