ReviewProteomics2012
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement.
Review in Proteomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed.
- Prioritizing peptides for targeted mass spectrometry experiments using deep learning.bioRxiv : the preprint server for biology · 2026Article
- Development of Highly Multiplex Targeted Proteomics Assays in Biofluids Using a Nominal Mass Ion Trap Mass Spectrometer.Molecular & cellular proteomics : MCP · 2026Article
- PII interactions with the acetyl-CoA carboxylase subunits BADC and BCCP co-regulate lipid and nitrogen metabolism in Arabidopsis.Plant physiology · 2025Article
- Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument.Journal of proteome research · 2025Article
- Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer.Journal of proteome research · 2025Article
- Systematic Evaluation of Chromatographic Peak Quality for Targeted Mass Spectrometry via Variational Autoencoder.Analytical chemistry · 2024Article
- Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry.Advances in experimental medicine and biology · 2024Article
- A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer's disease.Scientific data · 2023Article
- Application of Skyline software for detecting prohibited substances in doping control analysis.PloS one · 2023Article
- The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics.Antibiotics (Basel, Switzerland) · 2022Review
- Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma.Proteomes · 2022Article
- Effect of the Post-Harvest Processing on Protein Modification in Green Coffee Beans by Phenolic Compounds.Foods (Basel, Switzerland) · 2022Article
- Article
- Crosslinking mass spectrometry: A link between structural biology and systems biology.Protein science : a publication of the Protein Society · 2021Review
- Application of Proteomics in Sarcoidosis.American journal of respiratory cell and molecular biology · 2020Review
- Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling ofMetabolic engineering communications · 2020Article
- Comprehensive Characterization and Relative Quantification of α-Amylase/Trypsin Inhibitors from Wheat Cultivars by Targeted HPLC-MS/MS.Foods (Basel, Switzerland) · 2020Article
- Proteomics-Based Methodologies for the Detection and Quantification of Seafood Allergens.Foods (Basel, Switzerland) · 2020Review
- Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products.Foods (Basel, Switzerland) · 2020Review
- The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.Mass spectrometry reviews · 2020Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Software advancements in the last several years have had a significant impact on proteomics from method development to data analysis. Herein, we detail a method, which uses our in-house developed software tool termed Skyline, for empirical refinement of candidate peptides from targeted proteins. The method consists of four main steps from generation of a testable hypothesis, method development, peptide refinement, to peptide validation. The ultimate goal is to identify the best performing peptide in terms of ionization efficiency, reproducibility, specificity, and chromatographic characteristics to monitor as a proxy for protein abundance. It is important to emphasize that this method allows the user to perform this refinement procedure in the sample matrix and organism of interest with the instrumentation available. Finally, the method is demonstrated in a case study to determine the best peptide to monitor the abundance of surfactant protein B in lung aspirates.
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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.