1
|
Liang W, Zhu Z, Xu D, Wang P, Guo F, Xiao H, Hou C, Xue J, Zhi X, Ran R. The burgeoning spatial multi-omics in human gastrointestinal cancers. PeerJ 2024; 12:e17860. [PMID: 39285924 PMCID: PMC11404479 DOI: 10.7717/peerj.17860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/14/2024] [Indexed: 09/19/2024] Open
Abstract
The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body's three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.
Collapse
Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Zhenpeng Zhu
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Dandan Xu
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Peng Wang
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Fei Guo
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
| | - Haoshan Xiao
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Chenyang Hou
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
- Hebei North University, Zhangjiakou, Hebei Province, China
| | - Jun Xue
- Department of Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei Province, China
| | - Xuejun Zhi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
| | - Rensen Ran
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei province, China
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
2
|
Applications of mass spectroscopy in understanding cancer proteomics. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
|
3
|
Vandergrift GW, Kew W, Lukowski JK, Bhattacharjee A, Liyu AV, Shank EA, Paša-Tolić L, Prabhakaran V, Anderton CR. Imaging and Direct Sampling Capabilities of Nanospray Desorption Electrospray Ionization with Absorption-Mode 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2022; 94:3629-3636. [PMID: 35167251 DOI: 10.1021/acs.analchem.1c05216] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nanospray desorption electrospray ionization mass spectrometry, a powerful ambient sampling and imaging technique, is herein coupled as an isolated source with 21 Tesla (21T) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). Absorption-mode data, enabled by an external data acquisition system, is applied for improved mass resolution, accuracy, and dynamic range without compromising spectral acquisition rates. Isotopic fine structure (IFS) information is obtained from the ambient sampling of living Bacillus and Fusarium species, allowing for high confidence in molecular annotations with a resolution >830 k (at m/z 825). Tandem mass spectrometry experiments for biological samples are shown to retain the IFS in addition to gained fragmentation information, providing a further degree of annotation confidence from ambient analyses. Rat brain was imaged by nanospray desorption electrospray ionization (nano-DESI) 21T FTICR MS in ∼5 h using 768 ms transients, producing over 800 molecular annotations using the METASPACE platform and low-parts-per-billion mass accuracy at a spatial resolution of ∼25 × 180 μm. Finally, nano-DESI 21T FTICR MS imaging is demonstrated to reveal images corresponding to the IFS, as well as hundreds of additional molecular features (including demonstrated differences as low as 8.96 mDa) that are otherwise undetected by a more conventional imaging methodology.
Collapse
Affiliation(s)
- Gregory W Vandergrift
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jessica K Lukowski
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Elizabeth A Shank
- University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Venkateshkumar Prabhakaran
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,The Gene & Linda Voil and School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| |
Collapse
|
4
|
Luo S, Ling Y, Chen LP, Huang RP. Using Antibody Arrays for Biomarker Discovery. Methods Mol Biol 2020; 2237:237-245. [PMID: 33237423 DOI: 10.1007/978-1-0716-1064-0_20] [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] [Indexed: 03/13/2023]
Abstract
Biomarkers for diseases are important for the development of clinical diagnostic tests and can provide early intervention for cancer or cardiovascular patients. Over the past decade, antibody array technology has achieved significant technological improvement in the quantitative measurement of more than a thousand proteins simultaneously and has been utilized to screen and identify unique proteins as disease biomarkers. However, few biomarkers have been translated into clinical application. This chapter will discuss the protocol for the screening and validation of unique proteins that create a new avenue for biomarker discovery.
