ReviewProteomics2013
A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.
Review in Proteomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 86 citations in OpenAlex.
- A Bayesian framework for multivariate differential analysis.PLoS computational biology · 2026Article
- Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics.Journal of proteome research · 2026Article
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- Sample Preparation and Processing for Quick, Universal, and Insightful Microbial Proteomics.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition.ISME communications · 2025Article
- Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure.NPJ biofilms and microbiomes · 2024Article
- A compendium of multi-omics data illuminating host responses to lethal human virus infections.Scientific data · 2024Article
- Proteomics for Microalgae Extracts by High-Resolution Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts.Microbial cell factories · 2023Article
- Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity.Cell reports. Medicine · 2023Article
- LFQ-Based Peptide and Protein Intensity Differential Expression Analysis.Journal of proteome research · 2023Article
- Challenges and Opportunities for Single-cell Computational Proteomics.Molecular & cellular proteomics : MCP · 2023Review
- Itaconic acid production is regulated by LaeA inMetabolic engineering communications · 2022Article
- An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research.Cells · 2022Review
- Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?Journal of proteome research · 2022Article
- (Phospho)Proteomic dataset of ischemia- and ultrasound- stimulated mouse cardiac endothelial cells in vitro.Data in brief · 2021Article
- Phosphoproteomic response of cardiac endothelial cells to ischemia and ultrasound.Biochimica et biophysica acta. Proteins and proteomics · 2021Article
- Deciphering an AgRP-serotoninergic neural circuit in distinct control of energy metabolism from feeding.Nature communications · 2021Article
- Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production inFrontiers in bioengineering and biotechnology · 2021Article
- Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution.Nature communications · 2020Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g. disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred from one or more measured peptides. In recent years, many computational approaches to relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.
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Registered trials
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.