Raman2imzML Converts Raman Imaging Data into the Standard Mass Spectrometry Imaging Format

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2020 Oct 10

PMID 33036551

Citations 7

Authors

Stefania Alexandra Iakab

Lluc Semente

Maria Garcia-Altares

Xavier Correig

Pere Rafols

Affiliations

Soon will be listed here.

Abstract

Background: Multimodal imaging that combines mass spectrometry imaging (MSI) with Raman imaging is a rapidly developing multidisciplinary analytical method used by a growing number of research groups. Computational tools that can visualize and aid the analysis of datasets by both techniques are in demand.

Results: Raman2imzML was developed as an open-source converter that transforms Raman imaging data into imzML, a standardized common data format created and adopted by the mass spectrometry community. We successfully converted Raman datasets to imzML and visualized Raman images using open-source software designed for MSI applications.

Conclusion: Raman2imzML enables both MSI and Raman images to be visualized using the same file format and the same software for a straightforward exploratory imaging analysis.

Citing Articles

Advancing SERS as a quantitative technique: challenges, considerations, and correlative approaches to aid validation.

Sloan-Dennison S, Wallace G, Hassanain W, Laing S, Faulds K, Graham D Nano Converg. 2024; 11(1):33.

PMID: 39154073 PMC: 11330436. DOI: 10.1186/s40580-024-00443-4.

Correlative Raman Imaging: Development and Cancer Applications.

Khadem H, Mangini M, Farazpour S, De Luca A Biosensors (Basel). 2024; 14(7).

PMID: 39056600 PMC: 11274409. DOI: 10.3390/bios14070324.

Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level.

Chadha R, Guerrero J, Wei L, Sanchez L ACS Cent Sci. 2024; 10(4):758-774.

PMID: 38680555 PMC: 11046475. DOI: 10.1021/acscentsci.3c01438.

RaMALDI: Enabling simultaneous Raman and MALDI imaging of the same tissue section.

Yang E, Kim J, Tressler C, Shen X, Brown D, Johnson C Biosens Bioelectron. 2023; 239:115597.

PMID: 37597501 PMC: 10544780. DOI: 10.1016/j.bios.2023.115597.

SALDI-MS and SERS Multimodal Imaging: One Nanostructured Substrate to Rule Them Both.

Iakab S, Baquer G, Lafuente M, Pina M, Ramirez J, Rafols P Anal Chem. 2022; 94(6):2785-2793.

PMID: 35102738 PMC: 8851428. DOI: 10.1021/acs.analchem.1c04118.

References

Lasch P, Noda I . Two-Dimensional Correlation Spectroscopy for Multimodal Analysis of FT-IR, Raman, and MALDI-TOF MS Hyperspectral Images with Hamster Brain Tissue. Anal Chem. 2017; 89(9):5008-5016. DOI: 10.1021/acs.analchem.7b00332. View

Bocklitz T, Crecelius A, Matthaus C, Tarcea N, von Eggeling F, Schmitt M . Deeper understanding of biological tissue: quantitative correlation of MALDI-TOF and Raman imaging. Anal Chem. 2013; 85(22):10829-34. DOI: 10.1021/ac402175c. View

Ryabchykov O, Popp J, Bocklitz T . Fusion of MALDI Spectrometric Imaging and Raman Spectroscopic Data for the Analysis of Biological Samples. Front Chem. 2018; 6:257. PMC: 6055053. DOI: 10.3389/fchem.2018.00257. View

Rafols P, Vilalta D, Brezmes J, Canellas N, Del Castillo E, Yanes O . Signal preprocessing, multivariate analysis and software tools for MA(LDI)-TOF mass spectrometry imaging for biological applications. Mass Spectrom Rev. 2016; 37(3):281-306. DOI: 10.1002/mas.21527. View

Neumann E, Comi T, Spegazzini N, Mitchell J, Rubakhin S, Gillette M . Multimodal Chemical Analysis of the Brain by High Mass Resolution Mass Spectrometry and Infrared Spectroscopic Imaging. Anal Chem. 2018; 90(19):11572-11580. PMC: 6168410. DOI: 10.1021/acs.analchem.8b02913. View

Race A, Palmer A, Dexter A, Steven R, Styles I, Bunch J . SpectralAnalysis: Software for the Masses. Anal Chem. 2016; 88(19):9451-9458. DOI: 10.1021/acs.analchem.6b01643. View

Cerruti C, Benabdellah F, Laprevote O, Touboul D, Brunelle A . MALDI imaging and structural analysis of rat brain lipid negative ions with 9-aminoacridine matrix. Anal Chem. 2012; 84(5):2164-71. DOI: 10.1021/ac2025317. View

Buchberger A, DeLaney K, Johnson J, Li L . Mass Spectrometry Imaging: A Review of Emerging Advancements and Future Insights. Anal Chem. 2017; 90(1):240-265. PMC: 5959842. DOI: 10.1021/acs.analchem.7b04733. View

Fagerer S, Schmid T, Ibanez A, Pabst M, Steinhoff R, Jefimovs K . Analysis of single algal cells by combining mass spectrometry with Raman and fluorescence mapping. Analyst. 2013; 138(22):6732-6. DOI: 10.1039/c3an01135f. View

10.

Porta Siegel T, Hamm G, Bunch J, Cappell J, Fletcher J, Schwamborn K . Mass Spectrometry Imaging and Integration with Other Imaging Modalities for Greater Molecular Understanding of Biological Tissues. Mol Imaging Biol. 2018; 20(6):888-901. PMC: 6244545. DOI: 10.1007/s11307-018-1267-y. View

11.

Schramm T, Hester Z, Klinkert I, Both J, Heeren R, Brunelle A . imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data. J Proteomics. 2012; 75(16):5106-5110. DOI: 10.1016/j.jprot.2012.07.026. View

12.

Van de Plas R, Yang J, Spraggins J, Caprioli R . Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping. Nat Methods. 2015; 12(4):366-72. PMC: 4382398. DOI: 10.1038/nmeth.3296. View

13.

Bemis K, Harry A, Eberlin L, Ferreira C, van de Ven S, Mallick P . Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments. Bioinformatics. 2015; 31(14):2418-20. PMC: 4495298. DOI: 10.1093/bioinformatics/btv146. View

14.

Bergholt M, Serio A, McKenzie J, Boyd A, Soares R, Tillner J . Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis. ACS Cent Sci. 2018; 4(1):39-51. PMC: 5785772. DOI: 10.1021/acscentsci.7b00367. View

15.

Kallback P, Nilsson A, Shariatgorji M, Andren P . msIQuant--Quantitation Software for Mass Spectrometry Imaging Enabling Fast Access, Visualization, and Analysis of Large Data Sets. Anal Chem. 2016; 88(8):4346-53. DOI: 10.1021/acs.analchem.5b04603. View

16.

Ahlf D, Masyuko R, Hummon A, Bohn P . Correlated mass spectrometry imaging and confocal Raman microscopy for studies of three-dimensional cell culture sections. Analyst. 2014; 139(18):4578-85. DOI: 10.1039/c4an00826j. View

17.

Lenz B, Brink A, Siam M, De Paepe A, Bassett S, Eichinger-Chapelon A . Application of Imaging Techniques to Cases of Drug-Induced Crystal Nephropathy in Preclinical Studies. Toxicol Sci. 2017; 163(2):409-419. DOI: 10.1093/toxsci/kfx044. View

18.

McDonnell L, Heeren R . Imaging mass spectrometry. Mass Spectrom Rev. 2007; 26(4):606-43. DOI: 10.1002/mas.20124. View

19.

Robichaud G, Garrard K, Barry J, Muddiman D . MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform. J Am Soc Mass Spectrom. 2013; 24(5):718-21. PMC: 3693088. DOI: 10.1007/s13361-013-0607-z. View

20.

Rafols P, Vilalta D, Torres S, Calavia R, Heijs B, McDonnell L . Assessing the potential of sputtered gold nanolayers in mass spectrometry imaging for metabolomics applications. PLoS One. 2018; 13(12):e0208908. PMC: 6291137. DOI: 10.1371/journal.pone.0208908. View