Distinguishing Isomeric Peptides: The Unimolecular Reactivity and Structures of (LeuPro)M⁺ and (ProLeu)M⁺ (M = Alkali Metal)

The unimolecular chemistries and structures of gas-phase (ProLeu)­M⁺ and (LeuPro)­M⁺ complexes when M = Li, Na, Rb, and Cs have been explored using a combination of SORI-CID, IRMPD spectroscopy, and computational methods. CID of both (LeuPro)­M⁺ and (ProLeu)­M⁺ showed identical fragmentation pathways and could not be differentiated. Two of the fragmentation routes of both peptides produced ions at the same nominal mass as (Pro)­M⁺ and (Leu)­M⁺, respectively. For the litiated peptides, experiments revealed identical IRMPD spectra for each of the <i>m</i>/<i>z</i> 122 and 138 ions coming from both peptides. Comparison with computed IR spectra identified them as the (Pro)­Li⁺ and (Leu)­Li⁺, and it is concluded that both zwitterionic and canonical forms of (Pro)­Li⁺ exist in the ion population from CID of both (ProLeu)­Li⁺ and (LeuPro)­Li⁺. The two isomeric peptide complexes could be distinguished using IRMPD spectroscopy in both the fingerprint and the CH/NH/OH regions. The computed IR spectra for the lowest energy structures of each charge solvated complexes are consistent with the IRMPD spectra in both regions for all metal cation complexes. Through comparison between the experimental spectra, it was determined that in lithiated and sodiated ProLeu, metal cation is bound to both carbonyl oxygens and the amine nitrogen. In contrast, the larger metal cations are bound to the two carbonyls, while the amine nitrogen is hydrogen bonded to the amide hydrogen. In the lithiated and sodiated LeuPro complexes, the metal cation is bound to the amide carbonyl and the amine nitrogen while the amine nitrogen is hydrogen bonded to the carboxylic acid carbonyl. However, there is no hydrogen bond in the rubidiated and cesiated complexes; the metal cation is bound to both carbonyl oxygens and the amine nitrogen. Details of the position of the carboxylic acid CO stretch were especially informative in the spectroscopic confirmation of the lowest energy computed structures

High-Field Asymmetric Waveform Ion Mobility Spectrometry Interface Enhances Parallel Reaction Monitoring on an Orbitrap Mass Spectrometer

High-field asymmetric waveform ion mobility spectrometry (FAIMS) enables gas-phase separations on a chromatographic time scale and has become a useful tool for proteomic applications. Despite its emerging utility, however, the molecular determinants underlying peptide separation by FAIMS have not been systematically investigated. Here, we characterize peptide transmission in a FAIMS device across a broad range of compensation voltages (CVs) and used machine learning to identify charge state and three-dimensional (3D) electrostatic peptide potential as major contributors to peptide intensity at a given CV. We also demonstrate that the machine learning model can be used to predict optimized CV values for peptides, which significantly improves parallel reaction monitoring workflows. Together, these data provide insight into peptide separation by FAIMS and highlight its utility in targeted proteomic applications

Additional file 3 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 3: Table S2. List of MORC7 interacting proteins

Additional file 4 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 4: Table S3. Expression level of LUG directly regulated genes in Ler and lug mutant

Additional file 6 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 6: Table S5. Published ChIP-seq data used for ChromHMM states analysis

Additional file 2 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 2: Table S1. Genes proximal to MORC7A-unique, MORC7B-unique, MORC7-Pol V Common, and Pol V-unique peaks

Additional file 7 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 7. Review history

Additional file 5 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 5: Table S4. Primers used in this study

Additional file 1 of MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions

Additional file 1: Figure S1. Chromatin states of MORC7. Figure S2. Small RNA data over MORC7 peaks. Figure S3. Examples showing MORC7 enrichment over the promoter regions of the TOPLESS genes. Figure S4. MORC7 associates with some TFs. Figure S5. Metaplot and heatmap showing chromatin accessibility changes. Figure S6. Volcano plot showing TF changes for ZF off-target sites. Figure S7. Expression levels of genes in the primary shoot apical meristem specification pathway, with and without heat treatment, in Col-0 and morchex mutants. Figure S8. Motif enrichment of TPL and LUG peaks identified in Col-0 or morchex mutant. Figure S9. Metaplot and heatmap showing ChIP-seq signals over peaks detected in morchex mutant