High Resolution Is Not a Strict Requirement for Characterization and Quantification of Histone Post-Translational Modifications

• Published in: Journal of proteome research Vol. 13; no. 12; pp. 6152 - 6159
• Main Authors: Karch, Kelly R, Zee, Barry M, Garcia, Benjamin A
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 05.12.2014
• Subjects: Acetylation; Amino Acid Sequence; Chromatography, Liquid - methods; HeLa Cells; Histones - metabolism; Humans; Lysine - metabolism; Mass Spectrometry - instrumentation; Mass Spectrometry - methods; Methylation; Peptides - metabolism; Protein Processing, Post-Translational; Proteomics - methods; Reproducibility of Results; Tandem Mass Spectrometry - instrumentation; Tandem Mass Spectrometry - methods; Technical Note; quantification; proteomics; PTM; mass spectrometry; histone; stable isotope; chromatin; modification; epigenetics
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/pr500902f

Mass spectrometry (MS) is a powerful tool to accurately identify and quantify histone post-translational modifications (PTMs). High-resolution mass analyzers have been regarded as essential for these PTM analyses because the mass accuracy afforded is sufficient to differentiate trimethylation versus acetylation (42.0470 and 42.0106 Da, respectively), whereas lower-resolution mass analyzers cannot. Noting this limitation, we sought to determine whether lower-resolution detectors are nonetheless adequate for histone PTM analysis by comparing the low-resolution LTQ Velos Pro with the high-resolution LTQ-Orbitrap Velos Pro. We first determined that the optimal scan mode on the LTQ Velos Pro is the Enhanced scan mode with respect to apparent resolution, number of MS and MS/MS scans per run, and reproducibility of label-free quantifications. We next compared the performance of the LTQ Velos Pro to the LTQ-Orbitrap Velos Pro using the same criteria for comparison, and we found that the main difference is that the LTQ-Orbitrap Velos Pro is able to resolve the difference between acetylation and trimethylation while the LTQ Velos Pro cannot. However, using heavy isotope labeled synthetic peptide standards and retention time information enables confident assignment of these modifications and comparable quantification between the instruments. Therefore, lower-resolution instruments can confidently be utilized for histone PTM analysis.