ReviewProteomics. Clinical applications2015
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.
Review in Proteomics. Clinical applications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 193 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
193 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Phosphorylation in theJournal of proteome research · 2024Pooled it
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
- TurboID proximity labeling reveals protein interaction networks for germline Argonautes.bioRxiv : the preprint server for biology · 2026Article
- A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs.Scientific data · 2026Article
- Change in the chondroitin/dermatan structure in distal lung tissue from COPD patients.Scientific reports · 2026Article
- Prioritization of Therapeutic Targets of Inflammation Using Proteomics, Bioinformatics, and In Silico Cell-Cell Interactomics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella).Advanced biotechnology · 2025Article
- GPBD: high-confidence N-glycopeptide identification via glycopeptide boundary discriminator.Analytical and bioanalytical chemistry · 2025Article
- Mass spectrometry-based proteomics of FFPE tissues: progress, limitations, and clinical translation barriers.Clinical proteomics · 2025Review
- Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes.Nature communications · 2025Article
- Restricting metabolic plasticity enhances stress adaptation through the modulation of PDH and HIF1A in TRAP1-depleted colon cancer.Cancer letters · 2025Article
- Human iPSC-Derived Mononuclear Phagocytes Improve Cognition and Neural Health across Multiple Mouse Models of Aging and Alzheimer's Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- UBR-1 enzyme network regulates glutamate homeostasis to affect organismal behavior and developmental viability.bioRxiv : the preprint server for biology · 2025Article
- Article
- PyViscount: Validating False Discovery Rate Estimation Methods via Random Search Space Partition.Journal of proteome research · 2025Article
- Shotgun Proteomics Protocol for Insects.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.Journal of proteome research · 2024Article
- Borrelia PeptideAtlas: A proteome resource of common Borrelia burgdorferi isolates for Lyme research.Scientific data · 2024Article
- Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases.Computational and structural biotechnology journal · 2024Article
- Mannose-6-Phosphate Isomerase Functional Status Shapes a Rearrangement in the Proteome and Degradome of Mannose-Treated Melanoma Cells.Journal of proteome research · 2024Article
133 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features.
Indexed as
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What OpenQuestion holds
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.