Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data

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Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/ACS.JPROTEOME.5B00536
P932PMC publication ID4859434
P698PubMed publication ID26390080
P5875ResearchGate publication ID282047047

P50authorQuanhu ShengQ42122644
Chengjian TuQ59707162
Danjun MaQ59945212
P2093author name stringJun Li
Xue Wang
Yu Shyr
Jun Qu
Zhengping Yi
Xiaomeng Shen
P2860cites workSpectral probabilities and generating functions of tandem mass spectra: a strike against decoy databasesQ37209690
MS-GF+ makes progress towards a universal database search tool for proteomicsQ37283260
A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteomeQ37324346
The one hour yeast proteomeQ37428852
Fast and accurate database searches with MS-GF+PercolatorQ37684591
Quantitative phosphoproteomics reveals novel phosphorylation events in insulin signaling regulated by protein phosphatase 1 regulatory subunit 12A.Q38980335
MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectraQ42113410
Accurate and sensitive peptide identification with Mascot PercolatorQ42538465
Combining percolator with X!Tandem for accurate and sensitive peptide identificationQ45748238
Semi-supervised learning for peptide identification from shotgun proteomics datasets.Q45965072
Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologiesQ47992982
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.Q51897865
Estimating the confidence of peptide identifications without decoy databasesQ84194234
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysisQ24657366
Probability-based protein identification by searching sequence databases using mass spectrometry dataQ27860736
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein databaseQ27861106
Large-scale analysis of the yeast proteome by multidimensional protein identification technologyQ28131778
OLAV: towards high-throughput tandem mass spectrometry data identificationQ28202185
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database searchQ28211385
BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomicsQ28256669
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modelingQ28260951
Open mass spectrometry search algorithmQ28286936
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometryQ29547311
TANDEM: matching proteins with tandem mass spectraQ29615238
Andromeda: a peptide search engine integrated into the MaxQuant environmentQ29615816
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identificationQ30490288
Ion-current-based proteomic profiling of the retina in a rat model of Smith-Lemli-Opitz syndrome.Q30559384
ICan: an optimized ion-current-based quantification procedure with enhanced quantitative accuracy and sensitivity in biomarker discoveryQ30606993
Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.Q30779337
Visualization of LC-MS/MS proteomics data in MaxQuantQ30887155
Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databasesQ30912264
Improved classification of mass spectrometry database search results using newer machine learning approachesQ33228309
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data setsQ33433611
Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patientsQ33815640
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimatesQ34005153
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigationsQ34445192
A cross-validation scheme for machine learning algorithms in shotgun proteomicsQ34486815
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer.Q34629866
A proteomics search algorithm specifically designed for high-resolution tandem mass spectraQ36650680
Selected reaction monitoring for quantitative proteomics: a tutorialQ36973024
Combining results of multiple search engines in proteomicsQ37160902
P433issue11
P304page(s)4662-4673
P577publication date2015-09-30
P1433published inJournal of Proteome ResearchQ3186939
P1476titleOptimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data
P478volume14

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cites work (P2860)
Q98303596Combined proximity labeling and affinity purification-mass spectrometry workflow for mapping and visualizing protein interaction networks
Q64086703Comparison of data-acquisition methods for the identification and quantification of histone post-translational modifications on a Q Exactive HF hybrid quadrupole Orbitrap mass spectrometer
Q28553325Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument
Q63352285Quantitative Proteomics Data in the Public Domain: Challenges and Opportunities
Q35911728Rapid high mass resolution mass spectrometry using matrix-assisted ionization
Q48228108Unambiguous Identification of β-Tubulin as the Direct Cellular Target Responsible for the Cytotoxicity of Chalcone by Photoaffinity Labeling
Q36329329Using the entrapment sequence method as a standard to evaluate key steps of proteomics data analysis process

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