MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species
Abstract
Selected reaction monitoring (SRM), sometimes called multiple reaction monitoring (MRM), is becoming the tool of choice for targeted quantitative proteomics in the plant science community. Key to a successful SRM experiment is prior identification of the distinct peptides for the proteins of interest and the determination of the so-called transitions that can be programmed into an LC-MS/MS to monitor those peptides. The transition for a given peptide comprises the intact peptide m/z and a high intensity product ion that can be monitored at a characteristic retention time (RT). To aid the design of SRM experiments, several online tools and databases have been produced to help researchers select transitions for their proteins of interest, but many of these tools are limited to the most popular model organisms such as human, yeast, and mouse or require the experimental acquisition of local spectral libraries. In this paper we present MRMaid, a web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. By using data from this large public repository, MRMaid is able to cover a wide range of species that can increase as the coverage of PRIDE grows. In this paper MRMaid transitions for 25 Arabidopsis thaliana proteins are evaluated experimentally, and found capable of quantifying 23 of these proteins. This performance was found to be comparable with the more time consuming approach of designing transitions using locally acquired orbitrap data, indicating that MRMaid is a valuable tool for targeted Arabidopsis proteomics.
Related
- A PCR-based assay for the sensitive and accurate determination of malaria parasite species that commonly infect humans, including discrimination of Plasmodium ovalecurtisi and Plasmodium ovalewallikeri
- The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species
- Short TALE-binding domains enable mitochondrial genome editing in Arabidopsis thaliana
- Loss‐of‐function of gynoecium‐expressed phospholipase pPLAIIγ triggers maternal haploid induction in Arabidopsis
- Antagonistic DNA methylation dynamics at a single locus controls pollen tube guidance in Arabidopsis
BibTeX
@article{fan2026mrmaid,
title = {{MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species}},
author = {Jun Fan and Fady Mohareb and Alexandra Jones and Conrad Bessant},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2012.00164},
url = {https://hal.science/hal-05788747v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species
AU - Jun Fan
AU - Fady Mohareb
AU - Alexandra Jones
AU - Conrad Bessant
PY - 2026
DA - 2026/10/09
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2012.00164
UR - https://hal.science/hal-05788747v1
AB - Selected reaction monitoring (SRM), sometimes called multiple reaction monitoring (MRM), is becoming the tool of choice for targeted quantitative proteomics in the plant science community. Key to a successful SRM experiment is prior identification of the distinct peptides for the proteins of interest and the determination of the so-called transitions that can be programmed into an LC-MS/MS to monitor those peptides. The transition for a given peptide comprises the intact peptide m/z and a high intensity product ion that can be monitored at a characteristic retention time (RT). To aid the design of SRM experiments, several online tools and databases have been produced to help researchers select transitions for their proteins of interest, but many of these tools are limited to the most popular model organisms such as human, yeast, and mouse or require the experimental acquisition of local spectral libraries. In this paper we present MRMaid, a web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database. By using data from this large public repository, MRMaid is able to cover a wide range of species that can increase as the coverage of PRIDE grows. In this paper MRMaid transitions for 25 Arabidopsis thaliana proteins are evaluated experimentally, and found capable of quantifying 23 of these proteins. This performance was found to be comparable with the more time consuming approach of designing transitions using locally acquired orbitrap data, indicating that MRMaid is a valuable tool for targeted Arabidopsis proteomics.
SN - 1664-462X
ER -