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

Data Standardization and Sharing—The work of the HUPO-PSI

(2013) Sandra Orchard   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Pattern recognition in bioinformatics

(2013) D. de Ridder et al.   BRIEFINGS IN BIOINFORMATICS

ProteinLasso: A Lasso regression approach to protein inference problem in shotgun proteomics

(2013) Ting Huang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles

(2013) Thomas Fannes et al.   JOURNAL OF PROTEOME RESEARCH

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

(2013) Harald Marx et al.   NATURE BIOTECHNOLOGY

Extending the coverage of spectral libraries: A neighbor-based approach to predicting intensities of peptide fragmentation spectra

(2013) Chao Ji et al.   PROTEOMICS

Interlaboratory studies and initiatives developing standards for proteomics

(2013) Alexander R. Ivanov et al.   PROTEOMICS

A review of statistical methods for protein identification using tandem mass spectrometry

(2013) William Noble et al.   Statistics and Its Interface

A linear programming model for protein inference problem in shotgun proteomics

(2012) Ting Huang et al.   BIOINFORMATICS

A cross-validation scheme for machine learning algorithms in shotgun proteomics

(2012) Viktor Granholm et al.   BMC BIOINFORMATICS

Protein inference: a review

(2012) T. Huang et al.   BRIEFINGS IN BIOINFORMATICS

Current algorithmic solutions for peptide-based proteomics data generation and identification

(2012) Michael R Hoopmann et al.   CURRENT OPINION IN BIOTECHNOLOGY

Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration

(2012) O. Serang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides

(2012) Banu Dost et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator

(2012) James C. Wright et al.   MOLECULAR & CELLULAR PROTEOMICS

Inference and Validation of Protein Identifications

(2012) Manfred Claassen   MOLECULAR & CELLULAR PROTEOMICS

Prediction of Missed Proteolytic Cleavages for the Selection of Surrogate Peptides for Quantitative Proteomics

(2012) Craig Lawless et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Computational structural analysis of protein interactions and networks

(2012) Yogesh Hooda et al.   PROTEOMICS

Chromatographic retention time prediction for posttranslationally modified peptides

(2012) Luminita Moruz et al.   PROTEOMICS

A SURVEY OF COMPUTATIONAL METHODS FOR PROTEIN COMPLEX PREDICTION FROM PROTEIN INTERACTION NETWORKS

(2012) SRIGANESH SRIHARI et al.   Journal of Bioinformatics and Computational Biology

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

Proteome Coverage Prediction for Integrated Proteomics Datasets

(2011) Manfred Claassen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The importance of the digest: Proteolysis and absolute quantification in proteomics

(2011) Philip Brownridge et al.   METHODS

Direct Maximization of Protein Identifications from Tandem Mass Spectra

(2011) Marina Spivak et al.   MOLECULAR & CELLULAR PROTEOMICS

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

CONSeQuence: Prediction of Reference Peptides for Absolute Quantitative Proteomics Using Consensus Machine Learning Approaches

(2011) Claire E. Eyers et al.   MOLECULAR & CELLULAR PROTEOMICS

Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data

(2011) Christine Vogel et al.   Nature Protocols

Unsupervised 2D gel electrophoresis image segmentation based on active contours

(2011) Michalis A. Savelonas et al.   PATTERN RECOGNITION

Protein spot detection and quantification in 2-DE gel images using machine-learning methods

(2011) Panagiotis Tsakanikas et al.   PROTEOMICS

Mining proteomic data for biomedical research

(2011) Laura L. Elo et al.   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

Predicting Retention Time Shifts Associated with Variation of the Gradient Slope in Peptide RP-HPLC

(2010) Vic Spicer et al.   ANALYTICAL CHEMISTRY

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

(2010) Sujun Li et al.   ANALYTICAL CHEMISTRY

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

(2010) B.-J. M. Webb-Robertson et al.   BIOINFORMATICS

Retention Characteristics of Peptides in RP-LC: Peptide Retention Prediction

(2010) Valeri I. Babushok et al.   CHROMATOGRAPHIA

The Importance of Peptide Detectability for Protein Identification, Quantification, and Experiment Design in MS/MS Proteomics

(2010) Yong Fuga Li et al.   JOURNAL OF PROTEOME RESEARCH

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

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

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

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

Image analysis tools and emerging algorithms for expression proteomics

(2010) Andrew W. Dowsey et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

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

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

A model for predicting slopes S in the basic equation for the linear-solvent-strength theory of peptide separation by reversed-phase high-performance liquid chromatography

(2009) Hoangkim Vu et al.   JOURNAL OF CHROMATOGRAPHY A

Predicting Intensity Ranks of Peptide Fragment Ions

(2009) Ari M. Frank   JOURNAL OF PROTEOME RESEARCH

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

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

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

Improvements to the Percolator Algorithm for Peptide Identification from Shotgun Proteomics Data Sets

(2009) Marina Spivak et al.   JOURNAL OF PROTEOME RESEARCH

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance

(2009) Amanda G. Paulovich et al.   MOLECULAR & CELLULAR PROTEOMICS

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

(2009) Vincent A Fusaro et al.   NATURE BIOTECHNOLOGY

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

SitePredicting the cleavage of proteinase substrates

(2009) Jelle Verspurten et al.   TRENDS IN BIOCHEMICAL SCIENCES

An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identifications from Tandem Mass Spectra

(2009) Nathan Edwards et al.   Clinical Proteomics

A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data

(2008) Cong Zhou et al.   BMC BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results

(2008) John C Braisted et al.   BMC BIOINFORMATICS

Adaptive Discriminant Function Analysis and Reranking of MS/MS Database Search Results for Improved Peptide Identification in Shotgun Proteomics

(2008) Ying Ding et al.   JOURNAL OF PROTEOME RESEARCH

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

(2008) Christopher Y. Park et al.   JOURNAL OF PROTEOME RESEARCH

Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors

(2008) Sheila J. Barton et al.   MASS SPECTROMETRY REVIEWS

Assessment of PLSDA cross validation

(2008) Johan A. Westerhuis et al.   Metabolomics

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

(2008) Michael Mueller et al.   PROTEOMICS

Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression Data

(2007) Paul Kearney et al.   JOURNAL OF PROTEOME RESEARCH