2 research outputs found
Improving Ion Mobility Mass Spectrometry of Proteins through Tristate Gating and Optimization of Multiplexing Parameters
Coupling drift tube
ion mobility (IM) to Fourier transform mass
spectrometry (FT-MS) affords the opportunity for gas-phase separation
of ions based on size and conformation with high-resolution mass analysis.
However, combining IM and FT-MS is challenging because ions exit the
drift tube on a much faster time scale than the rate of mass analysis.
Fourier transform (FT) and Hadamard transform multiplexing methods
have been implemented to overcome the duty-cycle mismatch, offering
new avenues for obtaining high-resolution, high-mass-accuracy analysis
of mobility-selected ions. The gating methods used to integrate the
drift tube with the FT mass analyzer discriminate against the transmission
of large, low-mobility ions owing to the well-known gate depletion
effect. Tristate gating strategies have been shown to increase ion
transmission for drift tube IM-FT-MS systems through implementation
of dual ion gating, controlling the quantity and timing of ions through
the drift tube to reduce losses of slow-moving ions. Here we present
an optimized set of multiplexing parameters for tristate gating ion
mobility of several proteins on an Orbitrap mass spectrometer and
further report parameters for increased ion transmission and mobility
resolution as well as decreased experimental times from 15 min down
to 30 s. On average, peak intensities in the arrival time distributions
(ATDs) for ubiquitin increased 2.1× on average, while those of
myoglobin increased by 1.5× with a resolving power increase on
average of 11%
Distinctive interactomes of RNA polymerase II phosphorylation during different stages of transcription
Summary: During eukaryotic transcription, RNA polymerase II undergoes dynamic post-translational modifications on the C-terminal domain (CTD) of the largest subunit, generating an information-rich PTM landscape that transcriptional regulators bind. The phosphorylation of Ser5 and Ser2 of CTD heptad occurs spatiotemporally with the transcriptional stages, recruiting different transcriptional regulators to Pol II. To delineate the protein interactomes at different transcriptional stages, we reconstructed phosphorylation patterns of the CTD at Ser5 and Ser2 in vitro. Our results showed that distinct protein interactomes are recruited to RNA polymerase II at different stages of transcription by the phosphorylation of Ser2 and Ser5 of the CTD heptads. In particular, we characterized calcium homeostasis endoplasmic reticulum protein (CHERP) as a regulator bound by phospho-Ser2 heptad. Pol II association with CHERP recruits an accessory splicing complex whose loss results in broad changes in alternative splicing events. Our results shed light on the PTM-coded recruitment process that coordinates transcription