piNET: a versatile web platform for downstream analysis and visualization of proteomics data

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

(2018) Alexandra B. Keenan et al.   Cell Systems

DeepPhos: prediction of protein phosphorylation sites with deep learning

(2018) Fenglin Luo et al.   BIOINFORMATICS

A curated resource for phosphosite-specific signature analysis

(2018) Karsten Krug et al.   MOLECULAR & CELLULAR PROTEOMICS

qPhos: a database of protein phosphorylation dynamics in humans

(2018) Kai Yu et al.   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms

(2018) Peter V Hornbeck et al.   NUCLEIC ACIDS RESEARCH

dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications

(2018) Kai-Yao Huang et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

iPTMnet: an integrated resource for protein post-translational modification network discovery

(2017) Hongzhan Huang et al.   NUCLEIC ACIDS RESEARCH

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

(2017) Amar Koleti et al.   NUCLEIC ACIDS RESEARCH

Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing

(2016) Ludovic C. Gillet et al.   Annual Review of Analytical Chemistry

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes

(2016) Jennifer G. Abelin et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics: Fig. 1.

(2015) Yasset Perez-Riverol et al.   BIOINFORMATICS

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

SIGNOR: a database of causal relationships between biological entities

(2015) Livia Perfetto et al.   NUCLEIC ACIDS RESEARCH

Applications of targeted proteomics in systems biology and translational medicine

(2015) H. Alexander Ebhardt et al.   PROTEOMICS

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

(2015) Yasset Perez-Riverol et al.   PROTEOMICS

Processing strategies and software solutions for data-independent acquisition in mass spectrometry

(2015) Aivett Bilbao et al.   PROTEOMICS

KinomeXplorer: an integrated platform for kinome biology studies

(2014) Heiko Horn et al.   NATURE METHODS

A fast Peptide Match service for UniProt Knowledgebase

(2013) Chuming Chen et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

PHOSIDA 2011: the posttranslational modification database

(2010) F. Gnad et al.   NUCLEIC ACIDS RESEARCH

RegPhos: a system to explore the protein kinase–substrate phosphorylation network in humans

(2010) Tzong-Yi Lee et al.   NUCLEIC ACIDS RESEARCH

Pathway Palette: A rich internet application for peptide-, protein- and network-oriented analysis of MS data

(2010) Manor Askenazi et al.   PROTEOMICS

PhosphoPep—a database of protein phosphorylation sites in model organisms

(2008) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY