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For: Guo D, Föll MC, Volkmann V, Enderle-Ammour K, Bronsert P, Schilling O, Vitek O. Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. Bioinformatics 2021;36:i300-i308. [PMID: 32657378 PMCID: PMC7355295 DOI: 10.1093/bioinformatics/btaa436] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
Number Cited by Other Article(s)
1
HUANG D, LIU X, XU G. [Research progress of deep learning applications in mass spectrometry imaging data analysis]. Se Pu 2024;42:669-680. [PMID: 38966975 PMCID: PMC11224939 DOI: 10.3724/sp.j.1123.2023.10035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Indexed: 07/06/2024]  Open
2
Gardner W, Winkler DA, Bamford SE, Muir BW, Pigram PJ. Markedly Enhanced Analysis of Mass Spectrometry Images Using Weakly Supervised Machine Learning. SMALL METHODS 2024;8:e2301230. [PMID: 38204217 DOI: 10.1002/smtd.202301230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/03/2023] [Indexed: 01/12/2024]
3
Beck A, Muhoberac M, Randolph CE, Beveridge CH, Wijewardhane PR, Kenttämaa HI, Chopra G. Recent Developments in Machine Learning for Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024;4:233-246. [PMID: 38910862 PMCID: PMC11191731 DOI: 10.1021/acsmeasuresciau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 06/25/2024]
4
Piga I, Magni F, Smith A. The journey towards clinical adoption of MALDI-MS-based imaging proteomics: from current challenges to future expectations. FEBS Lett 2024;598:621-634. [PMID: 38140823 DOI: 10.1002/1873-3468.14795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
5
Bi S, Wang M, Pu Q, Yang J, Jiang N, Zhao X, Qiu S, Liu R, Xu R, Li X, Hu C, Yang L, Gu J, Du D. Multi-MSIProcessor: Data Visualizing and Analysis Software for Spatial Metabolomics Research. Anal Chem 2024;96:339-346. [PMID: 38102989 DOI: 10.1021/acs.analchem.3c04192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
6
Bemis KA, Föll MC, Guo D, Lakkimsetty SS, Vitek O. Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis. Nat Methods 2023;20:1883-1886. [PMID: 37996752 DOI: 10.1038/s41592-023-02070-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/06/2023] [Indexed: 11/25/2023]
7
Bemis KA, Föll MC, Guo D, Lakkimsetty SS, Vitek O. Cardinal v3 - a versatile open source software for mass spectrometry imaging analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529280. [PMID: 36865170 PMCID: PMC9980127 DOI: 10.1101/2023.02.20.529280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
8
Guo D, Föll MC, Bemis KA, Vitek O. A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images. Bioinformatics 2023;39:btad067. [PMID: 36744928 PMCID: PMC9942547 DOI: 10.1093/bioinformatics/btad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/23/2022] [Accepted: 02/06/2023] [Indexed: 02/07/2023]  Open
9
Guo L, Dong J, Xu X, Wu Z, Zhang Y, Wang Y, Li P, Tang Z, Zhao C, Cai Z. Divide and Conquer: A Flexible Deep Learning Strategy for Exploring Metabolic Heterogeneity from Mass Spectrometry Imaging Data. Anal Chem 2023;95:1924-1932. [PMID: 36633187 PMCID: PMC9878502 DOI: 10.1021/acs.analchem.2c04045] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023]
10
Development of Non-Targeted Mass Spectrometry Method for Distinguishing Spelt and Wheat. Foods 2022;12:foods12010141. [PMID: 36613357 PMCID: PMC9818861 DOI: 10.3390/foods12010141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022]  Open
11
Hu H, Laskin J. Emerging Computational Methods in Mass Spectrometry Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022;9:e2203339. [PMID: 36253139 PMCID: PMC9731724 DOI: 10.1002/advs.202203339] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/17/2022] [Indexed: 05/10/2023]
12
Guo L, Liu X, Zhao C, Hu Z, Xu X, Cheng KK, Zhou P, Xiao Y, Shah M, Xu J, Dong J, Cai Z. iSegMSI: An Interactive Strategy to Improve Spatial Segmentation of Mass Spectrometry Imaging Data. Anal Chem 2022;94:14522-14529. [PMID: 36223650 DOI: 10.1021/acs.analchem.2c01456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
13
Yamada H, Xu L, Eto F, Takeichi R, Islam A, Mamun MA, Zhang C, Yao I, Sakamoto T, Aramaki S, Kikushima K, Sato T, Takahashi Y, Machida M, Kahyo T, Setou M. Changes of Mass Spectra Patterns on a Brain Tissue Section Revealed by Deep Learning with Imaging Mass Spectrometry Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022;33:1607-1614. [PMID: 35881989 DOI: 10.1021/jasms.2c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
14
Plyusnin I, Truong Nguyen PT, Sironen T, Vapalahti O, Smura T, Kant R. ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. BMC Bioinformatics 2022;23:196. [PMID: 35643449 PMCID: PMC9143711 DOI: 10.1186/s12859-022-04709-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/04/2022] [Indexed: 11/12/2022]  Open
15
Missinou AA, Ferreira de Carvalho J, Marnet N, Delhaye T, Hamzaoui O, Abdel Sayed D, Guitton Y, Lebreton L, Langrume C, Laperche A, Delourme R, Manzanares-Dauleux MJ, Bouchereau A, Gravot A. Identification and Quantification of Glucosinolates and Phenolics in a Large Panel of Brassica napus Highlight Valuable Genetic Resources for Chemical Ecology and Breeding. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022;70:5245-5261. [PMID: 35420430 DOI: 10.1021/acs.jafc.1c08118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
16
Abdelmoula WM, Stopka SA, Randall EC, Regan M, Agar JN, Sarkaria JN, Wells WM, Kapur T, Agar NYR. massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation. Bioinformatics 2022;38:2015-2021. [PMID: 35040929 PMCID: PMC8963284 DOI: 10.1093/bioinformatics/btac032] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 01/21/2023]  Open
17
Pino L, Schilling B. Proximity labeling and other novel mass spectrometric approaches for spatiotemporal protein dynamics. Expert Rev Proteomics 2021;18:757-765. [PMID: 34496693 PMCID: PMC8650568 DOI: 10.1080/14789450.2021.1976149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
18
Tuck M, Blanc L, Touti R, Patterson NH, Van Nuffel S, Villette S, Taveau JC, Römpp A, Brunelle A, Lecomte S, Desbenoit N. Multimodal Imaging Based on Vibrational Spectroscopies and Mass Spectrometry Imaging Applied to Biological Tissue: A Multiscale and Multiomics Review. Anal Chem 2020;93:445-477. [PMID: 33253546 DOI: 10.1021/acs.analchem.0c04595] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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