Evidence map›Paper›PMID 31602691›Full record

ReviewMass spectrometry reviews2020

Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry.

Nico Verbeeck, Richard M Caprioli, Raf Van de Plas

Open access · hybridAbstract readReview
In one paragraph

Review in Mass spectrometry reviews, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
97citing papers in PubMed, 1 pooled it
15.0field-weighted citation impact, top 1% of its field
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

97 citing papers in PubMed, 1 synthesis or guideline pooled it, 278 citations in OpenAlex.

  1. Pooled it
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  14. Topological segmentation of mass spectrometry imaging data.Journal of mass spectrometry and advances in the clinical lab · 2025
    Article
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  20. Mass Spectrometry Imaging.Analytical chemistry · 2025
    Review

37 more citing papers are in PubMed but not listed here.

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

3 authors at 3 institutions in 3 countries.

Nico VerbeeckDelft Center for Systems and Control, Delft University of Technology - TU Delft, Delft, The Netherlands.
Richard M CaprioliMass Spectrometry Research Center, Vanderbilt University, Nashville, TN.
Raf Van de PlasDelft Center for Systems and Control, Delft University of Technology - TU Delft, Delft, The Netherlands.
Delft University of Technology · NLKU Leuven · BEVanderbilt University · US

Funding

Training (pp 214-245)P41GM103391 · NIGMS · VANDERBILT UNIVERSITY · PI CAPRIOLI, RICHARD M · 2012 to 2020
$17.7M
Vanderbilt University Biomolecular Multimodal Imaging Center for 3-Dimensional Tissue MappingU54DK120058 · NIDDK · VANDERBILT UNIVERSITY · PI HARRIS, RAYMOND C. · 2018 to 2021
$5.7M
Molecular mapping of microbial communities at the host-pathogen interface by multi-modal 3-dimensional imaging mass spectrometryR01AI138581 · NIAID · VANDERBILT UNIVERSITY MEDICAL CENTER · PI Eric P Skaar, Jeffrey M Spraggins · 2018 to 2026
$5.2M
15 Tesla Bruker SolariX FT-ICR mass spectrometerS10OD012359 · OD · VANDERBILT UNIVERSITY · PI CAPRIOLI, RICHARD M · 2012 to 2012
$1.6M
NIAID NIH HHS R01 AI138581NIDDK NIH HHS U54 DK120058NIGMS NIH HHS P41 GM103391NIH HHS S10 OD012359
6 · The paper itself

Abstract

Imaging mass spectrometry (IMS) is a rapidly advancing molecular imaging modality that can map the spatial distribution of molecules with high chemical specificity. IMS does not require prior tagging of molecular targets and is able to measure a large number of ions concurrently in a single experiment. While this makes it particularly suited for exploratory analysis, the large amount and high-dimensional nature of data generated by IMS techniques make automated computational analysis indispensable. Research into computational methods for IMS data has touched upon different aspects, including spectral preprocessing, data formats, dimensionality reduction, spatial registration, sample classification, differential analysis between IMS experiments, and data-driven fusion methods to extract patterns corroborated by both IMS and other imaging modalities. In this work, we review unsupervised machine learning methods for exploratory analysis of IMS data, with particular focus on (a) factorization, (b) clustering, and (c) manifold learning. To provide a view across the various IMS modalities, we have attempted to include examples from a range of approaches including matrix assisted laser desorption/ionization, desorption electrospray ionization, and secondary ion mass spectrometry-based IMS. This review aims to be an entry point for both (i) analytical chemists and mass spectrometry experts who want to explore computational techniques; and (ii) computer scientists and data mining specialists who want to enter the IMS field. © 2019 The Authors. Mass Spectrometry Reviews published by Wiley Periodicals, Inc. Mass SpecRev 00:1-47, 2019.

Indexed as

Unsupervised Machine LearningAnimalsData AnalysisHumansMass SpectrometryMolecular Imagingclusteringdata analysisDESIimaging mass spectrometryLAESILAICPmachine learningMALDImanifold learningmatrix factorizationSIMSunsupervised

Identifiers

PMID31602691
PMCPMC7187435
OpenAlexW2979874034

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.