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

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

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

Multiplexed peptide analysis using data-independent acquisition and Skyline

(2015) Jarrett D Egertson et al.   Nature Protocols

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

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

Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry

(2014) Michael W. Burgess et al.   MOLECULAR & CELLULAR PROTEOMICS

MixGF: Spectral Probabilities for Mixture Spectra from more than One Peptide

(2014) Jian Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Neutron Encoded Labeling for Peptide Identification

(2013) Christopher M. Rose et al.   ANALYTICAL CHEMISTRY

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

(2013) John D. Chapman et al.   MASS SPECTROMETRY REVIEWS

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Multiplexed MS/MS for improved data-independent acquisition

(2013) Jarrett D Egertson et al.   NATURE METHODS

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

(2012) Chad R. Weisbrod et al.   JOURNAL OF PROTEOME RESEARCH

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Targeted proteomics

(2012) Vivien Marx   NATURE METHODS

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

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

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library

(2011) Chia-Yu Yen et al.   MOLECULAR & CELLULAR PROTEOMICS

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

XDIA: improving on the label-free data-independent analysis

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

The Importance of Peptide Detectability for Protein Identification, Quantification, and Experiment Design in MS/MS Proteomics

(2010) Yong Fuga Li et al.   JOURNAL OF PROTEOME RESEARCH

Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies

(2010) Stephane Houel et al.   JOURNAL OF PROTEOME RESEARCH

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Deconvolution of Mixture Spectra from Ion-Trap Data-Independent-Acquisition Tandem Mass Spectrometry

(2009) Marshall Bern et al.   ANALYTICAL CHEMISTRY

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

(2009) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures

(2009) Guo-Zhong Li et al.   PROTEOMICS

Precursor-Ion Mass Re-Estimation Improves Peptide Identification on Hybrid Instruments

(2008) Roland Luethy et al.   JOURNAL OF PROTEOME RESEARCH

A Fast SEQUEST Cross Correlation Algorithm

(2008) Jimmy K. Eng et al.   JOURNAL OF PROTEOME RESEARCH

Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics

(2008) Thomas Koenig 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

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS