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

Biosaur: An open‐source Python software for LC/MS1 peptide feature detection with ion‐mobility support

(2021) Daniil A. Abdrakhimov et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Deep learning the collisional cross sections of the peptide universe from a million experimental values

(2021) Florian Meier et al.   Nature Communications

Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

(2021) Mark V. Ivanov et al.   JOURNAL OF PROTEOME RESEARCH

Deep Learning Based Prediction of Gas Chromatographic Retention Indices for a Wide Variety of Polar and Mid-Polar Liquid Stationary Phases

(2021) Dmitriy D. Matyushin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry

(2021) Chih-Hsiang Chang et al.   JOURNAL OF PROTEOME RESEARCH

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

(2021) Robbin Bouwmeester et al.   NATURE METHODS

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics

(2020) Yi Yang et al.   Nature Communications

Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times

(2020) Robbin Bouwmeester et al.   ANALYTICAL CHEMISTRY

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

(2020) Nikita Prianichnikov et al.   MOLECULAR & CELLULAR PROTEOMICS

Predicting Ion Mobility Collision Cross-Sections Using a Deep Neural Network: DeepCCS

(2019) Pier-Luc Plante et al.   ANALYTICAL CHEMISTRY

Improved Descriptors for the Quantitative Structure–Activity Relationship Modeling of Peptides and Proteins

(2018) Mark H. Barley et al.   Journal of Chemical Information and Modeling

Improved Peptide Retention Time Prediction in Liquid Chromatography through Deep Learning

(2018) Chunwei Ma et al.   ANALYTICAL CHEMISTRY

Discrimination of Leucine and Isoleucine in Peptides Sequencing with Orbitrap Fusion Mass Spectrometer

(2014) Albert T. Lebedev et al.   ANALYTICAL CHEMISTRY

Protein Analysis by Shotgun/Bottom-up Proteomics

(2013) Yaoyang Zhang et al.   CHEMICAL REVIEWS

Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters

(2011) Stephen J. Valentine et al.   JOURNAL OF PROTEOME RESEARCH

Machine learning based prediction for peptide drift times in ion mobility spectrometry

(2010) Anuj R. Shah et al.   BIOINFORMATICS

An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies

(2009) Erin Shammel Baker et al.   JOURNAL OF PROTEOME RESEARCH

Ion mobility-mass spectrometry

(2008) Abu B. Kanu et al.   JOURNAL OF MASS SPECTROMETRY

New descriptors of amino acids and their application to peptide QSAR study

(2008) Zhi-hua Lin et al.   PEPTIDES