Re-analysis of ProteomicsDB using an accurate, sensitive and scalable false discovery rate estimation approach for protein groups

Pout2Prot: An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files

(2022) Kay Schallert et al.   JOURNAL OF PROTEOME RESEARCH

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

(2021) Edward L. Huttlin et al.   CELL

Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

(2021) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

ProteomicsDB: toward a FAIR open-source resource for life-science research

(2021) Ludwig Lautenbacher et al.   NUCLEIC ACIDS RESEARCH

EPIFANY: A Method for Efficient High-Confidence Protein Inference

(2020) Julianus Pfeuffer et al.   JOURNAL OF PROTEOME RESEARCH

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

(2019) Dongxue Wang et al.   Molecular Systems Biology

PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides

(2018) Laurent Jacob et al.   BIOSTATISTICS

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics

(2017) Enrique Audain et al.   Journal of Proteomics

Alternative Splicing May Not Be the Key to Proteome Complexity

(2017) Michael L. Tress et al.   TRENDS IN BIOCHEMICAL SCIENCES

DeepPep: Deep proteome inference from peptide profiles

(2017) Minseung Kim et al.   PLoS Computational Biology

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

How to talk about protein-level false discovery rates in shotgun proteomics

(2016) Matthew The et al.   PROTEOMICS

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

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

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

(2015) Nathan J. Edwards et al.   JOURNAL OF PROTEOME RESEARCH

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

(2015) Federico Abascal et al.   PLoS Computational Biology

Analyzing the First Drafts of the Human Proteome

(2014) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Statistical Approach to Protein Quantification

(2013) Sarah Gerster et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides

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

Recognizing Uncertainty Increases Robustness and Reproducibility of Mass Spectrometry-based Protein Inferences

(2012) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

(2012) Viktor Granholm et al.   Journal of Proteomics

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

(2010) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

(2009) Yong Fuga Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS