In-depth evaluation of software tools for data-independent acquisition based label-free quantification

Qualitative and Quantitative Characterization of Plasma Proteins When Incorporating Traveling Wave Ion Mobility into a Liquid Chromatography–Mass Spectrometry Workflow for Biomarker Discovery: Use of Product Ion Quantitation As an Alternative Data Analysis Tool for Label Free Quantitation

(2014) Charlotte E. Daly et al.   ANALYTICAL CHEMISTRY

General Statistical Framework for Quantitative Proteomics by Stable Isotope Labeling

(2014) Pedro Navarro et al.   JOURNAL OF PROTEOME RESEARCH

Empirical Bayesian Random Censoring Threshold Model Improves Detection of Differentially Abundant Proteins

(2014) Frank Koopmans et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Data processing methods and quality control strategies for label-free LC–MS protein quantification

(2013) Marianne Sandin et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Improving Qualitative and Quantitative Performance for MSE-based Label-free Proteomics

(2013) Nicholas J. Bond et al.   JOURNAL OF PROTEOME RESEARCH

Effects of Traveling Wave Ion Mobility Separation on Data Independent Acquisition in Proteomics Studies

(2013) Pavel V. Shliaha et al.   JOURNAL OF PROTEOME RESEARCH

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

(2013) Ute Distler et al.   NATURE METHODS

Exploring skyline for both MSE-based label-free proteomics and HRMS quantitation of small molecules

(2013) Shanshan Liu et al.   PROTEOMICS

Current challenges in software solutions for mass spectrometry-based quantitative proteomics

(2012) Salvatore Cappadona et al.   AMINO ACIDS

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Benchmarking stable isotope labeling based quantitative proteomics

(2012) A.F. Maarten Altelaar et al.   Journal of Proteomics

Tools for Label-free Peptide Quantification

(2012) Sven Nahnsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

(2012) Melissa M. Matzke et al.   PROTEOMICS

The use of selected reaction monitoring in quantitative proteomics

(2012) Stephen W Holman et al.   Bioanalysis

Computational and Statistical Analysis of Protein Mass Spectrometry Data

(2012) William Stafford Noble et al.   PLoS Computational Biology

RIBAR and xRIBAR: Methods for Reproducible Relative MS/MS-based Label-Free Protein Quantification

(2011) Niklaas Colaert et al.   JOURNAL OF PROTEOME RESEARCH

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

The importance of the digest: Proteolysis and absolute quantification in proteomics

(2011) Philip Brownridge et al.   METHODS

Absolute Quantification of the Glycolytic Pathway in Yeast:

(2011) Kathleen M. Carroll et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS

(2009) Scott J. Geromanos et al.   PROTEOMICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

(2008) Eva Lange et al.   BMC BIOINFORMATICS

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