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

Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines

(2015) Ludger J. E. Goeminne et al.   JOURNAL OF PROTEOME RESEARCH

Importance of Host Cell Arginine Uptake in Francisella Phagosomal Escape and Ribosomal Protein Amounts

(2015) Elodie Ramond et al.   MOLECULAR & CELLULAR PROTEOMICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Aivett Bilbao et al.   PROTEOMICS

Improved Normalization of Systematic Biases Affecting Ion Current Measurements in Label-free Proteomics Data

(2014) Paul A. Rudnick 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

Protein Analysis by Shotgun/Bottom-up Proteomics

(2013) Yaoyang Zhang et al.   CHEMICAL REVIEWS

Quantifying the Effect of Competition for Detection between Coeluting Peptides on Detection Probabilities in Mass-Spectrometry-Based Proteomics

(2013) Paul Schliekelman et al.   JOURNAL OF PROTEOME RESEARCH

Assessment and Improvement of Statistical Tools for Comparative Proteomics Analysis of Sparse Data Sets with Few Experimental Replicates

(2013) Veit Schwämmle et al.   JOURNAL OF PROTEOME RESEARCH

Accurate Label-Free Protein Quantitation with High- and Low-Resolution Mass Spectrometers

(2013) Jocelyn F. Krey et al.   JOURNAL OF PROTEOME RESEARCH

Analyzing LC-MS/MS data by spectral count and ion abundance: two case studies

(2013) Thomas I. Milac 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

Normalization and missing value imputation for label-free LC-MS analysis

(2012) Yuliya V Karpievitch et al.   BMC BIOINFORMATICS

Mass Spectrometry: Reconnaissance at the Frontiers of Biology

(2012) Alma L. Burlingame et al.   MOLECULAR & CELLULAR PROTEOMICS

Investigation of the adaptation of Lactococcus lactis to isoleucine starvation integrating dynamic transcriptome and proteome information

(2011) Clémentine Dressaire et al.   Microbial Cell Factories

Peptide polarity and the position of arginine as sources of selectivity during positive electrospray ionisation mass spectrometry

(2011) Daniel A. Abaye et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

A statistical framework for protein quantitation in bottom-up MS-based proteomics

(2009) Yuliya Karpievitch et al.   BIOINFORMATICS

Testing significance relative to a fold-change threshold is a TREAT

(2009) D. J. McCarthy et al.   BIOINFORMATICS

Protein Quantification in Label-Free LC-MS Experiments

(2009) Timothy Clough et al.   JOURNAL OF PROTEOME RESEARCH

A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches

(2009) Vibhuti J. Patel et al.   JOURNAL OF PROTEOME RESEARCH

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance

(2009) Amanda G. Paulovich et al.   MOLECULAR & CELLULAR PROTEOMICS

Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling

(2009) Lily Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

Mixed-Effects Statistical Model for Comparative LC−MS Proteomics Studies†

(2008) D. S. Daly et al.   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

Does Trypsin Cut Before Proline?

(2007) Jesse Rodriguez et al.   JOURNAL OF PROTEOME RESEARCH