Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

Cleaning out the Litterbox of Proteomic Scientists’ Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts

(2016) Matthias Schittmayer et al.   JOURNAL OF PROTEOME RESEARCH

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics

(2016) Matthew The et al.   JOURNAL OF PROTEOME RESEARCH

Design and Development of a Medical Big Data Processing System Based on Hadoop

(2015) Qin Yao et al.   JOURNAL OF MEDICAL SYSTEMS

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

(2015) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

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

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Macroporous reversed-phase separation of proteins combined with reversed-phase separation of phosphopeptides and tandem mass spectrometry for profiling the phosphoproteome of MDA-MB-231 cells

(2014) Xiaoxia Ye et al.   ELECTROPHORESIS

Hunting for Unexpected Post-Translational Modifications by Spectral Library Searching with Tier-Wise Scoring

(2014) Chun Wai Manson Ma et al.   JOURNAL OF PROTEOME RESEARCH

Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation

(2014) Mark O. Collins et al.   Journal of Proteomics

Environmental Stress Affects the Activity of Metabolic and Growth Factor Signaling Networks and Induces Autophagy Markers in MCF7 Breast Cancer Cells

(2014) Pedro Casado et al.   MOLECULAR & CELLULAR PROTEOMICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

How to submit MS proteomics data to ProteomeXchange via the PRIDE database

(2014) Tobias Ternent et al.   PROTEOMICS

Sequential Phosphoproteomic Enrichment through Complementary Metal-Directed Immobilized Metal Ion Affinity Chromatography

(2013) Chia-Feng Tsai et al.   ANALYTICAL CHEMISTRY

Chromosome-8-Coded Proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with Partial Immunohistochemical Verifications

(2013) Yang Liu et al.   JOURNAL OF PROTEOME RESEARCH

Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications

(2013) Yingwei Hu et al.   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

PRIDE Cluster: building a consensus of proteomics data

(2013) Johannes Griss et al.   NATURE METHODS

Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells

(2013) P. Casado et al.   Science Signaling

The use of mass defect in modern mass spectrometry

(2012) Lekha Sleno   JOURNAL OF MASS SPECTROMETRY

Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment

(2012) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Data extraction from proteomics raw data: An evaluation of nine tandem MS tools using a large Orbitrap data set

(2012) Francesco Mancuso et al.   Journal of Proteomics

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Spectral archives: a vision for future proteomics data repositories

(2011) Henry Lam   NATURE METHODS

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

(2011) Ari M Frank et al.   NATURE METHODS

Exploring the Human Leukocyte Phosphoproteome Using a Microfluidic Reversed-Phase−TiO2−Reversed-Phase High-Performance Liquid Chromatography Phosphochip Coupled to a Quadrupole Time-of-Flight Mass Spectrometer

(2010) Reinout Raijmakers et al.   ANALYTICAL CHEMISTRY

Peptide Identification from Mixture Tandem Mass Spectra

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

Quantitative erythrocyte membrane proteome analysis with Blue-Native/SDS PAGE

(2009) Renske A. van Gestel et al.   Journal of Proteomics

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring

(2008) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH