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

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 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 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.

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

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.

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