Collapse
Affiliation(s)
| | - Yunbiao Ling
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li-Pai Chen
- Department of Gynaecologic Oncology, Cancer Institute and Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruo-Pan Huang
- RayBiotech, Peachtree Corners, GA, USA
- RayBiotech, Inc., Guangzhou, Guangdong, China
- South China Biochip Research Center, Guangzhou, Guangdong, China
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
5
|
Kotowska AM, Trindade GF, Mendes PM, Williams PM, Aylott JW, Shard AG, Alexander MR, Scurr DJ. Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling. Nat Commun 2020; 11:5832. [PMID: 33203841 PMCID: PMC7672064 DOI: 10.1038/s41467-020-19445-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023] Open
Abstract
Label-free protein characterization at surfaces is commonly achieved using digestion and/or matrix application prior to mass spectrometry. We report the assignment of undigested proteins at surfaces in situ using secondary ion mass spectrometry (SIMS). Ballistic fragmentation of proteins induced by a gas cluster ion beam (GCIB) leads to peptide cleavage producing fragments for subsequent OrbitrapTM analysis. In this work we annotate 16 example proteins (up to 272 kDa) by de novo peptide sequencing and illustrate the advantages of this approach by characterizing a protein monolayer biochip and the depth distribution of proteins in human skin.
Collapse
Affiliation(s)
- Anna M Kotowska
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Philip M Williams
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jonathan W Aylott
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander G Shard
- National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
| | | | - David J Scurr
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK.
| |
Collapse
|
6
|
Bowman AP, Blakney GT, Hendrickson CL, Ellis SR, Heeren RMA, Smith DF. Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS. Anal Chem 2020; 92:3133-3142. [PMID: 31955581 PMCID: PMC7031845 DOI: 10.1021/acs.analchem.9b04768] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Detailed characterization
of complex biological surfaces by matrix-assisted
laser desorption/ionization (MALDI) mass spectrometry imaging (MSI)
requires instrumentation that is capable of high mass resolving power,
mass accuracy, and dynamic range. Fourier transform ion cyclotron
resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral
performance for MALDI MSI experiments, and often reveals molecular
features that are unresolved on lower performance instrumentation.
Higher magnetic field strength improves all performance characteristics
of FT-ICR; mass resolving power improves linearly, while mass accuracy
and dynamic range improve quadratically with magnetic field strength.
Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving
power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below
100 ppb, and dynamic range per pixel over 500:1 were obtained from
the direct analysis of biological tissue sections. Molecular features
with m/z differences as small as
1.79 mDa were resolved and identified with high mass accuracy. These
features allow for the separation and identification of lipids to
the underlying structures of tissues. The unique molecular detail,
accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR
MSI experiment enable researchers to visualize molecular structures
in complex tissues that have remained hidden until now. The instrument
described allows for future innovative, such as high-end studies to
unravel the complexity of biological, geological, and engineered organic
material surfaces with an unsurpassed detail.
Collapse
Affiliation(s)
- Andrew P Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Greg T Blakney
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States.,Department of Chemistry and Biochemistry , Florida State University , 95 Chieftain Way , Tallahassee , Florida 32306 , United States
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Donald F Smith
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States
| |
Collapse
|
7
|
Belianinov A, Ievlev AV, Lorenz M, Borodinov N, Doughty B, Kalinin SV, Fernández FM, Ovchinnikova OS. Correlated Materials Characterization via Multimodal Chemical and Functional Imaging. ACS NANO 2018; 12:11798-11818. [PMID: 30422627 PMCID: PMC9850281 DOI: 10.1021/acsnano.8b07292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Multimodal chemical imaging simultaneously offers high-resolution chemical and physical information with nanoscale and, in select cases, atomic resolution. By coupling modalities that collect physical and chemical information, we can address scientific problems in biological systems, battery and fuel cell research, catalysis, pharmaceuticals, photovoltaics, medicine, and many others. The combined systems enable the local correlation of material properties with chemical makeup, making fundamental questions of how chemistry and structure drive functionality approachable. In this Review, we present recent progress and offer a perspective for chemical imaging used to characterize a variety of samples by a number of platforms. Specifically, we present cases of infrared and Raman spectroscopies combined with scanning probe microscopy; optical microscopy and mass spectrometry; nonlinear optical microscopy; and, finally, ion, electron, and probe microscopies with mass spectrometry. We also discuss the challenges associated with the use of data originated by the combinatorial hardware, analysis, and machine learning as well as processing tools necessary for the interpretation of multidimensional data acquired from multimodal studies.
