ArticleMolecular & cellular proteomics : MCP2008
Significance analysis of spectral count data in label-free shotgun proteomics.
Article in Molecular & cellular proteomics : MCP, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 182 papers, 1 of them a synthesis that pooled it.
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.
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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
182 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Reproducibility Crossroads: Impact of Statistical Choices on Proteomics Functional Enrichment.International journal of molecular sciences · 2025Pooled it
- Hemoglobin depletion from plasma: considerations for proteomic discovery in sickle cell disease and other hemolytic processes.Proteomics. Clinical applications · 2010Trial
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- Proteomic Insights into the Antibacterial Mechanism of Brevibacillus brevis HK544 Producing Edeine B1 against Erwinia amylovora.The plant pathology journal · 2026Article
- KANK2 at focal adhesions regulates their maintenance and dynamics, while at fibrillar adhesions it influences cell migration via microtubule-dependent mechanism.Cell communication and signaling : CCS · 2026Article
- On the question of correct use of replicates in quantitative label-free proteomics.Analytical and bioanalytical chemistry · 2025Article
- Deciphering Functions of a Putative Histidinol Dehydrogenase in Acidovorax citrulli by Phenotypic and Proteomic Analyses.The plant pathology journal · 2025Article
- A putative glucose-1-phosphate thymidylyltransferase is required for virulence, membrane-associated mechanisms, and tolerance to external stresses inFrontiers in plant science · 2025Article
- Framework for analyzing MAE-derived immunopeptidomes from cell lines with shared HLA haplotypes.PloS one · 2025Article
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- Non-targeted N-glycome profiling reveals multiple layers of organ-specific diversity in mice.Nature communications · 2024Article
- A kalihinol analog disrupts apicoplast function and vesicular trafficking inScience (New York, N.Y.) · 2024Article
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- An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited FungusJournal of fungi (Basel, Switzerland) · 2024Article
- The extracellular matrix component perlecan/HSPG2 regulates radioresistance in prostate cancer cells.Frontiers in cell and developmental biology · 2024Article
- The antiproliferative effect of FGF2 in K-Ras-driven tumor cells involves modulation of rRNA and the nucleolus.Journal of cell science · 2023Article
- EGFR-T790M Mutation-Derived Interactome Rerouted EGFR Translocation Contributing to Gefitinib Resistance in Non-Small Cell Lung Cancer.Molecular & cellular proteomics : MCP · 2023Article
- Proteomic and Phenotypic Analyses of a Putative YggS Family Pyridoxal Phosphate-Dependent Enzyme in Acidovorax citrulli.The plant pathology journal · 2023Article
- Mass spectrometry-based retina proteomics.Mass spectrometry reviews · 2023Review
122 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Spectral counting has become a commonly used approach for measuring protein abundance in label-free shotgun proteomics. At the same time, the development of data analysis methods has lagged behind. Currently most studies utilizing spectral counts rely on simple data transforms and posthoc corrections of conventional signal-to-noise ratio statistics. However, these adjustments can neither handle the bias toward high abundance proteins nor deal with the drawbacks due to the limited number of replicates. We present a novel statistical framework (QSpec) for the significance analysis of differential expression with extensions to a variety of experimental design factors and adjustments for protein properties. Using synthetic and real experimental data sets, we show that the proposed method outperforms conventional statistical methods that search for differential expression for individual proteins. We illustrate the flexibility of the model by analyzing a data set with a complicated experimental design involving cellular localization and time course.
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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.