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Fig. 1 | Epigenetics & Chromatin

Fig. 1

From: Systematic quantitative analysis of H2A and H2B variants by targeted proteomics

Fig. 1

Principles of discovery and targeted proteomics approaches. Major steps of discovery and targeted mass spectrometry analyses are schematized. Discovery proteomics (top panel) characterizes the global composition of a protein sample. With the quadrupole-orbitrap technology, peptide ions within a small window of mass-to-charge (m/z) ratio are isolated in the first quadrupole (Q1) and then fragmented in a collision cell; all ion fragments are finally monitored in the orbitrap analyzer. The processing of resulting MS/MS spectra allows identifying the proteins initially present in the samples (not shown). Targeted proteomics (bottom panel) precisely quantifies a predefined set of proteins. The SRM methodology first selects peptide ions representative of the proteins of interest in the first quadrupole (Q1); they are fragmented in the second quadrupole (Q2); finally, predefined representative ion fragments (F1, F2 and F3) are recorded in the last quadrupole (Q3). The reconstitution of each peptide elution profile, named SRM trace, allows for the integration and quantification of its abundance. The PRM methodology is similar to the SRM pipeline but the last quantification step is not restricted to a predefined set of fragment ions and can consider all of them, recorded in the Orbitrap analyzer

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