Published in Mol Cell Proteomics on December 17, 2012
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics (2014) 5.09
Quantitative proteomic analysis of histone modifications. Chem Rev (2015) 1.32
Recent advances in quantitative neuroproteomics. Methods (2013) 1.23
Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics (2014) 1.07
Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum. Plant Cell (2014) 0.96
Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. Proc Natl Acad Sci U S A (2014) 0.92
Quantitative profiling of the protein coronas that form around nanoparticles. Nat Protoc (2014) 0.89
Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics (2014) 0.89
Mechanism of super-assembly of respiratory complexes III and IV. Nature (2016) 0.88
SILAC-iPAC: a quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture. J Proteomics (2014) 0.88
Global analysis of cellular proteolysis by selective enzymatic labeling of protein N-termini. Methods Enzymol (2014) 0.83
Chemical proteomics approaches for identifying the cellular targets of natural products. Nat Prod Rep (2016) 0.83
Mass spectrometry-based proteomics in Chest Medicine, Gerontology, and Nephrology: subgroups omics for personalized medicine. Biomedicine (Taipei) (2014) 0.80
Proteomics for systems toxicology. Comput Struct Biotechnol J (2014) 0.79
Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. Biomolecules (2015) 0.79
Glycoproteins identified from heart failure and treatment models. Proteomics (2014) 0.79
Proteomics approaches shed new light on hibernation physiology. J Comp Physiol B (2015) 0.78
Regulation of highly homologous major urinary proteins in house mice quantified with label-free proteomic methods. Mol Biosyst (2016) 0.78
A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation. Elife (2016) 0.78
Algorithms and design strategies towards automated glycoproteomics analysis. Mass Spectrom Rev (2016) 0.77
Probing structures of large protein complexes using zero-length cross-linking. Methods (2015) 0.77
Decoding protein networks during virus entry by quantitative proteomics. Virus Res (2015) 0.77
Proteomics analysis of human tears from aqueous-deficient and evaporative dry eye patients. Sci Rep (2016) 0.76
A proteomic approach to obesity and type 2 diabetes. J Cell Mol Med (2015) 0.76
Human Urine Proteomics: Analytical Techniques and Clinical Applications in Renal Diseases. Int J Proteomics (2015) 0.76
Proteomic tools to decipher microbial community structure and functioning. Environ Sci Pollut Res Int (2014) 0.76
The Use of Advanced Mass Spectrometry to Dissect the Life-Cycle of Photosystem II. Front Plant Sci (2016) 0.76
Understanding the rules of the road: proteomic approaches to interrogate the blood brain barrier. Front Neurosci (2015) 0.76
The presence of prolines in the flanking region of an immunodominant HIV-2 gag epitope influences the quality and quantity of the epitope generated. Eur J Immunol (2015) 0.75
Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. Mol Cell Proteomics (2016) 0.75
Characterization of the human aqueous humour proteome: A comparison of the genders. PLoS One (2017) 0.75
A strong neutrophil elastase proteolytic fingerprint marks the carcinoma tumor proteome. Mol Cell Proteomics (2016) 0.75
Proteome Profiling of Wheat Shoots from Different Cultivars. Front Plant Sci (2017) 0.75
Mass spectrometric determination of early and advanced glycation in biology. Glycoconj J (2016) 0.75
Shotgun Proteomics Analysis of Estrogen Effects in the Uterus Using Two-Dimensional Liquid Chromatography and Tandem Mass Spectrometry. Methods Mol Biol (2016) 0.75
Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis. Data Brief (2017) 0.75
A Survey of the Impact of Deyolking on Biological Processes Covered by Shotgun Proteomic Analyses of Zebrafish Embryos. Zebrafish (2015) 0.75
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics (2002) 30.58
Mass spectrometry-based proteomics. Nature (2003) 28.94
Global quantification of mammalian gene expression control. Nature (2011) 22.36
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol (1999) 21.92
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics (2004) 19.05
Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics (2005) 10.67
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol (2006) 9.95
ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics (2008) 9.47
Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol (2005) 7.52
Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem (2007) 6.80
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem (2003) 6.63
Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol (2007) 6.56
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res (2006) 6.43
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics (2010) 5.77
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
The quantitative proteome of a human cell line. Mol Syst Biol (2011) 4.57
OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics (2008) 4.41
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics (2007) 3.60
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res (2008) 3.36
A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods (2008) 3.35
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics (2006) 3.32
A protein complex network of Drosophila melanogaster. Cell (2011) 3.31
Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem (2011) 3.19
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res (2006) 3.10
Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol (2005) 2.98
Proteomics: a pragmatic perspective. Nat Biotechnol (2010) 2.81
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet (2009) 2.44
Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol (2003) 2.37
Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics (2005) 2.24
Quantitation in mass-spectrometry-based proteomics. Annu Rev Plant Biol (2010) 2.14
Role of spectral counting in quantitative proteomics. Expert Rev Proteomics (2010) 2.00
A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics (2005) 1.91
Normalization regarding non-random missing values in high-throughput mass spectrometry data. Pac Symp Biocomput (2006) 1.86
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics (2008) 1.80
Comparative LC-MS: a landscape of peaks and valleys. Proteomics (2008) 1.73
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Mol Syst Biol (2007) 1.50
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics (2008) 1.48
The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol (2011) 1.44
A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics (2007) 1.44
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J Proteome Res (2012) 1.39
Alignment of LC-MS images, with applications to biomarker discovery and protein identification. Proteomics (2008) 1.22
Computational mass spectrometry-based proteomics. PLoS Comput Biol (2011) 1.18
Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides. Mol Cell Proteomics (2009) 1.18
Bioinformatics analysis of mass spectrometry-based proteomics data sets. FEBS Lett (2009) 1.16
Protein quantification across hundreds of experimental conditions. Proc Natl Acad Sci U S A (2009) 1.10
Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res (2006) 1.07
msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies. Mol Cell Proteomics (2012) 1.01
A serum protein profile predictive of the resistance to neoadjuvant chemotherapy in advanced breast cancers. Mol Cell Proteomics (2011) 0.97
The proteomic profile of circulating pentraxin 3 (PTX3) complex in sepsis demonstrates the interaction with azurocidin 1 and other components of neutrophil extracellular traps. Mol Cell Proteomics (2012) 0.96
Glycomic and proteomic profiling of pancreatic cyst fluids identifies hyperfucosylated lactosamines on the N-linked glycans of overexpressed glycoproteins. Mol Cell Proteomics (2012) 0.94
Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. BMC Bioinformatics (2008) 0.93
Analysis of the human pituitary proteome by data independent label-free liquid chromatography tandem mass spectrometry. Proteomics (2011) 0.92
MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data. J Chromatogr A (2011) 0.84
RIBAR and xRIBAR: Methods for reproducible relative MS/MS-based label-free protein quantification. J Proteome Res (2011) 0.82
Retention time alignment of LC/MS data by a divide-and-conquer algorithm. J Am Soc Mass Spectrom (2012) 0.80
Recent segmental duplications in the human genome. Science (2002) 21.30
SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics (2008) 17.31
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
RazerS--fast read mapping with sensitivity control. Genome Res (2009) 6.53
Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A (2004) 6.08
Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics (2008) 4.41
TOPP--the OpenMS proteomics pipeline. Bioinformatics (2007) 4.37
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res (2005) 4.15
NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity. Nucleic Acids Res (2011) 3.19
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Simultaneous alignment of short reads against multiple genomes. Genome Biol (2009) 2.79
BNDB - the Biochemical Network Database. BMC Bioinformatics (2007) 2.75
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell (2013) 2.64
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics (2006) 2.40
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics (2009) 2.35
High-accuracy peak picking of proteomics data using wavelet techniques. Pac Symp Biocomput (2006) 1.77
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics (2008) 1.77
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics (2007) 1.61
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics (2009) 1.55
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics (2007) 1.51
RazerS 3: faster, fully sensitive read mapping. Bioinformatics (2012) 1.47
Segment-based multiple sequence alignment. Bioinformatics (2008) 1.46
A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics (2011) 1.44
A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics (2007) 1.44
YLoc--an interpretable web server for predicting subcellular localization. Nucleic Acids Res (2010) 1.43
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics (2009) 1.41
An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res (2013) 1.39
SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res (2006) 1.33
Going from where to why--interpretable prediction of protein subcellular localization. Bioinformatics (2010) 1.32
A combinatorial approach to protein docking with flexible side chains. J Comput Biol (2002) 1.29
