Deep learning embedder method and tool for mass spectra similarity search

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

(2019) Siegfried Gessulat et al.   NATURE METHODS

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

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

Application of targeted mass spectrometry in bottom-up proteomics for systems biology research

(2018) Nathan P. Manes et al.   Journal of Proteomics

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification

(2017) Jin-Young Cho et al.   JOURNAL OF PROTEOME RESEARCH

The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

(2017) Meghan C. Burke et al.   JOURNAL OF PROTEOME RESEARCH

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics

(2016) Matthew The et al.   JOURNAL OF PROTEOME RESEARCH

A Pipeline for Differential Proteomics in Unsequenced Species

(2016) Şule Yılmaz et al.   JOURNAL OF PROTEOME RESEARCH

Tandem mass spectral libraries of peptides and their roles in proteomics research

(2016) Wenguang Shao et al.   MASS SPECTROMETRY REVIEWS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

(2016) Johannes Griss et al.   NATURE METHODS

Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries

(2015) Oliver Horlacher et al.   JOURNAL OF PROTEOME RESEARCH

Deep learning

(2015) Yann LeCun et al.   NATURE

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

(2015) Jian Wang et al.   NATURE METHODS

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

(2015) Sven Degroeve et al.   NUCLEIC ACIDS RESEARCH

Proteome Analysis of a Hepatocyte-Specific BIRC5 (Survivin)-Knockout Mouse Model during Liver Regeneration

(2014) Thilo Bracht et al.   JOURNAL OF PROTEOME RESEARCH

Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring

(2014) Chun Wai Manson Ma et al.   JOURNAL OF PROTEOME RESEARCH

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

(2014) Sangtae Kim et al.   Nature Communications

Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner

(2014) Allyson M. MacLean et al.   PLOS BIOLOGY

A novel spectral library workflow to enhance protein identifications

(2013) Haomin Li et al.   Journal of Proteomics

PRIDE Cluster: building a consensus of proteomics data

(2013) Johannes Griss et al.   NATURE METHODS

Refining similarity scoring to enable decoy-free validation in spectral library searching

(2013) Wenguang Shao et al.   PROTEOMICS

Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment

(2012) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data

(2012) Yassene Mohammed et al.   JOURNAL OF PROTEOME RESEARCH

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

(2011) Lydia Ashleigh Baumgardner et al.   JOURNAL OF PROTEOME RESEARCH

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

(2010) Ding Ye et al.   BIOINFORMATICS

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

Clustering Millions of Tandem Mass Spectra

(2007) Ari M. Frank et al.   JOURNAL OF PROTEOME RESEARCH