Testing and Validation of Computational Methods for Mass Spectrometry.

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of Proteome Research

• Publication date

  2016-03-04

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/acs.jproteome.5b00852PMID 26549429PMCID PMC4804830
• 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.

• Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

  2015cited by this paper
• Dynamic profiling of the protein life cycle in response to pathogens

  2015cited by this paper
• Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less.

  2015cited by this paper
• EBprot: Statistical analysis of labeling‐based quantitative proteomics data

  2015cited by this paper
• Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research

  2015cited by this paper
• In‐depth evaluation of software tools for data‐independent acquisition based label‐free quantification

  2015cited by this paper
• Managing expectations when publishing tools and methods for computational proteomics.

  2015cited by this paper
• Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data

  2015cited by this paper
• JAMSS: proteomics mass spectrometry simulation in Java

  2015cited by this paper
• A Statistical Framework for Hypothesis Testing in Real Data Comparison Studies

  2015cited by this paper
• ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination

  2014cited by this paper
• Cross-study validation for the assessment of prediction algorithms

  2014cited by this paper
• Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata

  2014cited by this paper
• Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

  2014cited by this paper
• Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

  2014cited by this paper
• Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis

  2014cited by this paper
• Identification of Trans-Golgi Network Proteins in Arabidopsis thaliana Root Tissue

  2013cited by this paper
• Improving qualitative and quantitative performance for MS(E)-based label-free proteomics.

  2013cited by this paper
• Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data.

  2013cited by this paper
• The effect of organelle discovery upon sub-cellular protein localisation.

  2013cited by this paper
• Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

  2013cited by this paper
• On representative and illustrative comparisons with real data in bioinformatics: response to the letter to the editor by Smith et al

  2013cited by this paper
• Novel algorithms and the benefits of comparative validation

  2013cited by this paper
• Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

  2012cited by this paper
• A Plea for Neutral Comparison Studies in Computational Sciences

  2012cited by this paper
• MSSimulator: Simulation of mass spectrometry data.

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

  2011cited by this paper
• ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

  2011cited by this paper
• Editorial: From Data to Results

  2011cited by this paper
• ms3 eliminates ratio distortion in isobaric multiplexed quantitative

  2011cited by this paper
• Data-driven assessment of eQTL mapping methods

  2010cited by this paper
• Papers on normalization, variable selection, classification or clustering of microarray data

  2009cited by this paper
• LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

  2008cited by this paper
• SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling

  2007cited by this paper
• Posttranscriptional Expression Regulation: What Determines Translation Rates?

  2007cited by this paper
• Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale*S

  2004cited by this paper
• Faculty Opinions recommendation of Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

  2004cited by this paper

• Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future

  2025cites this paper
• Mass spectrometry-based proteomics in glioblastoma - current understanding and future impact.

  2025cites this paper
• Redefining Root Exudation with Proteins at the Forefront of Rhizosphere Function.

  2025cites this paper
• Expert Algorithm for Substance Identification Using Mass Spectrometry: Statistical Foundations in Unimolecular Reaction Rate Theory

  2023cites this paper
• Expert Algorithm for Substance Identification Using Mass Spectrometry: Application to the Identification of Cocaine on Different Instruments Using Binary Classification Models

  2023cites this paper
• Simulation of mass spectrometry-based proteomics data with Synthedia

  2022cites this paper
• Complementary hepatic metabolomics and proteomics reveal the adaptive mechanisms of dairy cows to the transition period.

  2022cites this paper
• Over‐optimism in benchmark studies and the multiplicity of design and analysis options when interpreting their results

  2021cites this paper
• Metabolomics-based predictive biomarkers of radiation injury and countermeasure efficacy: current status and future perspectives

  2021cites this paper
• ScholarWorks at University of Montana ScholarWorks at University of Montana

  2020cites this paper
• Advanced mono- and multi-dimensional GC-MS techniques for oxygen-containing compound characterization in biomass and biofuel samples.

  2020cites this paper
• A Systematic Review of Metabolomic and Lipidomic Candidates for Biomarkers in Radiation Injury

  2020cites this paper
• Translating ‘big data’: better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

  2020cites this paper
• Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains*

  2019cites this paper
• ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

  2019cites this paper
• pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data

  2019cites this paper
• XNet: A Bayesian approach to Extracted Ion Chromatogram Clustering for Precursor Mass Spectrometry Data.

  2019cites this paper
• Real-time feature detection in mass spectrometer data

  2018cites this paper
• Explanatory note on the determination of newly expressed protein levels in the context of genetically modified plant applications for EU market authorisation

  2018cites this paper
• Comparison of measured and recommended acceptance criteria for the analysis of seized drugs using Gas Chromatography–Mass Spectrometry (GC–MS)

  2018cites this paper
• Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.

  2018cites this paper
• The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models

  2018cites this paper
• Fast open modification spectral library searching through approximate nearest neighbor indexing

  2018cites this paper
• Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

  2018cites this paper
• Quality control in mass spectrometry-based proteomics.

  2018cites this paper
• Evaluating de novo sequencing in proteomics: already an accurate alternative to database‐driven peptide identification?

  2018cites this paper
• A Peptide-Level Fully Annotated Data Set for Quantitative Evaluation of Precursor-Aware Mass Spectrometry Data Processing Algorithms.

  2018cites this paper
• A Golden Age for Working with Public Proteomics Data

  2017cites this paper
• Searching molecular structure databases using tandem MS data: are we there yet?

  2017cites this paper
• Proteomics and metabolomics characterizing the pathophysiology of adaptive reactions to the metabolic challenges during the transition from late pregnancy to early lactation in dairy cows.

  2017cites this paper
• Improving cross‐study prediction through addon batch effect adjustment or addon normalization

  2016cites this paper
• A multi-center study benchmarks software tools for label-free proteome quantification

  2016cites this paper
• Boulesteix Improving cross-study prediction through addon batch effect adjustment and addon normalization

  2016cites this paper
• Challenges in Large-Scale Computational Mass Spectrometry and Multiomics.

  2016cites this paper