Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020
出版年份 2020 全文链接
标题
Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020
作者
关键词
-
出版物
PROTEOMICS
Volume -, Issue -, Pages 1900276
出版商
Wiley
发表日期
2020-04-10
DOI
10.1002/pmic.201900276
参考文献
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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。- Proteogenomic Characterization of Endometrial Carcinoma
- (2020) Yongchao Dou et al. CELL
- Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression
- (2020) Bing Bai et al. NEURON
- Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma
- (2019) Ying Jiang et al. NATURE
- MaxQuant.Live enables global targeting of more than 25,000 peptides
- (2019) Christoph Wichmann et al. MOLECULAR & CELLULAR PROTEOMICS
- Analysis of 1508 plasma samples by capillary flow data-independent acquisition profiles proteomics of weight loss and maintenance
- (2019) Roland Bruderer et al. MOLECULAR & CELLULAR PROTEOMICS
- Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
- (2019) Siegfried Gessulat et al. NATURE METHODS
- High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis
- (2019) Shivani Tiwary et al. NATURE METHODS
- MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning
- (2019) Wen-Feng Zeng et al. ANALYTICAL CHEMISTRY
- Thesaurus: quantifying phosphopeptide positional isomers
- (2019) Brian C. Searle et al. NATURE METHODS
- Speeding Up Percolator
- (2019) John T. Halloran et al. JOURNAL OF PROTEOME RESEARCH
- Systematic Assessment of the Effect of Internal Library in Targeted Analysis of SWATH-MS
- (2019) Chuan-Qi Zhong et al. JOURNAL OF PROTEOME RESEARCH
- DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
- (2019) Vadim Demichev et al. NATURE METHODS
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics
- (2018) Ryan Peckner et al. NATURE METHODS
- MaxQuant goes Linux
- (2018) Pavel Sinitcyn et al. NATURE METHODS
- BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes
- (2018) Florian Meier et al. NATURE METHODS
- Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM-DIA, and Untargeted DIA
- (2018) Frank Koopmans et al. PROTEOMICS
- A proteomic landscape of diffuse-type gastric cancer
- (2018) Sai Ge et al. Nature Communications
- Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
- (2018) Christina Ludwig et al. Molecular Systems Biology
- Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine
- (2018) Hao Chi et al. NATURE BIOTECHNOLOGY
- Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry
- (2018) Ngoc Hieu Tran et al. NATURE METHODS
- Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
- (2018) Brian C. Searle et al. Nature Communications
- Scanning Quadrupole Data-Independent Acquisition, Part A: Qualitative and Quantitative Characterization
- (2017) M. Arthur Moseley et al. JOURNAL OF PROTEOME RESEARCH
- Optimization of Acquisition and Data-Processing Parameters for Improved Proteomic Quantification by Sequential Window Acquisition of All Theoretical Fragment Ion Mass Spectrometry
- (2017) Shanshan Li et al. JOURNAL OF PROTEOME RESEARCH
- The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics
- (2017) Lindsay K. Pino et al. MASS SPECTROMETRY REVIEWS
- Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS
- (2017) George Rosenberger et al. NATURE BIOTECHNOLOGY
- PIQED: automated identification and quantification of protein modifications from DIA-MS data
- (2017) Jesse G Meyer et al. NATURE METHODS
- PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data
- (2017) Ying S Ting et al. NATURE METHODS
- Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
- (2017) George Rosenberger et al. NATURE METHODS
- MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
- (2017) Andy T Kong et al. NATURE METHODS
- Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome
- (2016) Ulrike Kusebauch et al. CELL
- SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries
- (2016) Jemma X. Wu et al. MOLECULAR & CELLULAR PROTEOMICS
- Mass-spectrometric exploration of proteome structure and function
- (2016) Ruedi Aebersold et al. NATURE
- Proteogenomics connects somatic mutations to signalling in breast cancer
- (2016) Philipp Mertins et al. NATURE
- A multicenter study benchmarks software tools for label-free proteome quantification
- (2016) Pedro Navarro et al. NATURE BIOTECHNOLOGY
- TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
- (2016) Hannes L Röst et al. NATURE METHODS
- Spectral library searching in proteomics
- (2016) Johannes Griss PROTEOMICS
- Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses
- (2016) Sarah J. Parker et al. PROTEOMICS
- SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools
- (2016) Peter Blattmann et al. PLoS One
- Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics
- (2015) Tomas Cajka et al. ANALYTICAL CHEMISTRY
- Efficient visualization of high-throughput targeted proteomics experiments: TAPIR: Fig. 1.
- (2015) Hannes L. Röst et al. BIOINFORMATICS
- specL—an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics
- (2015) Christian Panse et al. BIOINFORMATICS
- Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet
- (2015) Andrew Keller et al. MOLECULAR & CELLULAR PROTEOMICS
- Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry
- (2015) Sarah J. Parker et al. MOLECULAR & CELLULAR PROTEOMICS
- Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues
- (2015) Roland Bruderer et al. MOLECULAR & CELLULAR PROTEOMICS
- A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
- (2015) Joel M Chick et al. NATURE BIOTECHNOLOGY
- Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
- (2015) Tiannan Guo et al. NATURE MEDICINE
- Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files
- (2015) Yuanyue Li et al. NATURE METHODS
- MSPLIT-DIA: sensitive peptide identification for data-independent acquisition
- (2015) Jian Wang et al. NATURE METHODS
- DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
- (2015) Chih-Chiang Tsou et al. NATURE METHODS
- Building high-quality assay libraries for targeted analysis of SWATH MS data
- (2015) Olga T Schubert et al. Nature Protocols
- Visualization of LC-MS/MS proteomics data in MaxQuant
- (2015) Stefka Tyanova et al. PROTEOMICS
- Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics
- (2015) Eric W. Deutsch et al. Proteomics Clinical Applications
- An open-source computational and data resource to analyze digital maps of immunopeptidomes
- (2015) Etienne Caron et al. eLife
- DIANA—algorithmic improvements for analysis of data-independent acquisition MS data
- (2014) Johan Teleman et al. BIOINFORMATICS
- Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics
- (2014) Umut H. Toprak et al. MOLECULAR & CELLULAR PROTEOMICS
- OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
- (2014) Hannes L Röst et al. NATURE BIOTECHNOLOGY
- MS-GF+ makes progress towards a universal database search tool for proteomics
- (2014) Sangtae Kim et al. Nature Communications
- A repository of assays to quantify 10,000 human proteins by SWATH-MS
- (2014) George Rosenberger et al. Scientific Data
- Improving Qualitative and Quantitative Performance for MSE-based Label-free Proteomics
- (2013) Nicholas J. Bond et al. JOURNAL OF PROTEOME RESEARCH
- Multiplexed MS/MS for improved data-independent acquisition
- (2013) Jarrett D Egertson et al. NATURE METHODS
- Proteoform: a single term describing protein complexity
- (2013) Lloyd M Smith et al. NATURE METHODS
- Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification
- (2012) Chad R. Weisbrod et al. JOURNAL OF PROTEOME RESEARCH
- Proteomic Study and Marker Protein Identification ofCaenorhabditis elegansLipid Droplets
- (2012) Peng Zhang et al. MOLECULAR & CELLULAR PROTEOMICS
- Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics
- (2012) Amelia C. Peterson et al. MOLECULAR & CELLULAR PROTEOMICS
- Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis
- (2012) Ludovic C. Gillet et al. MOLECULAR & CELLULAR PROTEOMICS
- Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing
- (2012) Marco Gerlinger et al. NEW ENGLAND JOURNAL OF MEDICINE
- Using iRT, a normalized retention time for more targeted measurement of peptides
- (2012) Claudia Escher et al. PROTEOMICS
- mProphet: automated data processing and statistical validation for large-scale SRM experiments
- (2011) Lukas Reiter et al. NATURE METHODS
- XDIA: improving on the label-free data-independent analysis
- (2010) Paulo C. Carvalho et al. BIOINFORMATICS
- Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
- (2010) Brendan MacLean et al. BIOINFORMATICS
- Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation
- (2010) Tamar Geiger et al. MOLECULAR & CELLULAR PROTEOMICS
- Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean
- (2009) Alexandre Panchaud et al. ANALYTICAL CHEMISTRY
- Selected reaction monitoring for quantitative proteomics: a tutorial
- (2008) Vinzenz Lange et al. Molecular Systems Biology
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