Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides

Tandem Mass Spectrum Identification via Cascaded Search

(2015) Attila Kertesz-Farkas et al.   JOURNAL OF PROTEOME RESEARCH

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

(2015) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

(2015) Joel M Chick et al.   NATURE BIOTECHNOLOGY

Mass spectrometrists should search only for peptides they care about

(2015) William Stafford Noble   NATURE METHODS

Analyzing the First Drafts of the Human Proteome

(2014) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

ISPTM: An Iterative Search Algorithm for Systematic Identification of Post-translational Modifications from Complex Proteome Mixtures

(2013) Xin Huang et al.   JOURNAL OF PROTEOME RESEARCH

When Target–Decoy False Discovery Rate Estimations Are Inaccurate and How to Spot Instances

(2013) Robert J. Chalkley   JOURNAL OF PROTEOME RESEARCH

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Bayesian false discovery rates for post-translational modification proteomics

(2013) Yan Fu   Statistics and Its Interface

Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

(2012) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Mass spectrometry in high-throughput proteomics: ready for the big time

(2010) Tommy Nilsson et al.   NATURE METHODS

Mascot-Derived False Positive Peptide Identifications Revealed by Manual Analysis of Tandem Mass Spectra

(2009) Yue Chen 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

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

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

Unrestricted identification of modified proteins using MS/MS

(2009) Erik Ahrné et al.   PROTEOMICS

Separating the Wheat from the Chaff: Unbiased Filtering of Background Tandem Mass Spectra Improves Protein Identification

(2008) Magno Junqueira et al.   JOURNAL OF PROTEOME RESEARCH

Factors That Contribute to the Misidentification of Tyrosine Nitration by Shotgun Proteomics

(2008) Stanley M. Stevens et al.   MOLECULAR & CELLULAR PROTEOMICS

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