Published in Anal Chem on August 15, 2006
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 13.35
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A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics (2010) 3.78
Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J Proteome Res (2009) 3.44
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods (2011) 2.02
Clustering millions of tandem mass spectra. J Proteome Res (2007) 1.98
Building consensus spectral libraries for peptide identification in proteomics. Nat Methods (2008) 1.96
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods (2011) 1.95
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res (2008) 1.90
Wavelet- and Fourier-transform-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry. Anal Chem (2011) 1.49
Multiplexed MS/MS for improved data-independent acquisition. Nat Methods (2013) 1.48
Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Anal Chem (2010) 1.43
Compound identification using partial and semipartial correlations for gas chromatography-mass spectrometry data. Anal Chem (2012) 1.34
A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry. Bioinformatics (2012) 1.27
Peptide identification from mixture tandem mass spectra. Mol Cell Proteomics (2010) 1.22
Combining results of multiple search engines in proteomics. Mol Cell Proteomics (2013) 1.20
Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics (2010) 1.17
The spectral networks paradigm in high throughput mass spectrometry. Mol Biosyst (2012) 1.11
Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res (2009) 1.08
Methods for peptide identification by spectral comparison. Proteome Sci (2007) 1.05
File formats commonly used in mass spectrometry proteomics. Mol Cell Proteomics (2012) 1.01
Novor: Real-Time Peptide de Novo Sequencing Software. J Am Soc Mass Spectrom (2015) 1.00
Computational approaches to protein inference in shotgun proteomics. BMC Bioinformatics (2012) 0.99
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data. Mol Cell Proteomics (2015) 0.94
Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol Cell Proteomics (2011) 0.94
Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance. Proteomics Clin Appl (2009) 0.93
Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA). Mol Cell Proteomics (2013) 0.93
A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins. Mol Cell Proteomics (2008) 0.92
Exploring the potential of public proteomics data. Proteomics (2015) 0.90
De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics. J Am Soc Mass Spectrom (2012) 0.89
Building and searching tandem mass spectral libraries for peptide identification. Mol Cell Proteomics (2011) 0.88
Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol (2012) 0.85
Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. Mol Cell Proteomics (2014) 0.84
Identifying sources of tick blood meals using unidentified tandem mass spectral libraries. Nat Commun (2013) 0.84
On the estimation of false positives in peptide identifications using decoy search strategy. Proteomics (2009) 0.83
YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research. Genomics Proteomics Bioinformatics (2015) 0.83
On the accuracy and limits of peptide fragmentation spectrum prediction. Anal Chem (2010) 0.83
Expediting SRM assay development for large-scale targeted proteomics experiments. J Proteome Res (2014) 0.82
Proteomics data repositories. Proteomics (2009) 0.82
HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models. J Comput Biol (2007) 0.81
Assigning statistical significance to proteotypic peptides via database searches. J Proteomics (2010) 0.80
A novel spectral library workflow to enhance protein identifications. J Proteomics (2013) 0.80
Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries. Nat Protoc (2014) 0.80
Identification of tandem mass spectra of mixtures of isomeric peptides. J Proteome Res (2010) 0.79
Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Mol Cell Proteomics (2015) 0.77
Algorithms and design strategies towards automated glycoproteomics analysis. Mass Spectrom Rev (2016) 0.77
Kinetic analysis of BCL11B multisite phosphorylation-dephosphorylation and coupled sumoylation in primary thymocytes by multiple reaction monitoring mass spectroscopy. J Proteome Res (2014) 0.76
Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA). Mol Cell Proteomics (2014) 0.76
Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach. Mol Cell Proteomics (2012) 0.76
Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. BMC Bioinformatics (2010) 0.75
Large scale analysis of amino acid substitutions in bacterial proteomics. BMC Bioinformatics (2016) 0.75
Spectral library generating function for assessing spectrum-spectrum match significance. J Proteome Res (2013) 0.75
Compound Identification Using Penalized Linear Regression on Metabolomics. J Mod Appl Stat Methods (2016) 0.75
Scientific workflow optimization for improved peptide and protein identification. BMC Bioinformatics (2015) 0.75
Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra. Proteomics (2013) 0.75
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics (2010) 13.35
Quantifying similarity between motifs. Genome Biol (2007) 9.27
Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods (2007) 8.94
FIMO: scanning for occurrences of a given motif. Bioinformatics (2011) 8.89
An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (2012) 7.27
A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol (2003) 6.32
Searching for statistically significant regulatory modules. Bioinformatics (2003) 5.72
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res (2007) 5.57
Matrix2png: a utility for visualizing matrix data. Bioinformatics (2003) 5.31
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Nature (2006) 4.96
Aminoglycoside antibiotics induce bacterial biofilm formation. Nature (2005) 4.93
The spectrum kernel: a string kernel for SVM protein classification. Pac Symp Biocomput (2002) 4.90
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom (2004) 4.76
Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem (2002) 3.86
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
A statistical framework for genomic data fusion. Bioinformatics (2004) 3.64
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56
Kernel methods for predicting protein-protein interactions. Bioinformatics (2005) 3.52
Exploring gene expression data with class scores. Pac Symp Biocomput (2002) 3.51
Mismatch string kernels for discriminative protein classification. Bioinformatics (2004) 3.27
The KLHL12-Cullin-3 ubiquitin ligase negatively regulates the Wnt-beta-catenin pathway by targeting Dishevelled for degradation. Nat Cell Biol (2006) 3.22
Overexpression of catalase targeted to mitochondria attenuates murine cardiac aging. Circulation (2009) 2.96
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal Chem (2003) 2.89
Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data. Anal Chem (2008) 2.77
High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Anal Chem (2007) 2.75
Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics (2012) 2.66
Learning gene functional classifications from multiple data types. J Comput Biol (2002) 2.65
Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res (2007) 2.61
Code developments to improve the efficiency of automated MS/MS spectra interpretation. J Proteome Res (2003) 2.53
The effect of replication on gene expression microarray experiments. Bioinformatics (2003) 2.49
Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem (2004) 2.40
Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics (2006) 2.36
Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics (2012) 2.29
Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res (2012) 2.24
Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal Chem (2009) 2.20
Comparison of database search strategies for high precursor mass accuracy MS/MS data. J Proteome Res (2010) 2.17
A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J Proteome Res (2003) 2.16
Rapid and accurate peptide identification from tandem mass spectra. J Proteome Res (2008) 2.13
The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo. Proc Natl Acad Sci U S A (2013) 2.10
Effects of modified digestion schemes on the identification of proteins from complex mixtures. J Proteome Res (2006) 2.09
Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol (2003) 2.04
Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci U S A (2005) 2.03
Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods (2011) 2.02
Peptide charge state determination for low-resolution tandem mass spectra. Proc IEEE Comput Syst Bioinform Conf (2005) 1.97
Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem (2003) 1.94
Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data. J Proteome Res (2010) 1.91
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res (2008) 1.90
Learning to predict protein-protein interactions from protein sequences. Bioinformatics (2003) 1.84
Proteomic identification of the cerebral cavernous malformation signaling complex. J Proteome Res (2007) 1.83
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res (2009) 1.80
An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domain. Mol Cell (2010) 1.78
Direct qualitative analysis of triacylglycerols by electrospray mass spectrometry using a linear ion trap. J Am Soc Mass Spectrom (2005) 1.78
Proteomics of integral membrane proteins--theory and application. Chem Rev (2007) 1.76
Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci U S A (2004) 1.67
Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol (2008) 1.66
Support vector machine classification on the web. Bioinformatics (2004) 1.65
Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures. J Proteome Res (2009) 1.63
15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res (2007) 1.58
Shotgun proteomics: tools for the analysis of complex biological systems. Curr Opin Mol Ther (2002) 1.57
Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway. Mol Cell Proteomics (2007) 1.53
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput Biol (2010) 1.52
Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal Chem (2005) 1.52
Multiplexed MS/MS for improved data-independent acquisition. Nat Methods (2013) 1.48
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Bioinformatics (2008) 1.48
Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Res (2013) 1.47
Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics (2011) 1.47
Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics (2008) 1.47
Structure of the Golgi and distribution of reporter molecules at 20 degrees C reveals the complexity of the exit compartments. Mol Biol Cell (2002) 1.44
Predicting co-complexed protein pairs from heterogeneous data. PLoS Comput Biol (2008) 1.44
Statistical calibration of the SEQUEST XCorr function. J Proteome Res (2009) 1.43
Panorama: a targeted proteomics knowledge base. J Proteome Res (2014) 1.43
Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Anal Chem (2010) 1.43
Semi-supervised protein classification using cluster kernels. Bioinformatics (2005) 1.42
Proteomic insights into an expanded cellular role for cytoplasmic lipid droplets. J Lipid Res (2009) 1.41
Ranking predicted protein structures with support vector regression. Proteins (2008) 1.41
FIP3-endosome-dependent formation of the secondary ingression mediates ESCRT-III recruitment during cytokinesis. Nat Cell Biol (2012) 1.38
Sequential Cyk-4 binding to ECT2 and FIP3 regulates cleavage furrow ingression and abscission during cytokinesis. EMBO J (2008) 1.38
QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics (2009) 1.38
Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila. Genome Res (2009) 1.37
Using BiblioSpec for creating and searching tandem MS peptide libraries. Curr Protoc Bioinformatics (2007) 1.35
Organellar proteomics reveals Golgi arginine dimethylation. Mol Biol Cell (2004) 1.35
Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res (2011) 1.33