Predictive chromatography of peptides and proteins as a complementary tool for proteomics

Application of Statistical Thermodynamics To Predict the Adsorption Properties of Polypeptides in Reversed-Phase HPLC

(2015) Irina A. Tarasova et al.   ANALYTICAL CHEMISTRY

Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches

(2015) Fabian Aicheler et al.   ANALYTICAL CHEMISTRY

Applicability of the critical chromatography concept to proteomics problems: I. Effect of the stationary phase and the size of the chromatographic column on the dependence of the retention time of peptides and proteins on the amino acid sequence

(2015) A. V. Gorshkov et al.   JOURNAL OF ANALYTICAL CHEMISTRY

Solvent selectivity and strength in reversed-phase liquid chromatography separation of peptides

(2014) Martin Gilar et al.   JOURNAL OF CHROMATOGRAPHY A

Empirical Multidimensional Space for Scoring Peptide Spectrum Matches in Shotgun Proteomics

(2014) Mark V. Ivanov et al.   JOURNAL OF PROTEOME RESEARCH

Predicting retention time in hydrophilic interaction liquid chromatography mass spectrometry and its use for peak annotation in metabolomics

(2014) Mingshu Cao et al.   Metabolomics

Confetti: A Multiprotease Map of theHeLaProteome for Comprehensive Proteomics

(2014) Xiaofeng Guo et al.   MOLECULAR & CELLULAR PROTEOMICS

Optimized Nonlinear Gradients for Reversed-Phase Liquid Chromatography in Shotgun Proteomics

(2013) Luminita Moruz et al.   ANALYTICAL CHEMISTRY

Mass Fingerprinting of Complex Mixtures: Protein Inference from High-Resolution Peptide Masses and Predicted Retention Times

(2013) Luminita Moruz et al.   JOURNAL OF PROTEOME RESEARCH

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

(2013) Anton A. Goloborodko et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Machine learning applications in proteomics research: How the past can boost the future

(2013) Pieter Kelchtermans et al.   PROTEOMICS

In silico design of targeted SRM-based experiments

(2012) Sven Nahnsen et al.   BMC BIOINFORMATICS

Design of peptide standards with the same composition and minimal sequence variation to monitor performance/selectivity of reversed-phase matrices

(2012) Colin T. Mant et al.   JOURNAL OF CHROMATOGRAPHY A

Application of modern reversed-phase peptide retention prediction algorithms to the Houghten and DeGraw dataset: Peptide helicity and its effect on prediction accuracy

(2012) Janice Reimer et al.   JOURNAL OF CHROMATOGRAPHY A

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

(2012) Hannes Röst et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Instant spectral assignment for advanced decision tree-driven mass spectrometry

(2012) D. J. Bailey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatographic retention time prediction for posttranslationally modified peptides

(2012) Luminita Moruz et al.   PROTEOMICS

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

On the utility of predictive chromatography to complement mass spectrometry based intact protein identification

(2011) Marina L. Pridatchenko et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

(2011) Mi-Youn K Brusniak et al.   BMC BIOINFORMATICS

Sequence-specific predictive chromatography to assist mass spectrometric analysis of asparagine deamidation and aspartate isomerization in peptides

(2011) Nadezda P. Sargaeva et al.   ELECTROPHORESIS

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Applicability of the critical chromatography concept to proteomics problems: Experimental study of the dependence of peptide retention time on the sequence of amino acids in the chain

(2011) I. A. Tarasova et al.   POLYMER SCIENCE SERIES A

Applicability of the critical-chromatography concept to analysis of proteins: Dependence of retention times on the sequence of amino acid residues in a chain

(2011) A. V. Gorshkov et al.   POLYMER SCIENCE SERIES A

Prediction of peptide retention volumes in gradient reversed phase HPLC

(2011) I. N. Azarova et al.   RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

EFFECT OF PHOSPHORYLATION ON THE RETENTION BEHAVIOR OF PEPTIDES IN ION PAIRING REVERSED-PHASE HPLC BASED ON A PREDICTION MODEL

(2010) Yanjun Yu et al.   JOURNAL OF LIQUID CHROMATOGRAPHY & RELATED TECHNOLOGIES

Training, Selection, and Robust Calibration of Retention Time Models for Targeted Proteomics

(2010) Luminita Moruz et al.   JOURNAL OF PROTEOME RESEARCH

Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysis

(2010) Tatiana Yu Perlova et al.   PROTEOMICS

Utility of Retention Prediction Model for Investigation of Peptide Separation Selectivity in Reversed-Phase Liquid Chromatography: Impact of Concentration of Trifluoroacetic Acid, Column Temperature, Gradient Slope and Type of Stationary Phase

(2009) Martin Gilar et al.   ANALYTICAL CHEMISTRY

Retention time alignment algorithms for LC/MS data must consider non-linear shifts

(2009) Katharina Podwojski et al.   BIOINFORMATICS

Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach

(2009) Nico Pfeifer et al.   JOURNAL OF PROTEOME RESEARCH

MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly

(2009) Carly A. Sherwood et al.   JOURNAL OF PROTEOME RESEARCH

Predictions of peptides' retention times in reversed-phase liquid chromatography as a new supportive tool to improve protein identification in proteomics

(2009) Tomasz Bączek et al.   PROTEOMICS

Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics

(2008) Ravi C. Dwivedi et al.   ANALYTICAL CHEMISTRY

Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments

(2008) K. Shinoda et al.   BIOINFORMATICS

Predicting protein retention time in ion-exchange chromatography based on three-dimensional protein characterization

(2008) Li Xu et al.   JOURNAL OF CHROMATOGRAPHY A

Methods of calculating protein hydrophobicity and their application in developing correlations to predict hydrophobic interaction chromatography retention

(2008) Andrea Mahn et al.   JOURNAL OF CHROMATOGRAPHY A

Standardization of retention time data for AMT tag proteomics database generation

(2008) I.A. Tarasova et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions

(2008) Jennifer A. Mead et al.   MOLECULAR & CELLULAR PROTEOMICS

Informatics for peptide retention properties in proteomic LC-MS

(2008) Kosaku Shinoda et al.   PROTEOMICS

Prediction of protein retention times in gradient hydrophobic interaction chromatographic systems

(2007) Jie Chen et al.   JOURNAL OF CHROMATOGRAPHY A