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Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units

Journal of proteome research, 2019-10, Vol.18 (10), p.3792-3799

2019

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Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry

Journal of proteome research, 2024-04

2024

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Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

Journal of proteome research, 2018-10, Vol.17 (10), p.3463-3474

2018

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Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate

Journal of proteome research, 2019-02, Vol.18 (2), p.585-593

2019

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Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics

Journal of proteome research, 2015-08, Vol.14 (8), p.3148-3161

2015

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On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra

Journal of proteome research, 2015-02, Vol.14 (2), p.1147-1160

2015

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Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

Journal of proteome research, 2022-10, Vol.21 (10), p.2412-2420

2022

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Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

Journal of proteome research, 2008-01, Vol.7 (1), p.29-34

2008

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Tandem Mass Spectrum Identification via Cascaded Search

Journal of proteome research, 2015-08, Vol.14 (8), p.3027-3038

2015

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

Journal of proteome research, 2009-07, Vol.8 (7), p.3737-3745

2009

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Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

Journal of proteome research, 2008-01, Vol.7 (1), p.40-44

2008

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Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

Journal of proteome research, 2011-09, Vol.10 (9), p.3871-3879

2011

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Efficient Indexing of Peptides for Database Search Using Tide

Journal of proteome research, 2023-02, Vol.22 (2), p.577-584

2023

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Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra

Journal of proteome research, 2019-01, Vol.18 (1), p.86-94, Article acs.jproteome.8b00365

2019

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Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning

Journal of proteome research, 2022-07, Vol.21 (7), p.1771-1782

2022

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Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data

Journal of proteome research, 2018-11, Vol.17 (11), p.3644-3656

2018

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Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study

Journal of proteome research, 2017-08, Vol.16 (8), p.2663-2679

2017

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The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data

Journal of proteome research, 2023-02, Vol.22 (2), p.561-569

2023

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Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics

Journal of proteome research, 2022-04, Vol.21 (4), p.1204-1207

2022

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Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

Journal of proteome research, 2010-10, Vol.9 (10), p.5346-5357

2010

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Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

Journal of proteome research, 2014-10, Vol.13 (10), p.4488-4491

2014

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Speeding Up Percolator

Journal of proteome research, 2019-09, Vol.18 (9), p.3353-3359

2019

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On Using Samples of Known Protein Content to Assess the Statistical Calibration of Scores Assigned to Peptide-Spectrum Matches in Shotgun Proteomics

Journal of proteome research, 2011-05, Vol.10 (5), p.2671-2678

2011

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Statistical Calibration of the SEQUEST XCorr Function

Journal of proteome research, 2009-04, Vol.8 (4), p.2106-2113

2009

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Detecting Cross-Linked Peptides by Searching against a Database of Cross-Linked Peptide Pairs

Journal of proteome research, 2010-05, Vol.9 (5), p.2488-2495

2010

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Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units

Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate

Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics

On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra

Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

Tandem Mass Spectrum Identification via Cascaded Search

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

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

Efficient Indexing of Peptides for Database Search Using Tide

Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra

Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning

Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data

Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study

The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data

Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics

Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

Speeding Up Percolator

On Using Samples of Known Protein Content to Assess the Statistical Calibration of Scores Assigned to Peptide-Spectrum Matches in Shotgun Proteomics

Statistical Calibration of the SEQUEST XCorr Function

Detecting Cross-Linked Peptides by Searching against a Database of Cross-Linked Peptide Pairs

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