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

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

(2021) Florian Meier et al.   Nature Communications

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

(2020) Alyssa Q. Stiving et al.   ANALYTICAL CHEMISTRY

Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry

(2020) Denis Morsa et al.   ANALYTICAL CHEMISTRY

LESA Cyclic Ion Mobility Mass Spectrometry of Intact Proteins from Thin Tissue Sections

(2020) Emma K. Sisley et al.   ANALYTICAL CHEMISTRY

Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-Based Quantitation in Proteomic LC/MS/MS

(2020) Kosuke Ogata et al.   ANALYTICAL CHEMISTRY

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

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

Comment on Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry: TIMS Enables Native Mass Spectrometry Applications

(2020) Christian Bleiholder et al.   ANALYTICAL CHEMISTRY

First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes

(2020) Jacob W. McCabe et al.   ANALYTICAL CHEMISTRY

The proteome landscape of the kingdoms of life

(2020) Johannes B. Müller et al.   NATURE

Response to Comment on Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry

(2020) Denis Morsa et al.   ANALYTICAL CHEMISTRY

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

(2020) Florian Meier et al.   NATURE METHODS

Recommendations for reporting ion mobility Mass Spectrometry measurements

(2019) Valérie Gabelica et al.   MASS SPECTROMETRY REVIEWS

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

Separation of Isobaric Mono- and Dimethylated RGG-Repeat Peptides by Differential Ion Mobility-Mass Spectrometry

(2019) Daniel L. Winter et al.   ANALYTICAL CHEMISTRY

Trapped ion mobility spectrometry: A short review

(2018) Mark E. Ridgeway et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

A novel differential ion mobility device expands the depth of proteome coverage and the sensitivity of multiplex proteomic measurements

(2018) Sibylle Pfammatter et al.   MOLECULAR & CELLULAR PROTEOMICS

Improved Peptide Retention Time Prediction in Liquid Chromatography through Deep Learning

(2018) Chunwei Ma et al.   ANALYTICAL CHEMISTRY

Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility–Mass Spectrometry

(2018) Christopher D. Chouinard et al.   ANALYTICAL CHEMISTRY

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

(2017) Samaneh Ghassabi Kondalaji et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Building ProteomeTools based on a complete synthetic human proteome

(2017) Daniel P Zolg et al.   NATURE METHODS

PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration

(2017) Daniel Paul Zolg et al.   PROTEOMICS

Effect of charge on the conformation of highly basic peptides including the tail regions of histone proteins by ion mobility mass spectrometry

(2016) Satoko Akashi et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry

(2016) Zhiwei Zhou et al.   ANALYTICAL CHEMISTRY

3D HPLC-MS with Reversed-Phase Separation Functionality in All Three Dimensions for Large-Scale Bottom-Up Proteomics and Peptide Retention Data Collection

(2016) Vic Spicer et al.   ANALYTICAL CHEMISTRY

Improved Proteome and Phosphoproteome Analysis on a Cation Exchanger by a Combined Acid and Salt Gradient

(2016) Jun Adachi et al.   ANALYTICAL CHEMISTRY

Peptide retention time prediction

(2016) Luminita Moruz et al.   MASS SPECTROMETRY REVIEWS

Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions

(2015) Chunying Xiao et al.   ANALYST

Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

(2015) Florian Meier et al.   JOURNAL OF PROTEOME RESEARCH

How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

(2015) Shu-Hua Chen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A uniform field ion mobility study of melittin and implications of low-field mobility for resolving fine cross-sectional detail in peptide and protein experiments

(2015) Jody C. May et al.   PROTEOMICS

Enhancing bottom-up and top-down proteomic measurements with ion mobility separations

(2015) Erin Shammel Baker et al.   PROTEOMICS

N-Capping Motifs Promote Interaction of Amphipathic Helical Peptides with Hydrophobic Surfaces and Drastically Alter Hydrophobicity Values of Individual Amino Acids

(2014) Vic Spicer et al.   ANALYTICAL CHEMISTRY

Large-Scale Collision Cross-Section Profiling on a Traveling Wave Ion Mobility Mass Spectrometer

(2014) Christopher B. Lietz et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Fundamentals of Trapped Ion Mobility Spectrometry

(2014) Karsten Michelmann et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

Cis–Trans Isomerizations of Proline Residues Are Key to Bradykinin Conformations

(2013) Nicholas A. Pierson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Native ion mobility-mass spectrometry and related methods in structural biology

(2012) A. Konijnenberg et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Evidence for α-helices in the gas phase: A case study using Melittin from honey bee venom

(2011) Hannah V. Florance et al.   ANALYST

Defining intrinsic hydrophobicity of amino acids’ side chains in random coil conformation. Reversed-phase liquid chromatography of designed synthetic peptides vs. random peptide data sets

(2011) Dmitry Shamshurin et al.   JOURNAL OF CHROMATOGRAPHY A

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

Peptide Retention Standards and Hydrophobicity Indexes in Reversed-Phase High-Performance Liquid Chromatography of Peptides

(2009) Oleg V. Krokhin et al.   ANALYTICAL CHEMISTRY

Ion mobility mass spectrometry of proteins and proteinassemblies

(2009) Charlotte Uetrecht et al.   CHEMICAL SOCIETY REVIEWS

Factors That Influence Helical Preferences for Singly Charged Gas-Phase Peptide Ions: The Effects of Multiple Potential Charge-Carrying Sites

(2009) Janel R. McLean et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

(2009) Lei Tao et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

High‐field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high‐resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides

(2009) Yue Xuan et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Pseudorandom Sequence Modifications for Ion Mobility Orthogonal Time-of-Flight Mass Spectrometry

(2008) Brian H. Clowers et al.   ANALYTICAL CHEMISTRY

Ion mobility-mass spectrometry

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

Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis

(2008) Takeshi Masuda et al.   JOURNAL OF PROTEOME RESEARCH