Can IM-MS Collision Cross Sections of Biomolecules Be Rationalized Using Collision Cross-Section Trends of Polydisperse Synthetic Homopolymers?

2020 ◽  
Vol 31 (4) ◽  
pp. 990-995 ◽  
Author(s):  
Jean R. N. Haler ◽  
Philippe Massonnet ◽  
Johann Far ◽  
Gregory Upert ◽  
Nicolas Gilles ◽  
...  
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Collision Cross Sections

scholarly journals A parallelized molecular collision cross section package with optimized accuracy and efficiency

The Analyst ◽  
2019 ◽  
Vol 144 (5) ◽  
pp. 1660-1670 ◽  
Author(s):  
Christian Ieritano ◽  
Jeff Crouse ◽  
J. Larry Campbell ◽  
W. Scott Hopkins
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
High Accuracy ◽  
Molecular Collision ◽  
Collision Cross Sections

A new parallelized calculation package predicts collision cross sections with high accuracy and efficiency.

scholarly journals A Deep Convolutional Neural Network for Prediction of Peptide Collision Cross Sections in Ion Mobility Spectrometry

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1904
Author(s):  
Yulia V. Samukhina ◽  
Dmitriy D. Matyushin ◽  
Oksana I. Grinevich ◽  
Aleksey K. Buryak
Keyword(s):  
Neural Network ◽  
Mass Spectrometry ◽  
Convolutional Neural Network ◽  
Cross Section ◽  
Ion Mobility Spectrometry ◽  
Cross Sections ◽  
Ion Mobility ◽  
Collision Cross Section ◽  
Deep Convolutional Neural Network ◽  
Collision Cross Sections

Most frequently, the identification of peptides in mass spectrometry-based proteomics is carried out using high-resolution tandem mass spectrometry. In order to increase the accuracy of analysis, additional information on the peptides such as chromatographic retention time and collision cross section in ion mobility spectrometry can be used. An accurate prediction of the collision cross section values allows erroneous candidates to be rejected using a comparison of the observed values and the predictions based on the amino acids sequence. Recently, a massive high-quality data set of peptide collision cross sections was released. This opens up an opportunity to apply the most sophisticated deep learning techniques for this task. Previously, it was shown that a recurrent neural network allows for predicting these values accurately. In this work, we present a deep convolutional neural network that enables us to predict these values more accurately compared with previous studies. We use a neural network with complex architecture that contains both convolutional and fully connected layers and comprehensive methods of converting a peptide to multi-channel 1D spatial data and vector. The source code and pre-trained model are available online.

scholarly journals Collision Cross Sections of Charge-Reduced Proteins and Protein Complexes: A Database for Collision Cross Section Calibration

2020 ◽  
Vol 92 (6) ◽  
pp. 4475-4483 ◽  
Author(s):  
Alyssa Q. Stiving ◽  
Benjamin J. Jones ◽  
Jakub Ujma ◽  
Kevin Giles ◽  
Vicki H. Wysocki
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Protein Complexes ◽  
Collision Cross Sections

Collision cross sections and ion structures: development of a general calculation method via high-quality ion mobility measurements and theoretical modeling

The Analyst ◽  
2017 ◽  
Vol 142 (22) ◽  
pp. 4289-4298 ◽  
Author(s):  
Jong Wha Lee ◽  
Kimberly L. Davidson ◽  
Matthew F. Bush ◽  
Hugh I. Kim
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Ion Mobility ◽  
Calculation Method ◽  
Collision Cross Section ◽  
Theoretical Modeling ◽  
Structural Studies ◽  
High Quality ◽  
Collision Cross Sections

Theoretical collision cross section calculations revisited for reliable ion structural studies.

scholarly journals Collision cross section compendium to annotate and predict multi-omic compound identities

2019 ◽  
Vol 10 (4) ◽  
pp. 983-993 ◽  
Author(s):  
Jaqueline A. Picache ◽  
Bailey S. Rose ◽  
Andrzej Balinski ◽  
Katrina L. Leaptrot ◽  
Stacy D. Sherrod ◽  
...  
Keyword(s):  
Cross Section ◽  
Cross Sections ◽  
Ion Mobility ◽  
Collision Cross Section ◽  
Interactive Tool ◽  
Collision Cross Sections

The Unified Compendium is an online interactive tool that utilizes ion mobility collision cross sections to annotate biochemical molecules.

How useful is molecular modelling in combination with ion mobility mass spectrometry for ‘small molecule’ ion mobility collision cross-sections?

The Analyst ◽  
2015 ◽  
Vol 140 (20) ◽  
pp. 6814-6823 ◽  
Author(s):  
Cris Lapthorn ◽  
Frank S. Pullen ◽  
Babur Z. Chowdhry ◽  
Patricia Wright ◽  
George L. Perkins ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cross Section ◽  
Small Molecule ◽  
Cross Sections ◽  
Ion Mobility ◽  
Molecular Modelling ◽  
Collision Cross Section ◽  
Ion Mobility Mass Spectrometry ◽  
Collision Cross Sections

Evaluation of N2(g) and He(g) MOBCAL collision cross section values from 20 compounds ∼ m/z 122 to 609.

Electron energy distributions in uniform electric fields and the Townsend ionization coefficient

1958 ◽  
Vol 244 (1237) ◽  
pp. 166-185 ◽  
Keyword(s):  
Differential Equation ◽  
Cross Section ◽  
Electric Fields ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Present Theory ◽  
Uniform Electric Field ◽  
Ionization Coefficient ◽  
Special Cases ◽  
Wide Range

The second-order differential equation which expresses the equilibrium condition of an electron swarm in a uniform electric field in a gas, the electrons suffering both elastic and inelastic collisions with the gas molecules, is solved by the Jeffreys or W.K.B. method of approximation. The distribution function F(ε) of electrons of energy ε is obtained immediately in a general form involving the elastic and inelastic collision cross-sections and without any restriction on the range of E/p (electric strength/gas pressure) save that introduced in the original differential equation. In almost all applications the approximation is likely to be of high accuracy, and easy to use. Several of the earlier derivations of F(ε) are obtained as special cases. Using the function F(ε) an attempt is made to relate the Townsend ionization coefficient a to the properties of the gas in a more general manner than hitherto, using realistic functions for the collision cross-section. It is finally expressed by the equation α/ p = A exp ( — Bp/E ) in which A and B are functions involving the properties of the gas and the ratio E/p . The important coefficient B is directly related to the form and magnitude of the total inelastic cross-section below the ionization potential and can be evaluated for a particular gas once the cross-section is known experimentally. The present theory shows clearly the influence of E/p on both A and B, a matter which has not been satisfactorily discussed previously. The theory is illustrated by calculations of F (ε) and a/p for hydrogen over a range of E/p from 10 to 1000. The agreement between the calculated results and recent reliable observations of α/ p is surprisingly good considering the nature of the calculations and the wide range of E/p .

Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry

2012 ◽  
Vol 65 (5) ◽  
pp. 504 ◽  
Author(s):  
Antonio N. Calabrese ◽  
Lauren A. Speechley ◽  
Tara L. Pukala
Keyword(s):  
Mass Spectrometry ◽  
Cross Section ◽  
Cross Sections ◽  
Ion Mobility ◽  
Collision Cross Section ◽  
Travelling Wave ◽  
Ion Mobility Mass Spectrometry ◽  
Structural Transitions ◽  
Calmodulin Binding ◽  
Negative Mode

This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.

scholarly journals Some Recent Studies of Electron Swarms in Gases

1992 ◽  
Vol 45 (3) ◽  
pp. 365 ◽  
Author(s):  
H Tagashira
Keyword(s):  
Boltzmann Equation ◽  
Cross Section ◽  
Electric Fields ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Vibrational Excitation ◽  
Time Spectrum ◽  
Electron Collision ◽  
Electron Drift ◽  
Radio Frequency Electric Fields

Some recent studies of electron swarms in gases under the action of an electric field are introduced. The studies include a new type of continuity equation for electrons having a form in which the partial derivative of the electron density with respect to position and to time are interchanged, a method to deduce the time-of-flight and arrival-time-spectrum swarm parameters based on a Fourier-transformed Boltzmann equation, an examination of the correspondence between experimental and theoretical electron drift velocities, and an automatic technique to deduce the electron-gas molecule collision cross section from electron drift velocity data. We also briefly introduce a method for the deduction of electron collision cross sections with gas molecules having vibrational excitation cross sections greater than the elastic momentum transfer cross section by using a gas mixture technique, an integral type of method for solution of the Boltzmann equation with salient numerical stability, a quantitative analysis of the effect of Penning ionisation, and the behaviour of electron swarms under radio frequency electric fields.

scholarly journals A novel framework for molecular characterization of atmospherically relevant organic compounds based on collision cross section and mass-to-charge ratio

2016 ◽  
Vol 16 (20) ◽  
pp. 12945-12959 ◽  
Author(s):  
Xuan Zhang ◽  
Jordan E. Krechmer ◽  
Michael Groessl ◽  
Wen Xu ◽  
Stephan Graf ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Cross Section ◽  
Cross Sections ◽  
Collision Cross Section ◽  
Molecular Structures ◽  
Molecular Signature ◽  
Charge Ratio ◽  
Dynamics Simulations ◽  
Chemical Class ◽  
Atmospherically Relevant

Abstract. A new metric is introduced for representing the molecular signature of atmospherically relevant organic compounds, the collision cross section (Ω), a quantity that is related to the structure and geometry of molecules and is derived from ion mobility measurements. By combination with the mass-to-charge ratio (m∕z), a two-dimensional Ω − m∕z space is developed to facilitate the comprehensive investigation of the complex organic mixtures. A unique distribution pattern of chemical classes, characterized by functional groups including amine, alcohol, carbonyl, carboxylic acid, ester, and organic sulfate, is developed on the 2-D Ω − m∕z space. Species of the same chemical class, despite variations in the molecular structures, tend to situate as a narrow band on the space and follow a trend line. Reactions involving changes in functionalization and fragmentation can be represented by the directionalities along or across these trend lines, thus allowing for the interpretation of atmospheric transformation mechanisms of organic species. The characteristics of trend lines for a variety of functionalities that are commonly present in the atmosphere can be predicted by the core model simulations, which provide a useful tool to identify the chemical class to which an unknown species belongs on the Ω − m∕z space. Within the band produced by each chemical class on the space, molecular structural assignment can be achieved by utilizing collision-induced dissociation as well as by comparing the measured collision cross sections in the context of those obtained via molecular dynamics simulations.

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