ArticleMolecular & cellular proteomics : MCP2013
An adaptive alignment algorithm for quality-controlled label-free LC-MS.
Article in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Advances in the Design and Functionality of a Compact Multi-Reflecting Time-of-Flight Mass Spectrometer.Rapid communications in mass spectrometry : RCM · 2026Article
- The quantification of zebrafish ocular-associated proteins provides hints for sex-biased visual impairments and perception.Heliyon · 2024Article
- Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling.International journal of molecular sciences · 2021Article
- Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves.International journal of molecular sciences · 2019Article
- DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.Molecular & cellular proteomics : MCP · 2019Article
- The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function.Frontiers in cellular neuroscience · 2019Article
- A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.Briefings in bioinformatics · 2018Article
- Comparative Membrane-Associated Proteomics of Three Different Immune Reactions in Potato.International journal of molecular sciences · 2018Article
- Proteomic Analysis ofMolecular & cellular proteomics : MCP · 2017Article
- Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.Oncogene · 2016Article
- Dinosaur: A Refined Open-Source Peptide MS Feature Detector.Journal of proteome research · 2016Article
- Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling.Analytical chemistry · 2016Review
- Middle-Down and Chemical Proteomic Approaches to Reveal Histone H4 Modification Dynamics in Cell Cycle: Label-Free Semi-Quantification of Histone Tail Peptide Modifications Including Phosphorylation and Highly Sensitive Capture of Histone PTM Binding Proteins Using Photo-Reactive Crosslinkers.Mass spectrometry (Tokyo, Japan) · 2015Article
- Adaptive semantic tag mining from heterogeneous clinical research texts.Methods of information in medicine · 2015Article
- Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans.BMC plant biology · 2014Article
- Proteomics for systems toxicology.Computational and structural biotechnology journal · 2014Review
- Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions.BMC genomics · 2014Article
- Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.Journal of proteome research · 2014Article
- Numerical compression schemes for proteomics mass spectrometry data.Molecular & cellular proteomics : MCP · 2014Article
- Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach.BMC genomics · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Label-free quantification using precursor-based intensities is a versatile workflow for large-scale proteomics studies. The method however requires extensive computational analysis and is therefore in need of robust quality control during the data mining stage. We present a new label-free data analysis workflow integrated into a multiuser software platform. A novel adaptive alignment algorithm has been developed to minimize the possible systematic bias introduced into the analysis. Parameters are estimated on the fly from the data at hand, producing a user-friendly analysis suite. Quality metrics are output in every step of the analysis as well as actively incorporated into the parameter estimation. We furthermore show the improvement of this system by comprehensive comparison to classical label-free analysis methodology as well as current state-of-the-art software.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.