iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Bioinform.

• Publication date

  2016-04-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btv675PMID 26589272
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data

  2014cited by this paper
• Quantitative accuracy in mass spectrometry based proteomics of complex samples: the impact of labeling and precursor interference.

  2014cited by this paper
• Defining, Comparing, and Improving iTRAQ Quantification in Mass Spectrometry Proteomics Data*

  2013influential reference
• Impact of Peptide Modifications on iTRAQ Quantitation Accuracy

  2013cited by this paper
• MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

  2012influential reference
• PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios

  2012cited by this paper
• ms3 eliminates ratio distortion in isobaric multiplexed quantitative

  2011cited by this paper
• MS3 eliminates ratio distortion in isobaric labeling-based multiplexed quantitative proteomics

  2011cited by this paper
• Impact of peptide modifications on the isobaric tags for relative and absolute quantitation method accuracy.

  2011cited by this paper
• Relative quantification: characterization of bias, variability and fold changes in mass spectrometry data from iTRAQ-labeled peptides.

  2011cited by this paper
• General statistical modeling of data from protein relative expression isobaric tags.

  2011cited by this paper
• iTRAQ protein quantification: A quality‐controlled workflow

  2011cited by this paper
• Peptide and protein quantification: A map of the minefield

  2010cited by this paper
• Scaffold: A bioinformatic tool for validating MS/MS‐based proteomic studies

  2010cited by this paper
• Methods for combining peptide intensities to estimate relative protein abundance

  2010cited by this paper
• LTQ‐iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments

  2010cited by this paper
• Addressing Accuracy and Precision Issues in iTRAQ Quantitation*

  2010cited by this paper
• Computational protein profile similarity screening for quantitative mass spectrometry experiments

  2010cited by this paper
• MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics

  2009cited by this paper
• Prediction of high-responding peptides for targeted protein assays by mass spectrometry

  2009cited by this paper
• iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly".

  2009cited by this paper
• Robust and Sensitive iTRAQ Quantification on an LTQ Orbitrap Mass Spectrometer*S

  2008cited by this paper
• Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ).

  2007cited by this paper
• Precise protein quantification based on peptide quantification using iTRAQ™

  2007cited by this paper
• Semi-supervised learning for peptide identification from shotgun proteomics datasets

  2007cited by this paper
• Mass Spectrometry and Protein Analysis

  2006cited by this paper
• Multi-Q: a fully automated tool for multiplexed protein quantitation.

  2006cited by this paper
• Optimized proteomic analysis of a mouse model of cerebellar dysfunction using amine‐specific isobaric tags

  2006cited by this paper
• Absolute Quantification of Proteins by LCMSE

  2006cited by this paper
• A comparison of the consistency of proteome quantitation using two‐dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells

  2005cited by this paper
• i-Tracker: For quantitative proteomics using iTRAQ™

  2005cited by this paper
• Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S

  2004cited by this paper
• Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS.

  2003cited by this paper
• Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry.

  2003cited by this paper
• Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics*

  2002cited by this paper
• Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

  2002cited by this paper
• Variance stabilization applied to microarray data calibration and to the quantification of differential expression

  2002cited by this paper
• Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

  1999cited by this paper
• Total least squares problem - computational aspects and analysis

  1991cited by this paper

• Accounting for longitudinal peak quality metrics with MSstats+ enhances differential analysis in proteomic experiments with data-independent acquisition

  2025cites this paper
• Attribute-Weighted Aggregation of Tandem Mass Reporter Ion Intensity for Protein Quantification Using Isobaric Labeling.

  2025cites this paper
• IQUP identifies quantitatively unreliable spectra with machine learning for isobaric labeling-based proteomics

  2025cites this paper
• PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks

  2024cites this paper
• A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

  2023cites this paper
• TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.

  2023cites this paper
• Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter

  2023cites this paper
• A causal model of ion interference enables assessment and correction of ratio 1 compression in multiplex proteomics 2

  2022cites this paper
• Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage

  2021cites this paper
• VIQoR: a web service for Visually supervised protein Inference and protein Quantification

  2021cites this paper
• MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures

  2020cites this paper
• Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry.

  2019cites this paper
• Peptide-to-Protein Summarization: An Important Step for Accurate Quantification in Label-Based Proteomics.

  2019cites this paper
• IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments

  2018cites this paper
• DOSCHEDA: a web application for interactive chemoproteomics data analysis

  2017cites this paper
• IsoProt: A fully reproducible one-stop-shop for the analysis of iTRAQ/TMT data

  year unknowncites this paper