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics (2013) 1.28
Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med (2009) 1.27
Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci (2005) 1.23
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics (2008) 1.20
Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res (2013) 1.19
Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families. PLoS Comput Biol (2010) 1.19
Machine learning competition in immunology - Prediction of HLA class I binding peptides. J Immunol Methods (2011) 1.18
SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. J Proteome Res (2009) 1.17
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics (2009) 1.17
LC-MSsim--a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics (2008) 1.14
Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. J Comput Biol (2008) 1.12
BALL--biochemical algorithms library 1.3. BMC Bioinformatics (2010) 1.12
OpenMS and TOPP: open source software for LC-MS data analysis. Methods Mol Biol (2011) 1.12
Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome. PLoS Pathog (2010) 1.12
Prediction of dual protein targeting to plant organelles. New Phytol (2009) 1.10
OptiTope--a web server for the selection of an optimal set of peptides for epitope-based vaccines. Nucleic Acids Res (2009) 1.10
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics (2012) 1.10
Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res (2006) 1.07
BALLView: a tool for research and education in molecular modeling. Bioinformatics (2005) 1.07
MSSimulator: Simulation of mass spectrometry data. J Proteome Res (2011) 1.06
Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress. J Proteomics (2012) 1.06
A mathematical framework for the selection of an optimal set of peptides for epitope-based vaccines. PLoS Comput Biol (2008) 1.06
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics. BMC Bioinformatics (2007) 1.05
POPISK: T-cell reactivity prediction using support vector machines and string kernels. BMC Bioinformatics (2011) 1.03
Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. J Proteome Res (2011) 1.03
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. BMC Bioinformatics (2005) 1.01
Analytical model of peptide mass cluster centres with applications. Proteome Sci (2006) 1.00
Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays. Nucleic Acids Res (2013) 1.00
Comparative immunopeptidomics of humans and their pathogens. Proc Natl Acad Sci U S A (2004) 0.99
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol (2009) 0.99
Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. J Proteome Res (2010) 0.99
Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data. Mol Cell Proteomics (2013) 0.98
Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics (2004) 0.96
The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. Eur J Cell Biol (2010) 0.95
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis (2009) 0.95
Universal peptide vaccines - optimal peptide vaccine design based on viral sequence conservation. Vaccine (2011) 0.95
TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J Proteome Res (2012) 0.94
TOPPView: an open-source viewer for mass spectrometry data. J Proteome Res (2009) 0.94
Exploiting physico-chemical properties in string kernels. BMC Bioinformatics (2010) 0.93
From sequence to structure and back again: approaches for predicting protein-DNA binding. Proteome Sci (2004) 0.93
Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. BMC Bioinformatics (2008) 0.93
Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics (2007) 0.92
BALLDock/SLICK: a new method for protein-carbohydrate docking. J Chem Inf Model (2008) 0.92
STELLAR: fast and exact local alignments. BMC Bioinformatics (2011) 0.91
MicroRazerS: rapid alignment of small RNA reads. Bioinformatics (2009) 0.91
Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. J Proteome Res (2009) 0.91
EpiToolKit--a web server for computational immunomics. Nucleic Acids Res (2008) 0.91
Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments. BioData Min (2009) 0.90
Towards in silico design of epitope-based vaccines. Expert Opin Drug Discov (2009) 0.90
SNEP: SNP-derived epitope prediction program for minor H antigens. Immunogenetics (2005) 0.90
Epitope prediction algorithms for peptide-based vaccine design. Proc IEEE Comput Soc Bioinform Conf (2003) 0.89
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. J Proteomics (2013) 0.89
Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics (2005) 0.88
Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. Proteomics (2015) 0.87
Universality of protein reentrant condensation in solution induced by multivalent metal ions. Proteins (2010) 0.87
FRED--a framework for T-cell epitope detection. Bioinformatics (2009) 0.87
BALLView: an object-oriented molecular visualization and modeling framework. J Comput Aided Mol Des (2006) 0.87
Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways. Blood (2013) 0.87
Approaching clinical proteomics: current state and future fields of application in cellular proteomics. Cytometry A (2009) 0.86
Significantly improved prediction of subcellular localization by integrating text and protein sequence data. Pac Symp Biocomput (2006) 0.85