Published in Proteomics on March 01, 2009
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics (2011) 2.88
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog (2012) 1.44
A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics (2011) 1.34
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics (2014) 1.27
Comparison of extensive protein fractionation and repetitive LC-MS/MS analyses on depth of analysis for complex proteomes. J Proteome Res (2010) 1.25
FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines. J Proteome Res (2011) 1.14
An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome. PLoS One (2010) 1.05
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res (2012) 1.04
Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability. Genetics (2011) 1.01
Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol Cell Proteomics (2013) 0.97
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics (2013) 0.94
Ookinete-interacting proteins on the microvillar surface are partitioned into detergent resistant membranes of Anopheles gambiae midguts. J Proteome Res (2011) 0.91
Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation. Genome Biol (2013) 0.89
RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. PLoS One (2010) 0.89
Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol (2012) 0.85
Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines. Anal Bioanal Chem (2012) 0.83
The bacterial proteogenomic pipeline. BMC Genomics (2014) 0.80
Proteomics for systems toxicology. Comput Struct Biotechnol J (2014) 0.79
A novel algorithm for validating peptide identification from a shotgun proteomics search engine. J Proteome Res (2013) 0.79
LC-MS/MS suggests that hole hopping in cytochrome c peroxidase protects its heme from oxidative modification by excess H2O2. Chem Sci (2016) 0.77
Practical and Efficient Searching in Proteomics: A Cross Engine Comparison. Webmedcentral (2013) 0.77
A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome. PLoS One (2017) 0.76
Computational phosphoproteomics: from identification to localization. Proteomics (2015) 0.76
Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation. Mol Cell Proteomics (2015) 0.76
A multi-model statistical approach for proteomic spectral count quantitation. J Proteomics (2016) 0.75
LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database (Oxford) (2015) 0.75
PhosphoHunter: An Efficient Software Tool for Phosphopeptide Identification. Adv Bioinformatics (2015) 0.75
The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Mol Cell Proteomics (2017) 0.75
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods (2007) 25.29
Open mass spectrometry search algorithm. J Proteome Res (2004) 15.25
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol (2006) 9.95
Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics (2005) 8.14
The PeptideAtlas project. Nucleic Acids Res (2006) 7.87
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res (2007) 5.57
Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem (2002) 3.86
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics (2005) 3.51
A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal Chem (2003) 3.50
OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics (2003) 2.73
Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res (2007) 2.61
Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics (2007) 2.13
Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. J Proteome Res (2008) 1.81
The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation. Mol Cell Proteomics (2007) 1.53
ABRF-PRG04: differentiation of protein isoforms. J Biomol Tech (2007) 1.22
Methods, algorithms and tools in computational proteomics: a practical point of view. Proteomics (2007) 1.09
Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev Proteomics (2006) 1.08
Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom (2005) 0.89
Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data. Rapid Commun Mass Spectrom (2005) 0.86
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol (2004) 3.32
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J Biol Chem (2006) 2.66
A comprehensive collection of chicken cDNAs. Curr Biol (2002) 2.47
Differential expression of ion channel transcripts in atrial muscle and sinoatrial node in rabbit. Circ Res (2006) 2.17
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol Cell Biol (2005) 2.13
UKPMC: a full text article resource for the life sciences. Nucleic Acids Res (2010) 1.92
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS One (2008) 1.68
The chicken as a model for large-scale analysis of vertebrate gene function. Nat Rev Genet (2003) 1.57
Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol (2008) 1.54
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics (2009) 1.42
PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics (2004) 1.34
Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. Genome Res (2007) 1.28
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS (2012) 1.25
