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注意:仅列出部分参考文献,下载原文获取全部文献信息。Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape
Reta Birhanu Kitata et al.
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Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data
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Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation
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Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts
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NATURE COMMUNICATIONS (2022)
OmicsEV: a tool for comprehensive quality evaluation of omics data tables
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Sample Size-Comparable Spectral Library Enhances Data- Independent Acquisition-Based Proteome Coverage of Low-Input Cells
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ANALYTICAL CHEMISTRY (2021)
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JOURNAL OF PROTEOME RESEARCH (2021)
DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation
Ronghui Lou et al.
NATURE COMMUNICATIONS (2021)
pDeep3: Toward More Accurate Spectrum Prediction with Fast Few-Shot Learning
Ching Tarn et al.
ANALYTICAL CHEMISTRY (2021)
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data
Andrea Fossati et al.
NATURE METHODS (2021)
A data-independent acquisition-based global phosphoproteomics system enables deep profiling
Reta Birhanu Kitata et al.
NATURE COMMUNICATIONS (2021)
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data
Yang Young Lu et al.
BIOINFORMATICS (2021)
Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard
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JOURNAL OF PROTEOME RESEARCH (2021)
MaxDIA enables library-based and library-free data-independent acquisition proteomics
Pavel Sinitcyn et al.
NATURE BIOTECHNOLOGY (2021)
Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale
Martin Steger et al.
NATURE COMMUNICATIONS (2021)
Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes
Erli Gao et al.
MOLECULAR OMICS (2021)
Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction
HuiSong Pak et al.
MOLECULAR & CELLULAR PROTEOMICS (2021)
IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs
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Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition
Katalin Barkovits et al.
MOLECULAR & CELLULAR PROTEOMICS (2020)
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
Vadim Demichev et al.
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Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry
Kyung-Cho Cho et al.
ANALYTICAL CHEMISTRY (2020)
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
Thang V. Pham et al.
BIOINFORMATICS (2020)
In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics
Yi Yang et al.
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Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries
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Generating high quality libraries for DIA MS with empirically corrected peptide predictions
Brian C. Searle et al.
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Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries
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MOLECULAR & CELLULAR PROTEOMICS (2020)
Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments
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MOLECULAR & CELLULAR PROTEOMICS (2020)
Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant
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MOLECULAR & CELLULAR PROTEOMICS (2020)
Philosopher: a versatile toolkit for shotgun proteomics data analysis
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Identification of modified peptides using localization-aware open search
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NATURE COMMUNICATIONS (2020)
Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease
Aaron E. Robinson et al.
JOURNAL OF PROTEOME RESEARCH (2020)
diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition
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PDV: an integrative proteomics data viewer
Kai Li et al.
BIOINFORMATICS (2019)
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows
Dario Amodei et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2019)
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
Siegfried Gessulat et al.
NATURE METHODS (2019)
High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis
Shivani Tiwary et al.
NATURE METHODS (2019)
MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning
Wen-Feng Zeng et al.
ANALYTICAL CHEMISTRY (2019)
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
David J. Clark et al.
CELL (2019)
Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry
Philipp Mertins et al.
NATURE PROTOCOLS (2018)
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial
Christina Ludwig et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
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NATURE COMMUNICATIONS (2018)
PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data
Ying S. Ting et al.
NATURE METHODS (2017)
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
George Rosenberger et al.
NATURE METHODS (2017)
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Andy T. Kong et al.
NATURE METHODS (2017)
Data-Independent Acquisition of HLA Class I Peptidomes on the Q Exactive Mass Spectrometer Platform
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PROTEOMICS (2017)
pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning
Xie-Xuan Zhou et al.
ANALYTICAL CHEMISTRY (2017)
A multicenter study benchmarks software tools for label-free proteome quantification
Pedro Navarro et al.
NATURE BIOTECHNOLOGY (2016)
Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses
Sarah J. Parker et al.
PROTEOMICS (2016)
mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry
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JOURNAL OF PROTEOMICS (2015)
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data
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MOLECULAR & CELLULAR PROTEOMICS (2015)
Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues
Roland Bruderer et al.
MOLECULAR & CELLULAR PROTEOMICS (2015)
Quantitative variability of 342 plasma proteins in a human twin population
Yansheng Liu et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
MSPLIT-DIA: sensitive peptide identification for data-independent acquisition
Jian Wang et al.
NATURE METHODS (2015)
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
Chih-Chiang Tsou et al.
NATURE METHODS (2015)
An open-source computational and data resource to analyze digital maps of immunopeptidomes
Etienne Caron et al.
ELIFE (2015)
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
Juergen Cox et al.
MOLECULAR & CELLULAR PROTEOMICS (2014)
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
Hannes L. Roest et al.
NATURE BIOTECHNOLOGY (2014)
Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics
Viktor Granholm et al.
JOURNAL OF PROTEOMICS (2013)
Multiplexed MS/MS for improved data-independent acquisition
Jarrett D. Egertson et al.
NATURE METHODS (2013)
Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition
Jean-Philippe Lambert et al.
NATURE METHODS (2013)
Comet: An open-source MS/MS sequence database search tool
Jimmy K. Eng et al.
PROTEOMICS (2013)
A cross-platform toolkit for mass spectrometry and proteomics
Matthew C. Chambers et al.
NATURE BIOTECHNOLOGY (2012)
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Brendan MacLean et al.
BIOINFORMATICS (2010)
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
Alexey I. Nesvizhskii
JOURNAL OF PROTEOMICS (2010)
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Lukas Kall et al.
NATURE METHODS (2007)
TANDEM: matching proteins with tandem mass spectra
R Craig et al.
BIOINFORMATICS (2004)
A statistical model for identifying proteins by tandem mass spectrometry
AI Nesvizhskii et al.
ANALYTICAL CHEMISTRY (2003)
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
A Keller et al.
ANALYTICAL CHEMISTRY (2002)