One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

Simone Sidoli, Yekaterina Kori, Mariana Lopes, Zuo Fei Yuan, Hee Jong Kim, Katarzyna Kulej, Kevin A. Janssen, Laura M. Agosto, Julia Pinheiro Chagas Da Cunha, Andrew J. Andrews, Benjamin A. Garcia

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

DNA and histone proteins define the structure and composition of chromatin. Histone posttranslational modifications (PTMs) are covalent chemical groups capable of modeling chromatin accessibility, mostly due to their ability in recruiting enzymes responsible for DNA readout and remodeling. Mass spectrometry (MS)-based proteomics is the methodology of choice for large-scale identification and quantification of protein PTMs, including histones. High sensitivity proteomics requires online MS coupling with relatively low throughput and poorly robust nano-liquid chromatography (nanoLC) and, for histone proteins, a 2-d sample preparation that includes histone purification, derivatization, and digestion. We present a new protocol that achieves quantitative data on about 200 histone PTMs from tissue or cell lines in 7 h from start to finish. This protocol includes 4 h of histone extraction, 3 h of derivatization and digestion, and only 1 min of MS analysis via direct injection (DI-MS). We demonstrate that this sample preparation can be parallelized for 384 samples by using multichannel pipettes and 96-well plates. We also engineered the sequence of a synthetic "histone-like" peptide to spike into the sample, of which derivatization and digestion benchmarks the quality of the sample preparation. We ensure that DI-MS does not introduce biases in histone peptide ionization as compared to nanoLC-MS/MS by producing and analyzing a library of synthetically modified histone peptides mixed in equal molarity. Finally, we introduce EpiProfileLite for comprehensive analysis of this new data type. Altogether, our workflow is suitable for high-throughput screening of >1000 samples per day using a single mass spectrometer.

Original languageEnglish (US)
Pages (from-to)978-987
Number of pages10
JournalGenome research
Volume29
Issue number6
DOIs
StatePublished - Jan 1 2019

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Histone Code
Post Translational Protein Processing
Histones
Mass Spectrometry
Injections
Digestion
Liquid Chromatography
Proteomics
Peptides
Benchmarking
Proteins
Chromatin Assembly and Disassembly
Workflow
DNA
Tandem Mass Spectrometry
Libraries
Chromatin
Cell Line

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry. / Sidoli, Simone; Kori, Yekaterina; Lopes, Mariana; Yuan, Zuo Fei; Kim, Hee Jong; Kulej, Katarzyna; Janssen, Kevin A.; Agosto, Laura M.; Da Cunha, Julia Pinheiro Chagas; Andrews, Andrew J.; Garcia, Benjamin A.

In: Genome research, Vol. 29, No. 6, 01.01.2019, p. 978-987.

Research output: Contribution to journalArticle

Sidoli, S, Kori, Y, Lopes, M, Yuan, ZF, Kim, HJ, Kulej, K, Janssen, KA, Agosto, LM, Da Cunha, JPC, Andrews, AJ & Garcia, BA 2019, 'One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry', Genome research, vol. 29, no. 6, pp. 978-987. https://doi.org/10.1101/gr.247353.118
Sidoli, Simone ; Kori, Yekaterina ; Lopes, Mariana ; Yuan, Zuo Fei ; Kim, Hee Jong ; Kulej, Katarzyna ; Janssen, Kevin A. ; Agosto, Laura M. ; Da Cunha, Julia Pinheiro Chagas ; Andrews, Andrew J. ; Garcia, Benjamin A. / One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry. In: Genome research. 2019 ; Vol. 29, No. 6. pp. 978-987.
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