Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries

(2016) Jemma X. Wu et al.   MOLECULAR & CELLULAR PROTEOMICS

An Empirical Approach to Signature Peptide Choice for Selected Reaction Monitoring: Quantification of Uromodulin in Urine

(2015) Q. Fu et al.   CLINICAL CHEMISTRY

Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer

(2015) Jan Muntel et al.   JOURNAL OF PROTEOME RESEARCH

Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC–MS/MS

(2015) Aivett Bilbao et al.   JOURNAL OF PROTEOME RESEARCH

Quantifying Protein Measurands by Peptide Measurements: Where Do Errors Arise?

(2015) Irene van den Broek et al.   JOURNAL OF PROTEOME RESEARCH

Online Peptide Fractionation Using a Multiphasic Microfluidic Liquid Chromatography Chip Improves Reproducibility and Detection Limits for Quantitation in Discovery and Targeted Proteomics

(2015) Christoph Krisp et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry

(2015) Sarah J. Parker et al.   MOLECULAR & CELLULAR PROTEOMICS

Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files

(2015) Yuanyue Li et al.   NATURE METHODS

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

(2015) Jian Wang et al.   NATURE METHODS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Building high-quality assay libraries for targeted analysis of SWATH MS data

(2015) Olga T Schubert et al.   Nature Protocols

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

(2015) Aivett Bilbao et al.   PROTEOMICS

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

(2014) Meena Choi et al.   BIOINFORMATICS

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

(2014) Tanveer S. Batth et al.   JOURNAL OF PROTEOME RESEARCH

Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics

(2014) Umut H. Toprak et al.   MOLECULAR & CELLULAR PROTEOMICS

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis

(2013) Olga T. Schubert et al.   Cell Host & Microbe

Energy Dependence of HCD on Peptide Fragmentation: Stepped Collisional Energy Finds the Sweet Spot

(2013) Jolene K. Diedrich et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

(2013) Jean-Philippe Lambert et al.   NATURE METHODS

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

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

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

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

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS