scholarly journals Crown ethers as shift reagents in peptide epimer differentiation –conclusions from examination of ac-(H)FRW-NH2 petide sequences

2020 ◽  
Vol 23 (2) ◽  
pp. 177-188
Author(s):  
Magdalena M. Zimnicka
Keyword(s):  
Mass Spectrometry ◽  
Crown Ether ◽  
Crown Ethers ◽  
Ion Mobility ◽  
Ion Source ◽  
Peptide Sequence ◽  
Ion Mobility Mass Spectrometry ◽  
Peptide Molecule ◽  
Shift Reagents ◽  
Specific Association

Abstract Crown ethers with different ring sizes and substituents (18-crown-6, dibenzo-18-crown-6, dicyclohexano-18-crown-6, a chiral tetracarboxylic acid-18-crown-6 ether, dibenzo-21-crown-7, and dibenzo-30-crown-10) were evaluated as shift reagents to differentiate epimeric model peptides (tri-and tetrapeptides) using ion mobility mass spectrometry (IM-MS). The stable associates of peptide epimers with crown ethers were detected and examined using traveling-wave ion mobility time-of-flight mass spectrometer (Synapt G2-S HDMS) equipped with an electrospray ion source. The overall decrease of the epimer separation upon crown ether complexation was observed. The increase of the effectiveness of the microsolvation of a basic moiety - guanidine or ammonium group in the peptide had no or little effect on the epimer discrimination. Any increase of the epimer separation, which referred to the specific association mode between crown substituents and a given peptide sequence, was drastically reduced for the longer peptide sequence (tetrapeptide). The obtained results suggest that the application of the crown ethers as shift reagents in ion mobility mass spectrometry is limited to the formation of complexes differing in stoichiometry rather than it refers to a specific coordination mode between a crown ether and a peptide molecule.

scholarly journals Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source

2010 ◽  
Vol 45 (12) ◽  
pp. 1383-1393 ◽  
Author(s):  
Prabha Dwivedi ◽  
Geoffery Puzon ◽  
Maggie Tam ◽  
Denis Langlais ◽  
Shelley Jackson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Ion Mobility ◽  
Metabolic Profiling ◽  
Ion Source ◽  
Ion Mobility Mass Spectrometry

scholarly journals Native Tandem and Ion Mobility Mass Spectrometry Highlight Structural and Modular Similarities in Clustered-Regularly-Interspaced Shot-Palindromic-Repeats (CRISPR)-associated Protein Complexes From Escherichia coli and Pseudomonas aeruginosa

2012 ◽  
Vol 11 (11) ◽  
pp. 1430-1441 ◽  
Author(s):  
Esther van Duijn ◽  
Ioana M. Barbu ◽  
Arjan Barendregt ◽  
Matthijs M. Jore ◽  
Blake Wiedenheft ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Ion Mobility ◽  
Protein Complexes ◽  
Acquired Resistance ◽  
Native Mass Spectrometry ◽  
Ion Mobility Mass Spectrometry ◽  
E Coli ◽  
Ribonucleoprotein Complexes ◽  
Specific Association

The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA. Recently, a cryo-electron microscopy structure of Cascade revealed that the CRISPR RNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes.

Conformation of K+(Crown Ether) Complexes Revealed by Ion Mobility–Mass Spectrometry and Ultraviolet Spectroscopy

2020 ◽  
Vol 124 (48) ◽  
pp. 9980-9990
Author(s):  
Sota Tainaka ◽  
Tomoyuki Ujihira ◽  
Mayuko Kubo ◽  
Motoki Kida ◽  
Daisuke Shimoyama ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Crown Ether ◽  
Ion Mobility ◽  
Ion Mobility Mass Spectrometry ◽  
Ultraviolet Spectroscopy ◽  
Crown Ether Complexes

Organic acid shift reagents for the discrimination of carbohydrate isobars by ion mobility-mass spectrometry

The Analyst ◽  
2020 ◽  
Vol 145 (24) ◽  
pp. 8008-8015
Author(s):  
Kristin R. McKenna ◽  
Li Li ◽  
Ramanarayanan Krishnamurthy ◽  
Charles L. Liotta ◽  
Facundo M. Fernández
Keyword(s):  
Mass Spectrometry ◽  
Organic Acid ◽  
Ion Mobility ◽  
Traveling Wave ◽  
Drift Tube ◽  
Ion Mobility Mass Spectrometry ◽  
Mixture Analysis ◽  
Shift Reagents

Traveling wave and drift tube ion mobility were utilized to separate isomeric disaccharides. Organic acid shift reagents were necessary to increase the resolution of these separations for mixture analysis.

scholarly journals Gas-phase microsolvation of ubiquitin: investigation of crown ether complexation sites using ion mobility-mass spectrometry

The Analyst ◽  
2016 ◽  
Vol 141 (19) ◽  
pp. 5502-5510 ◽  
Author(s):  
Melanie Göth ◽  
Frederik Lermyte ◽  
Xiao Jakob Schmitt ◽  
Stephan Warnke ◽  
Gert von Helden ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Crown Ether ◽  
Gas Phase ◽  
Ion Mobility ◽  
Phase Structure ◽  
Side Chain ◽  
Ion Mobility Mass Spectrometry ◽  
Gas Phase Structure

The influence of side chain to backbone interactions on the gas-phase structure of ubiquitin and ubiquitin lysine-to-arginine mutants was analysed.

Rapid Diagnosis of Parkinson’s Disease from Sebum using Paper Spray Ionisation Ion Mobility Mass Spectrometry

2020 ◽  
Author(s):  
Depanjan Sarkar ◽  
Drupad Trivedi ◽  
Eleanor Sinclair ◽  
Sze Hway Lim ◽  
Caitlin Walton-Doyle ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Ion Mobility ◽  
Neurodegenerative Disorder ◽  
Treatment Options ◽  
Ion Mobility Mass Spectrometry ◽  
Paper Spray ◽  
Molecular Features ◽  
Validation Set

Parkinson’s disease (PD) is the second most common neurodegenerative disorder for which identification of robust biomarkers to complement clinical PD diagnosis would accelerate treatment options and help to stratify disease progression. Here we demonstrate the use of paper spray ionisation coupled with ion mobility mass spectrometry (PSI IM-MS) to determine diagnostic molecular features of PD in sebum. PSI IM-MS was performed directly from skin swabs, collected from 34 people with PD and 30 matched control subjects as a training set and a further 91 samples from 5 different collection sites as a validation set. PSI IM-MS elucidates ~ 4200 features from each individual and we report two classes of lipids (namely phosphatidylcholine and cardiolipin) that differ significantly in the sebum of people with PD. Putative metabolite annotations are obtained using tandem mass spectrometry experiments combined with accurate mass measurements. Sample preparation and PSI IM-MS analysis and diagnosis can be performed ~5 minutes per sample offering a new route to for rapid and inexpensive confirmatory diagnosis of this disease.

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