A Comprehensive Evaluation of MS/MS Spectrum Prediction Tools for Shotgun Proteomics

Mass-spectrometry-based draft of the Arabidopsis proteome

(2020) Julia Mergner et al.   NATURE

Generating high quality libraries for DIA MS with empirically corrected peptide predictions

(2020) Brian C. Searle et al.   Nature Communications

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

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

(2019) Siegfried Gessulat et al.   NATURE METHODS

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

(2019) Shivani Tiwary et al.   NATURE METHODS

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

(2019) Ralf Gabriels et al.   NUCLEIC ACIDS RESEARCH

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

(2019) Wen-Feng Zeng et al.   ANALYTICAL CHEMISTRY

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

(2019) Hao Yang et al.   BIOINFORMATICS

pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics

(2019) Wen-Jing Zhou et al.   JOURNAL OF PROTEOME RESEARCH

Prediction of LC-MS/MS properties of peptides from sequence by deep learning

(2019) Shenheng Guan et al.   MOLECULAR & CELLULAR PROTEOMICS

Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data

(2019) Rachel M. Miller et al.   JOURNAL OF PROTEOME RESEARCH

Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue

(2019) Jinshuai Sun et al.   JOURNAL OF PROTEOME RESEARCH

IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts

(2018) Xiaomeng Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors

(2018) Cheng Chang et al.   ANALYTICAL CHEMISTRY

Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine

(2018) Hao Chi et al.   NATURE BIOTECHNOLOGY

An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts

(2017) Xiaomeng Shen et al.   JOURNAL OF PROTEOME RESEARCH

Building ProteomeTools based on a complete synthetic human proteome

(2017) Daniel P Zolg et al.   NATURE METHODS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics

(2016) Erik Malmström et al.   Nature Communications

OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction

(2015) Yaojun Wang et al.   BMC BIOINFORMATICS

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

MS2PIP prediction server: compute and visualize MS2peak intensity predictions for CID and HCD fragmentation

(2015) Sven Degroeve et al.   NUCLEIC ACIDS RESEARCH

Prediction of Peptide Fragment Ion Mass Spectra by Data Mining Techniques

(2014) Nai-ping Dong et al.   ANALYTICAL CHEMISTRY

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

MS2PIP: a tool for MS/MS peak intensity prediction

(2013) Sven Degroeve et al.   BIOINFORMATICS

MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions

(2012) Shiwei Sun et al.   JOURNAL OF PROTEOME RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Prediction of Collision-Induced-Dissociation Spectra of Peptides with Post-translational or Process-Induced Modifications

(2011) Zhongqi Zhang   ANALYTICAL CHEMISTRY

SQID: An Intensity-Incorporated Protein Identification Algorithm for Tandem Mass Spectrometry

(2011) Wenzhou Li et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

(2010) Sujun Li et al.   ANALYTICAL CHEMISTRY

Predicting Intensity Ranks of Peptide Fragment Ions

(2009) Ari M. Frank   JOURNAL OF PROTEOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY