Computational Mass Spectrometry–Based Proteomics

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

(2011) Mi-Youn K Brusniak et al.   BMC BIOINFORMATICS

Added predictive value of high-throughput molecular data to clinical data and its validation

(2011) A.-L. Boulesteix et al.   BRIEFINGS IN BIOINFORMATICS

Advancing Next-Generation Proteomics through Computational Research

(2011) Nuno Bandeira et al.   JOURNAL OF PROTEOME RESEARCH

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

Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics

(2011) Henry Lam et al.   METHODS

Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra

(2011) Kyowon Jeong et al.   MOLECULAR & CELLULAR PROTEOMICS

Correct Interpretation of Comprehensive Phosphorylation Dynamics Requires Normalization by Protein Expression Changes

(2011) Ronghu Wu et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

(2011) Lukas Reiter et al.   NATURE METHODS

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

(2011) Tamar Geiger et al.   Nature Protocols

Quality assessments of peptide-spectrum matches in shotgun proteomics

(2011) Viktor Granholm et al.   PROTEOMICS

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases

(2011) Frank Emmert-Streib et al.   PLoS Computational Biology

Quantitation in Mass-Spectrometry-Based Proteomics

(2010) Waltraud X. Schulze et al.   Annual Review of Plant Biology

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Missing value imputation for gene expression data: computational techniques to recover missing data from available information

(2010) A. W.-C. Liew et al.   BRIEFINGS IN BIOINFORMATICS

Comprehensive proteomics

(2010) Martin Beck et al.   CURRENT OPINION IN BIOTECHNOLOGY

Role of spectral counting in quantitative proteomics

(2010) Deborah H Lundgren et al.   Expert Review of Proteomics

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

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

TagRecon: High-Throughput Mutation Identification through Sequence Tagging

(2010) Surendra Dasari et al.   JOURNAL OF PROTEOME RESEARCH

Optimal de novo Design of MRM Experiments for Rapid Assay Development in Targeted Proteomics

(2010) Andreas Bertsch et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

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

Back to the basics: Maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses

(2010) Luis Valledor et al.   Journal of Proteomics

The pros and cons of peptide-centric proteomics

(2010) Mark W Duncan et al.   NATURE BIOTECHNOLOGY

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

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

(2010) Tommy Nilsson et al.   NATURE METHODS

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Free computational resources for designing selected reaction monitoring transitions

(2010) Jennifer A. Cham Mead et al.   PROTEOMICS

Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry

(2010) Nitin Gupta et al.   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

A statistical framework for protein quantitation in bottom-up MS-based proteomics

(2009) Yuliya Karpievitch et al.   BIOINFORMATICS

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

Dealing with missing values in large-scale studies: microarray data imputation and beyond

(2009) T. Aittokallio   BRIEFINGS IN BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry

(2009) S. E. Abbatiello et al.   CLINICAL CHEMISTRY

Bioinformatics analysis of mass spectrometry-based proteomics data sets

(2009) Chanchal Kumar et al.   FEBS LETTERS

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Protein Quantification in Label-Free LC-MS Experiments

(2009) Timothy Clough et al.   JOURNAL OF PROTEOME RESEARCH

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg et al.   JOURNAL OF PROTEOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb 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

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis

(2009) Noelle M Griffin et al.   NATURE BIOTECHNOLOGY

A stress test for mass spectrometry–based proteomics

(2009) Ruedi Aebersold   NATURE METHODS

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

(2009) Alexander W Bell et al.   NATURE METHODS

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

(2009) Paola Picotti et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics☆

(2008) Neil R. Kitteringham et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data

(2008) Lukas N. Mueller et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry Based Targeted Protein Quantification: Methods and Applications

(2008) Sheng Pan et al.   JOURNAL OF PROTEOME RESEARCH

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

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

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Comparative LC-MS: A landscape of peaks and valleys

(2008) Antoine H. P. America et al.   PROTEOMICS

False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH