Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences

ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

(2017) Meena Choi et al.   JOURNAL OF PROTEOME RESEARCH

SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics

(2017) Susanna L. Lundström et al.   Scientific Reports

Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data

(2016) Zhibin Ning et al.   ANALYTICAL CHEMISTRY

DeMix-Q: Quantification-Centered Data Processing Workflow

(2016) Bo Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Multiple testing corrections in quantitative proteomics: A useful but blunt tool

(2016) Dana Pascovici et al.   PROTEOMICS

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

(2016) Matthew The et al.   PROTEOMICS

Proteomic maps of breast cancer subtypes

(2016) Stefka Tyanova et al.   Nature Communications

Abundant NDRG2 Expression Is Associated with Aggressiveness and Unfavorable Patients’ Outcome in Basal-Like Breast Cancer

(2016) Vera Kloten et al.   PLoS One

Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins

(2015) Tomi Suomi et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Novor: Real-Time Peptide de Novo Sequencing Software

(2015) Bin Ma   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

(2015) Ying S. Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics

(2015) Ludger J. E. Goeminne et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis

(2015) Agnieszka Latosinska et al.   PLoS One

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

Protein Inference Using Peptide Quantification Patterns

(2014) Pieter N. J. Lukasse et al.   JOURNAL OF PROTEOME RESEARCH

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry

(2014) Bo Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

(2014) B.-J. M. Webb-Robertson et al.   MOLECULAR & CELLULAR PROTEOMICS

SpliceVista, a Tool for Splice Variant Identification and Visualization in Shotgun Proteomics Data

(2014) Yafeng Zhu et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Segmentation of Precursor Mass Range Using “Tiling” Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification

(2013) Catherine E. Vincent et al.   ANALYTICAL CHEMISTRY

Breast cancer classification by proteomic technologies: Current state of knowledge

(2013) S.W. Lam et al.   CANCER TREATMENT REVIEWS

A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra

(2013) Craig D. Wenger et al.   JOURNAL OF PROTEOME RESEARCH

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

(2013) Thilo Muth et al.   JOURNAL OF PROTEOME RESEARCH

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

(2013) Anton A. Goloborodko et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics

(2013) Mohammad Pirmoradian et al.   MOLECULAR & CELLULAR PROTEOMICS

Statistical Approach to Protein Quantification

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

In SilicoInstrumental Response Correction Improves Precision of Label-free Proteomics and Accuracy of Proteomics-based Predictive Models

(2013) Yaroslav Lyutvinskiy et al.   MOLECULAR & CELLULAR PROTEOMICS

Coupling proteomics and transcriptomics in the quest of subtype-specific proteins in breast cancer

(2013) Maria P. Pavlou et al.   PROTEOMICS

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

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

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Efficient error correction for next-generation sequencing of viral amplicons

(2012) Pavel Skums et al.   BMC BIOINFORMATICS

Sequential Monte Carlo multiple testing

(2011) G. K. Sandve et al.   BIOINFORMATICS

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

Enhanced Information Output From Shotgun Proteomics Data by Protein Quantification and Peptide Quality Control (PQPQ)

(2011) Jenny Forshed et al.   MOLECULAR & CELLULAR PROTEOMICS

Distinct choline metabolic profiles are associated with differences in gene expression for basal-like and luminal-like breast cancer xenograft models

(2010) Siver A Moestue et al.   BMC CANCER

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

Intermediate filament dynamics and breast cancer: Aberrant promoter methylation of the Synemin gene is associated with early tumor relapse

(2010) E Noetzel et al.   ONCOGENE

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

(2009) Noelle M Griffin et al.   NATURE BIOTECHNOLOGY

How basal are triple-negative breast cancers?

(2008) François Bertucci et al.   INTERNATIONAL JOURNAL OF CANCER

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