Cargando…

Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes

Recent advances in mass spectrometry–based proteomics enable the acquisition of increasingly large datasets within relatively short times, which exposes bottlenecks in the bioinformatics pipeline. Although peptide identification is already scalable, most label-free quantification (LFQ) algorithms sc...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ammar, Constantin, Schessner, Julia Patricia, Willems, Sander, Michaelis, André C., Mann, Matthias
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Society for Biochemistry and Molecular Biology 2023
Materias:	Technological Innovation and Resources
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10315922/ https://www.ncbi.nlm.nih.gov/pubmed/37225017 http://dx.doi.org/10.1016/j.mcpro.2023.100581

Ejemplares similares

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
por: Cox, Jürgen, et al.
Publicado: (2014)

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs
por: Yu, Fengchao, et al.
Publicado: (2021)

pyQms enables universal and accurate quantification of mass spectrometry data
por: Leufken, Johannes, et al.
Publicado: (2017)

AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization
por: Willems, Sander, et al.
Publicado: (2021)

Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data
por: Kenar, Erhan, et al.
Publicado: (2014)

Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF
por: Skowronek, Patricia, et al.
Publicado: (2022)

Mass Spectrometric Quantification of Histone Post-translational Modifications by a Hybrid Chemical Labeling Method
por: Maile, Tobias M., et al.
Publicado: (2015)

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)

Index-ion Triggered MS2 Ion Quantification: A Novel Proteomics Approach for Reproducible Detection and Quantification of Targeted Proteins in Complex Mixtures
por: Yan, Wei, et al.
Publicado: (2011)

Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups
por: The, Matthew, et al.
Publicado: (2022)

PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts
por: Huang, Qingyao, et al.
Publicado: (2023)

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

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

Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics
por: Kulak, Nils A., et al.
Publicado: (2017)

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

SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering
por: Hamood, Firas, et al.
Publicado: (2022)

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)

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

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

Trimethylacetic Anhydride–Based Derivatization Facilitates Quantification of Histone Marks at the MS1 Level
por: Kuchaříková, Hana, et al.
Publicado: (2021)

NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions
por: Alvarez, Bruno, et al.
Publicado: (2019)

Initial Quantitative Proteomic Map of 28 Mouse Tissues Using the SILAC Mouse
por: Geiger, Tamar, et al.
Publicado: (2013)

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

Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning
por: Roux-Dalvai, Florence, et al.
Publicado: (2019)

A Standardized and Reproducible Workflow for Membrane Glass Slides in Routine Histology and Spatial Proteomics
por: Nordmann, Thierry M., et al.
Publicado: (2023)

Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs
por: Niinae, Tomoya, et al.
Publicado: (2021)

Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals
por: Hammond, Dean E., et al.
Publicado: (2022)

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

Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant
por: Chen, Zhuo A., et al.
Publicado: (2016)

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

MsImpute: Estimation of Missing Peptide Intensity Data in Label-Free Quantitative Mass Spectrometry
por: Hediyeh-Zadeh, Soroor, et al.
Publicado: (2023)

A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics
por: Bache, Nicolai, et al.
Publicado: (2018)

Stable Isotope Dynamic Labeling of Secretomes (SIDLS) Identifies Authentic Secretory Proteins Released by Cancer and Stromal Cells
por: Hammond, Dean E., et al.
Publicado: (2018)

Nic1 Inactivation Enables Stable Isotope Labeling with (13)C(6)(15)N(4)-Arginine in Schizosaccharomyces pombe
por: Carpy, Alejandro, et al.
Publicado: (2015)

Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits
por: Schober, Florian A., et al.
Publicado: (2021)

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

The One Hour Yeast Proteome
por: Hebert, Alexander S., et al.
Publicado: (2014)

A SILAC-based Approach Identifies Substrates of Caspase-dependent Cleavage upon TRAIL-induced Apoptosis
por: Stoehr, Gabriele, et al.
Publicado: (2013)

Expert System for Computer-assisted Annotation of MS/MS Spectra
por: Neuhauser, Nadin, et al.
Publicado: (2012)

Proteoform-Specific Insights into Cellular Proteome Regulation
por: Norris, Emma L., et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_2s22bgldt25gam83uk6l1or1aq