Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
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Title
Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification
Authors
Keywords
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Journal
Frontiers in Pharmacology
Volume 9, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2018-06-26
DOI
10.3389/fphar.2018.00681
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Note: Only part of the references are listed.- What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation
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- (2018) Lukas Krasny et al. Journal of Proteomics
- Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions
- (2018) Amir Ata Saei et al. MOLECULAR & CELLULAR PROTEOMICS
- Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder
- (2018) Weiwei Xue et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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- (2018) Feng Zhu et al. TRENDS IN PHARMACOLOGICAL SCIENCES
- Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals
- (2017) Pedro M. Quirós et al. JOURNAL OF CELL BIOLOGY
- Multiplex and Label-Free Relative Quantification Approach for Studying Protein Abundance of Drug Metabolizing Enzymes in Human Liver Microsomes Using SWATH-MS
- (2017) Rohitash Jamwal et al. JOURNAL OF PROTEOME RESEARCH
- Targeted Feature Detection for Data-Dependent Shotgun Proteomics
- (2017) Hendrik Weisser 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
- On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry
- (2017) Fränze Müller et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System
- (2017) J. F. Chignell et al. MICROBIAL ECOLOGY
- Comparison of computational model and X-ray crystal structure of human serotonin transporter: potential application for the pharmacology of human monoamine transporters
- (2017) Fengyuan Yang et al. MOLECULAR SIMULATION
- OUP accepted manuscript
- (2017) NUCLEIC ACIDS RESEARCH
- NOREVA: normalization and evaluation of MS-based metabolomics data
- (2017) Bo Li et al. NUCLEIC ACIDS RESEARCH
- Revealing vilazodone's binding mechanism underlying its partial agonism to the 5-HT1A receptor in the treatment of major depressive disorder
- (2017) Guoxun Zheng et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications
- (2017) Sandra Isabel Anjo et al. PROTEOMICS
- Trisomy 21 causes changes in the circulating proteome indicative of chronic autoinflammation
- (2017) Kelly D. Sullivan et al. Scientific Reports
- Proteome Speciation by Mass Spectrometry: Characterization of Composite Protein Mixtures in Milk Replacers
- (2016) Marco Gaspari et al. ANALYTICAL CHEMISTRY
- Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster
- (2016) Yanzhu Lin et al. BMC GENOMICS
- A systematic evaluation of normalization methods in quantitative label-free proteomics
- (2016) Tommi Välikangas et al. BRIEFINGS IN BIOINFORMATICS
- Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data
- (2016) Mun-Gwan Hong et al. JOURNAL OF PROTEOME RESEARCH
- Global proteomic profiling identifies etoposide chemoresistance markers in non-small cell lung carcinoma
- (2016) Debasish Paul et al. Journal of Proteomics
- 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
- A multicenter study benchmarks software tools for label-free proteome quantification
- (2016) Pedro Navarro et al. NATURE BIOTECHNOLOGY
- Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
- (2016) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study
- (2016) Weiwei Xue et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease
- (2016) Payam Emami Khoonsari et al. PLoS One
- SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity
- (2016) Ying Hong Li et al. PLoS One
- Advances in targeted proteomics and applications to biomedical research
- (2016) Tujin Shi et al. PROTEOMICS
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- (2016) Yvonne Aratyn-Schaus et al. Bioanalysis
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- (2016) Jingyu Xu et al. Biomed Research International
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- (2016) Allison B. Chambliss et al. Clinical Proteomics
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- (2016) Ying Hong Li et al. PLoS One
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- (2016) Guoxun Zheng et al. Scientific Reports
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- (2016) Bo Li et al. Scientific Reports
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- (2015) Andreas T. Roemmelt et al. ANALYTICAL CHEMISTRY
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- (2014) Hannes L Röst et al. NATURE BIOTECHNOLOGY
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- (2014) Z. Zhang BMJ Open
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- (2013) Dariusz Mrozek et al. BMC BIOINFORMATICS
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- (2012) Alysha M. De Livera et al. ANALYTICAL CHEMISTRY
- Normalization and missing value imputation for label-free LC-MS analysis
- (2012) Yuliya V Karpievitch et al. BMC BIOINFORMATICS
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- (2012) Ludovic C. Gillet et al. MOLECULAR & CELLULAR PROTEOMICS
- Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
- (2012) Jacek R Wiśniewski et al. Molecular Systems Biology
- Drug Discovery Prospect from Untapped Species: Indications from Approved Natural Product Drugs
- (2012) Feng Zhu et al. PLoS One
- Improved quality control processing of peptide-centric LC-MS proteomics data
- (2011) Melissa M. Matzke et al. BIOINFORMATICS
- State-of-the art data normalization methods improve NMR-based metabolomic analysis
- (2011) Stefanie M. Kohl et al. Metabolomics
- Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
- (2011) H. B. Rao et al. NUCLEIC ACIDS RESEARCH
- Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery
- (2011) F. Zhu et al. NUCLEIC ACIDS RESEARCH
- Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting
- (2011) F. Zhu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
- (2010) Brendan MacLean et al. BIOINFORMATICS
- Pharmacoproteomics: a chess game on a protein field
- (2010) Angelo D’Alessandro et al. DRUG DISCOVERY TODAY
- Comparison of Normalization Methods for the Identification of Biomarkers Using MALDI-TOF and SELDI-TOF Mass Spectra
- (2010) Sanket P. Borgaonkar et al. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
- Trends in the Exploration of Anticancer Targets and Strategies in Enhancing the Efficacy of Drug Targeting
- (2010) F. Zhu et al. Current Molecular Pharmacology
- What Are Next Generation Innovative Therapeutic Targets? Clues from Genetic, Structural, Physicochemical, and Systems Profiles of Successful Targets
- (2009) F. Zhu et al. JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS
- Update of TTD: Therapeutic Target Database
- (2009) Feng Zhu et al. NUCLEIC ACIDS RESEARCH
- Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines
- (2008) Y. Chen et al. CURRENT PROTEIN & PEPTIDE SCIENCE
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