Evidence map›Paper›PMID 41580616›Full record

ArticleBMC bioinformatics2026

mspms: an R package and GUI for multiplex substrate profiling by mass spectrometry.

Charlie Bayne, Brianna Hurysz, David J Gonzalez, Anthony O'Donoghue

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Charlie BayneBiomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA. chbayne@health.ucsd.edu.
Brianna HuryszBiomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
David J GonzalezDepartment of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.
Anthony O'DonoghueDepartment of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.

Funding

GRADUATE TRAINING IN CELLULAR &MOLECULAR PHARMACOLOGYT32GM007752 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BROWN, JOAN HELLER, HANDEL, TRACY M · 1985 to 2023
$13.5M
Tumor-specific drug activation by pericellular proteasesR21CA256460 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI O'DONOGHUE, ANTHONY JOHN, OWEN, SHAWN C · 2022 to 2023
$409k
National Institute of Allergy and Infectious Diseases R01AI158612NCI NIH HHS R21CA256460NIGMS NIH HHS T32 GM007752
6 · The paper itself

Abstract

backgroundMultiplex Substrate Profiling by Mass Spectrometry (MSP-MS) is a powerful method for determining the substrate specificity of proteolytic enzymes, which is essential for developing protease inhibitors, diagnostics, and protease-activated therapeutics. However, the complex datasets generated by MSP-MS pose significant analytical challenges and have limited accessibility for non-specialist users.

resultsWe developed mspms, a Bioconductor R package with an accompanying graphical interface, to streamline the analysis of MSP-MS data. Mspms standardizes workflows for data preparation, processing, statistical analysis, and visualization. The tool is designed for accessibility, serving advanced users through the R package and broader audiences through a web-based interface. We validated mspms using data from four well-characterized cathepsins (A-D), demonstrating that it reliably captures expected substrate specificities.

conclusionsmspms is the first publicly available, comprehensive platform for MSP-MS data analysis downstream of peptide identification and quantification. It integrates preprocessing, normalization, statistical testing, and visualization into a single, transparent, and user-friendly framework, making it a valuable resource for the protease research community. The package is distributed via Bioconductor, and a graphical interface is available online for interactive use.

Indexed as

BioconductorBioinformatics toolsComputational proteomicsData visualizationMass spectrometry data analysisMultiplex substrate profilingProtease specificityR package

Identifiers

PMID41580616
PMCPMC12934049

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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.