ArticleJournal of proteome research2023
LFQ-Based Peptide and Protein Intensity Differential Expression Analysis.
Article in Journal of proteome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
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Who cites it
15 citing papers in PubMed.
- MPOInt: An Epigenetics-Driven Workflow for Integrative Multi-Level Proteomics.Journal of proteome research · 2026Article
- Proteomic Mapping of Allergenic Proteins Reveals Key Differences Between Black Tiger Prawn (Journal of proteome research · 2026Article
- Mass Spectrometry Proteomics of the Nanoparticle Corona Is Highly Dependent on Sample Preparation Protocol.Proteomics · 2026Article
- Identification ofJournal of proteome research · 2025Article
- Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.Bioinformatics (Oxford, England) · 2025Article
- Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst.Journal of proteome research · 2024Article
- An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing.Nature protocols · 2024Review
- quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data.Nature methods · 2024Article
- Statistical Testing for Protein Equivalence Identifies Core Functional Modules Conserved across 360 Cancer Cell Lines and Presents a General Approach to Investigating Biological Systems.Journal of proteome research · 2024Article
- Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.bioRxiv : the preprint server for biology · 2024Article
- Application of SWATH Mass Spectrometry and Machine Learning in the Diagnosis of Inflammatory Bowel Disease Based on the Stool Proteome.Biomedicines · 2024Article
- Circulating Proteins as Diagnostic Markers in Gastric Cancer.International journal of molecular sciences · 2023Review
- Evaluating Proteomics Imputation Methods with Improved Criteria.Journal of proteome research · 2023Article
- Advances in proteomics: characterization of the innate immune system after birth and during inflammation.Frontiers in immunology · 2023Review
- Proteomic repository data submission, dissemination, and reuse: key messages.Expert review of proteomicsReview
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings.
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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.