Imaging mass spectrometry of proteins and peptides: 3d volume reconstruction

ABSTRACT As large genomic and proteomic datasets are generated from homogenates of various tissues, the need for information on the spatial localization of their encoded products has become

more pressing. Matrix-assisted laser desorption-ionization (MALDI) imaging mass spectrometry (IMS) offers investigators the means with which to unambiguously study peptides and proteins with

molecular specificity, and to determine their distribution in two and three dimensions1,2. In the past few years, several parameters have been optimized for IMS, including sample

preparation, matrix application and instrumental acquisition parameters3,4 (Box 1). These developments have resulted in a high degree of reproducibility in mass accuracy and peak intensities

(Supplementary Fig. 1 online). Recently, we have optimized our protocol to be able to increase the number of molecular species analyzed by collecting two sets of sections, covering one set

of sections with sinapinic acid for optimal detection of proteins and adjacent sections with 2,5-dihydroxybenzoic acid (DHB) matrix for the optimal detection of low-mass species, including

peptides. Approximately 1,000 peaks can be observed in each dataset (Fig. 1). Furthermore, the sections are collected at an equal distance, 200 μm instead of 400–500 μm used previously, thus

enabling the use of virtual _z_-stacks and three-dimensional (3D) volume renderings to investigate differential localization patterns in much smaller brain structures such as the substantia

nigra and the interpeduncular nucleus. Here we present our optimized step-by-step procedure based on previous work in our laboratory2, describing how to make 3D volume reconstructions of

MALDI IMS data, as applied to the rat brain. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access

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subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS TOWARD NANOSCALE MOLECULAR MASS SPECTROMETRY IMAGING VIA PHYSICALLY CONSTRAINED MACHINE

LEARNING ON CO-REGISTERED MULTIMODAL DATA Article Open access 26 June 2020 ON-TISSUE DATASET-DEPENDENT MALDI-TIMS-MS2 BIOIMAGING Article Open access 18 November 2023 AUTOMATED ANNOTATION AND

VISUALISATION OF HIGH-RESOLUTION SPATIAL PROTEOMIC MASS SPECTROMETRY IMAGING DATA USING HIT-MAP Article Open access 28 May 2021 REFERENCES * Caprioli, R.M., Farmer, T.B. & Gile, J.

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references ACKNOWLEDGEMENTS We thank D.S. Cornett (Vanderbilt University) for custom data preprocessing software, B. Dawant (Vanderbilt University) for assistance with registration

functions, P. Chaurand and L. Manier (Vanderbilt University) for assistance with MS/MS analyses, J. Morgan (St. Jude Children's Research Hospital, Memphis, Tennessee) for the kind gift

of PEP-19 antibody, and J. Smith (Vanderbilt University) for assistance with using the 3D Amira software. This work was supported by The National Parkinson Foundation Center of Excellence at

Vanderbilt, the National Institute of General Medical Science (GM58008-08), the Department of Defense (W81XWH-05-1-0179) and the National Cancer Institute of the US National Institutes of

Health (CA86243-03). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University Medical Center, 465 21st Avenue

south, Nashville, 37232, Tennessee, USA Malin Andersson, M Reid Groseclose & Richard M Caprioli * Departments of Psychiatry and Pharmacology, Vanderbilt University Medical Center, 465

21st Avenue south, Nashville, 37232, Tennessee, USA Malin Andersson & Ariel Y Deutch Authors * Malin Andersson View author publications You can also search for this author inPubMed 

Google Scholar * M Reid Groseclose View author publications You can also search for this author inPubMed Google Scholar * Ariel Y Deutch View author publications You can also search for this

author inPubMed Google Scholar * Richard M Caprioli View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to Richard M

Caprioli. SUPPLEMENTARY INFORMATION SUPPLEMENTARY TEXT AND FIGURES Supplementary Figures 1–3, Supplementary Methods (PDF 925 kb) SUPPLEMENTARY VIDEO 1 The movie shows the co-registered 3D

volumes of MS imaging data of SP and PEP-19 in the ventral midbrain rotating around its x axis. The movie starts with a frontal view of the midbrain, showing the tissue distribution of SP in

green and PEP-19 in purple. Overlap of peptide and protein distribution is signified by a white appearance. (MOV 1087 kb) SUPPLEMENTARY VIDEO 2 The 3D volumes of MS imaging data of SP and

PEP-19 in the ventral midbrain rotate around the y axis. The movie starts with a frontal view of the midbrain, showing the tissue distribution of SP in green and PEP-19 in purple. Overlap of

peptide and protein distribution is signified by a white appearance. (MOV 961 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Andersson, M.,

Groseclose, M., Deutch, A. _et al._ Imaging mass spectrometry of proteins and peptides: 3D volume reconstruction. _Nat Methods_ 5, 101–108 (2008). https://doi.org/10.1038/nmeth1145 Download

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