Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms
- 1Royal College of Surgeons in Ireland
Abstract
High-throughput proteomics now spans several technologies that differ in biological breadth, precision, specificity, sensitivity, cost, and method(s) of quantification; however, investigators currently lack an evidence-based framework to select or combine platforms. Here, we present the Atlas of Proteomic Technologies (APT) - a curated resource that evaluates six commercial platforms across ten analytical dimensions using published head-to-head evidence, expert evaluation, and iterative peer review. APT hosts two decision tools: the Help Me Choose tool maps a study's primary aim(s), scale, sample matrix, and technical constraints to a calibrated, weight-adjustable platform ranking, and the Help Me Combine tool ranks complementary platform pairs by their net-new protein coverage and user-specified technical priorities. Both tools were tested exhaustively across all possible combinations and behave in a balanced, merit-based manner. APT is openly accessible at https://aptatlas.org, providing downloadable tool specifications, seeded analysis scripts, and complete protein coverage lists, ensuring every score and recommendation is inspectable and reproducible.
Related
- Application of spectroscopic and multispectral imaging technologies on the assessment of ready-to-eat pineapple quality: A performance evaluation study of machine learning models generated from two commercial data analytics tools
- A Unified Framework for Batch Correction and Imputation in Modern Mass Spectrometry Proteomics
- PURELIGHT: a quantitative photon-counting framework unifying intensity and lifetime imaging at video rate across detector technologies
- Stoichiometry-Dependent Specificity in Biotin Enrichment: A Benchmarking Framework for Proximity-Labeling Proteomics.
- An integrated commercial poultry breeding framework for natural mating and animal welfare
BibTeX
@misc{whelan2026atlas,
title = {{Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms}},
author = {C. D. Whelan and K. Smith-Byrne},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.10.750723},
url = {https://www.biorxiv.org/content/10.64898/2026.09.10.750723v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Atlas of Proteomic Technologies: an evidence-based framework for selecting and combining commercial proteomics platforms
AU - C. D. Whelan
AU - K. Smith-Byrne
PY - 2026
DA - 2026/09/10
PB - bioRxiv
DO - 10.64898/2026.09.10.750723
UR - https://www.biorxiv.org/content/10.64898/2026.09.10.750723v1
AB - High-throughput proteomics now spans several technologies that differ in biological breadth, precision, specificity, sensitivity, cost, and method(s) of quantification; however, investigators currently lack an evidence-based framework to select or combine platforms. Here, we present the Atlas of Proteomic Technologies (APT) - a curated resource that evaluates six commercial platforms across ten analytical dimensions using published head-to-head evidence, expert evaluation, and iterative peer review. APT hosts two decision tools: the Help Me Choose tool maps a study's primary aim(s), scale, sample matrix, and technical constraints to a calibrated, weight-adjustable platform ranking, and the Help Me Combine tool ranks complementary platform pairs by their net-new protein coverage and user-specified technical priorities. Both tools were tested exhaustively across all possible combinations and behave in a balanced, merit-based manner. APT is openly accessible at https://aptatlas.org, providing downloadable tool specifications, seeded analysis scripts, and complete protein coverage lists, ensuring every score and recommendation is inspectable and reproducible.
ER -