Cargando…

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition

In bottom-up, label-free discovery proteomics, biological samples are acquired in a data-dependent (DDA) or data-independent (DIA) manner, with peptide signals recorded in an intact (MS1) and fragmented (MS2) form. While DDA has only the MS1 space for quantification, DIA contains both MS1 and MS2 at...

Descripción completa

Detalles Bibliográficos
Autores principales:	Huang, Ting, Bruderer, Roland, Muntel, Jan, Xuan, Yue, Vitek, Olga, Reiter, Lukas
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	The American Society for Biochemistry and Molecular Biology 2020
Materias:	Technological Innovation and Resources
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000113/ https://www.ncbi.nlm.nih.gov/pubmed/31888964 http://dx.doi.org/10.1074/mcp.RA119.001705

Ejemplares similares

Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results
por: Bruderer, Roland, et al.
Publicado: (2017)

Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition
por: Skowronek, Patricia, et al.
Publicado: (2022)

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry
por: Müller, Fränze, et al.
Publicado: (2019)

MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures
por: Huang, Ting, et al.
Publicado: (2020)

Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition
por: Ctortecka, Claudia, et al.
Publicado: (2021)

Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices With Zeno SWATH Data-Independent Acquisition
por: Sun, Weiwen, et al.
Publicado: (2023)

Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition
por: Barkovits, Katalin, et al.
Publicado: (2020)

Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences
por: Zhang, Bo, et al.
Publicado: (2017)

Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry
por: Amon, Sabine, et al.
Publicado: (2019)

MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets
por: Kovalchik, Kevin A., et al.
Publicado: (2021)

Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction
por: Pak, HuiSong, et al.
Publicado: (2021)

Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments
por: Bemis, Kyle D., et al.
Publicado: (2016)

Autoantibody Profiling in Multiple Sclerosis Using Arrays of Human Protein Fragments
por: Ayoglu, Burcu, et al.
Publicado: (2013)

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life
por: Wang, M., et al.
Publicado: (2012)

Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics
por: Furtwängler, Benjamin, et al.
Publicado: (2022)

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer
por: Meier, Florian, et al.
Publicado: (2018)

Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel Accumulation-Serial Fragmentation Mass Spectrometry
por: Phulphagar, Kshiti Meera, et al.
Publicado: (2023)

Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach
por: Carr, Steven A., et al.
Publicado: (2014)

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics
por: Fan, Jun, et al.
Publicado: (2015)

Platform-independent and Label-free Quantitation of Proteomic Data Using MS1 Extracted Ion Chromatograms in Skyline: APPLICATION TO PROTEIN ACETYLATION AND PHOSPHORYLATION
por: Schilling, Birgit, et al.
Publicado: (2012)

Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)
por: Renard, Bernhard Y., et al.
Publicado: (2012)

pepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information
por: Zhang, Yutong
Publicado: (2023)

Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator
por: Wright, James C., et al.
Publicado: (2012)

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis
por: Zhu, Yafeng, et al.
Publicado: (2020)

An Enhanced In Vivo Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Model for Quantification of Drug Metabolism Enzymes
por: MacLeod, A. Kenneth, et al.
Publicado: (2015)

A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling
por: Zappacosta, Francesca, et al.
Publicado: (2021)

In-Depth Comparison of Matrigel Dissolving Methods on Proteomic Profiling of Organoids
por: Wang, Man, et al.
Publicado: (2021)

A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos
por: Rosenthal, Shimon M., et al.
Publicado: (2021)

High Throughput Isolation and Glycosylation Analysis of IgG–Variability and Heritability of the IgG Glycome in Three Isolated Human Populations
por: Pučić, Maja, et al.
Publicado: (2011)

Comparative Performance of Four Methods for High-throughput Glycosylation Analysis of Immunoglobulin G in Genetic and Epidemiological Research
por: Huffman, Jennifer E., et al.
Publicado: (2014)

In Vivo Analysis of Proteomes and Interactomes Using Parallel Affinity Capture (iPAC) Coupled to Mass Spectrometry
por: Rees, Johanna S., et al.
Publicado: (2011)

Inferring Physical Protein Contacts from Large-Scale Purification Data of Protein Complexes
por: Schelhorn, Sven-Eric, et al.
Publicado: (2011)

Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data
por: Griss, Johannes, et al.
Publicado: (2011)

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library
por: Yen, Chia-Yu, et al.
Publicado: (2011)

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation
por: Thakur, Suman S., et al.
Publicado: (2011)

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification
por: Zhang, Jing, et al.
Publicado: (2012)

Antibody Colocalization Microarray: A Scalable Technology for Multiplex Protein Analysis in Complex Samples
por: Pla-Roca, M., et al.
Publicado: (2012)

TraML—A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists
por: Deutsch, Eric W., et al.
Publicado: (2012)

Proteomic Analysis and Discovery Using Affinity Proteomics and Mass Spectrometry
por: Olsson, Niclas, et al.
Publicado: (2011)

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer
por: Michalski, Annette, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_qnm72o3dk6k929njmarld3snib