SBRML: a markup language for associating systems biology data with models. Bioinformatics (2010) 1.24
GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast (2003) 1.22
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinformatics (2008) 1.20
The PSI formal document process and its implementation on the PSI website. Proteomics (2007) 1.20
Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics (2011) 1.16
FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines. J Proteome Res (2011) 1.14
Systematic integration of experimental data and models in systems biology. BMC Bioinformatics (2010) 1.13
CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. Mol Cell Proteomics (2011) 1.12
Conservation of orientation and sequence in protein domain--domain interactions. J Mol Biol (2004) 1.08
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J Proteome Res (2007) 1.07
Enzyme kinetics informatics: from instrument to browser. FEBS J (2010) 1.06
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res (2012) 1.04
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. Nucleic Acids Res (2006) 1.03
ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res (2008) 1.03
A critical and integrated view of the yeast interactome. Comp Funct Genomics (2004) 1.02
Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting. Proteomics (2002) 1.02
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins. Nucleic Acids Res (2010) 1.00
Analysis of gene expression in operons of Streptomyces coelicolor. Genome Biol (2006) 0.98
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics (2009) 0.97
Global mRNA selection mechanisms for translation initiation. Genome Biol (2015) 0.97
Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics. OMICS (2012) 0.97
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett (2013) 0.97
PepSeeker: mining information from proteomic data. Methods Mol Biol (2008) 0.96
e-Fungi: a data resource for comparative analysis of fungal genomes. BMC Genomics (2007) 0.96
Pedro: a configurable data entry tool for XML. Bioinformatics (2004) 0.96
Capture and analysis of quantitative proteomic data. Proteomics (2007) 0.96
A semantic sensor web for environmental decision support applications. Sensors (Basel) (2011) 0.94
An analysis of extensible modelling for functional genomics data. BMC Bioinformatics (2005) 0.94
A toolkit for capturing and sharing FuGE experiments. Bioinformatics (2008) 0.92
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics (2010) 0.91
Data capture in bioinformatics: requirements and experiences with Pedro. BMC Bioinformatics (2008) 0.91
Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics. Proteomics (2002) 0.91
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics (2009) 0.90
Human and mouse homo-oligomeric meprin A metalloendopeptidase: substrate and inhibitor specificities. Biol Chem (2007) 0.89
Investigating protein isoforms via proteomics: a feasibility study. Proteomics (2010) 0.88
Analysis of the trypanosome flagellar proteome using a combined electron transfer/collisionally activated dissociation strategy. J Am Soc Mass Spectrom (2008) 0.88
SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences. Nucleic Acids Res (2003) 0.88
Recent developments in proteome informatics for mass spectrometry analysis. Comb Chem High Throughput Screen (2009) 0.87
Guidelines for reporting the use of column chromatography in proteomics. Nat Biotechnol (2010) 0.86
Observations on the detection of b- and y-type ions in the collisionally activated decomposition spectra of protonated peptides. Rapid Commun Mass Spectrom (2009) 0.86
Quantitative analysis of chaperone network throughput in budding yeast. Proteomics (2013) 0.85
Information quality in proteomics. Brief Bioinform (2008) 0.85
Modeling and managing experimental data using FuGE. OMICS (2009) 0.84
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. BMC Bioinformatics (2006) 0.83
Information management for high content live cell imaging. BMC Bioinformatics (2009) 0.81
Puf3p induces translational repression of genes linked to oxidative stress. Nucleic Acids Res (2013) 0.81
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. BMC Genomics (2007) 0.80
Distributions of ion series in ETD and CID spectra: making a comparison. Methods Mol Biol (2011) 0.78
Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics (2008) 0.78
Conceptual data modelling for bioinformatics. Brief Bioinform (2002) 0.78
A critical assessment of the secondary structure alpha-helices and their termini in proteins. Protein Eng (2002) 0.78
Improved prediction for N-termini of alpha-helices using empirical information. Proteins (2004) 0.77
Expression screening and annotation of a zebrafish myoblast cDNA library. Gene Expr Patterns (2008) 0.77
Focus on Quantitative Proteomics. Proteomics (2015) 0.76
Computational phosphoproteomics: from identification to localization. Proteomics (2015) 0.76
An introduction to proteome bioinformatics. Methods Mol Biol (2010) 0.76
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics (2009) 0.75