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

Orbitrap Mass Spectrometry

(2013) Roman A. Zubarev et al.   ANALYTICAL CHEMISTRY

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

(2013) Harald Marx et al.   NATURE BIOTECHNOLOGY

The State of the Human Proteome in 2012 as Viewed through PeptideAtlas

(2012) Terry Farrah et al.   JOURNAL OF PROTEOME RESEARCH

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

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

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

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

Prediction of Collision-Induced-Dissociation Spectra of Peptides with Post-translational or Process-Induced Modifications

(2011) Zhongqi Zhang   ANALYTICAL CHEMISTRY

SQID: An Intensity-Incorporated Protein Identification Algorithm for Tandem Mass Spectrometry

(2011) Wenzhou Li et al.   JOURNAL OF PROTEOME RESEARCH

Improving SRM Assay Development: A Global Comparison between Triple Quadrupole, Ion Trap, and Higher Energy CID Peptide Fragmentation Spectra

(2011) Erik L. de Graaf et al.   JOURNAL OF PROTEOME RESEARCH

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur 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

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Peptide Identification from Mixture Tandem Mass Spectra

(2010) Jian Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures

(2009) Tonya Pekar Second et al.   ANALYTICAL CHEMISTRY

Phosphopeptide fragmentation and analysis by mass spectrometry

(2009) Paul J. Boersema et al.   JOURNAL OF MASS SPECTROMETRY

Correlation between y-Type Ions Observed in Ion Trap and Triple Quadrupole Mass Spectrometers

(2009) Carly A. Sherwood et al.   JOURNAL OF PROTEOME RESEARCH

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

Proteomics data repositories

(2009) Michael Riffle et al.   PROTEOMICS

Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides

(2009) King Wai Lau et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

(2008) Eric W Deutsch et al.   EMBO REPORTS

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE