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.

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.

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.

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.

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 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 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

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 Recommendations for Reporting Ion Mobility Mass Spectrometry Measurements

2018 ◽  
Author(s):  
Valerie Gabelica ◽  
Alexandre A. Shvartsburg ◽  
Carlos Afonso ◽  
Perdita E. Barran ◽  
Justin L. P. Benesch ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Cross Section ◽  
Ion Mobility ◽  
Collision Cross Section ◽  
Ion Mobility Mass Spectrometry ◽  
Gas Temperature ◽  
Mobility Data ◽  
Community Effort ◽  
Primary Standards ◽  
Definition Of

Here we present a guide on ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties on mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N, (ii) ion mobility does not measure surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model, (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort towards establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. <br><br><br>

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