Collapse
Affiliation(s)
- Alex Belianinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Anton V. Ievlev
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Matthias Lorenz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nikolay Borodinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Benjamin Doughty
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sergei V. Kalinin
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology and Petit Institute for Biochemistry and Bioscience, Atlanta, Georgia 30332, United States
| | - Olga S. Ovchinnikova
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Corresponding Author:
| |
Collapse
|
8
|
Osman H, Georges J, Elsahy D, Hattab EM, Yocom S, Cohen-Gadol AA. In Vivo Microscopy in Neurosurgical Oncology. World Neurosurg 2018; 115:110-127. [PMID: 29653276 DOI: 10.1016/j.wneu.2018.03.218] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Intraoperative neurosurgical histopathologic diagnoses rely on evaluation of rapid tissue preparations such as frozen sections and smears with conventional light microscopy. Although useful, these techniques are time consuming and therefore cannot provide real-time intraoperative feedback. In vivo molecular imaging techniques are emerging as novel methods for generating real-time diagnostic histopathologic images of tumors and their surrounding tissues. These imaging techniques rely on contrast generated by exogenous fluorescent dyes, autofluorescence of endogenous molecules, fluorescence decay of excited molecules, or light scattering. Large molecular imaging instruments are being miniaturized for clinical in vivo use. This review discusses pertinent imaging systems that have been developed for neurosurgical use and imaging techniques currently under development for neurosurgical molecular imaging.
Collapse
Affiliation(s)
- Hany Osman
- Massachusetts General Hospital and Harvard Medical School, Wellman Center for Photomedicine, Boston, Massachusetts, USA
| | - Joseph Georges
- Philadelphia College of Osteopathic Medicine, Department of Neurosurgery, Philadelphia, Pennsylvania, USA
| | - Deena Elsahy
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Eyas M Hattab
- University of Louisville, Department of Pathology and Laboratory Medicine, Louisville, Kentucky, USA
| | - Steven Yocom
- Philadelphia College of Osteopathic Medicine, Department of Neurosurgery, Philadelphia, Pennsylvania, USA
| | - Aaron A Cohen-Gadol
- Goodman Campbell Brain and Spine and Indiana University Department of Neurological Surgery, Indianapolis, Indiana, USA.
| |
Collapse
|
9
|
Subasi S, Altintas O, Kasap M, Guzel N, Akpinar G, Karaman S. Comparative proteomic analysis of amnion membrane transplantation and cross-linking treatments in an experimental alkali injury model. Int Ophthalmol 2017; 38:2563-2574. [PMID: 29170974 DOI: 10.1007/s10792-017-0770-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/16/2017] [Indexed: 11/28/2022]
Abstract
PURPOSE In this study, by using a two-dimensional (2D) electrophoresis-based experimental approach, we aimed at understanding the nature of alkali injuries and the underlying mechanisms. A secondary aim was to compare the effects of cross-linking (CXL) and amnion membrane transplantation (AMT) on corneal protein compositions at the end of the early repair phase after injured with alkali. METHOD The right corneas of 24 rabbits were injured with a 1 N solution of NaOH. Groups were formed based on the adjuvant therapies as (1) healthy group, (2) control group, (3) CXL group, (4) AMT group. In addition to the therapies, a conventional medical treatment was applied to all groups. Left eyes were used as within-subject healthy corneas (1). The corneas were excised at day 21, and a comparative proteomic analysis was performed using 2D gel electrophoresis coupled with MALDI-TOF/TOF. RESULT 2D gel electrophoresis revealed the presence seven protein spots whose abundance changed among the groups. Those proteins were SH3 domain-binding protein, plant homeodomain finger protein 23, S100 calcium binding protein A-11(S100 A11), keratin type 2 cytoskeletal 1 and 2, transketolase and glyceraldehyde 3-phosphate dehydrogenase. Ingenuity pathway analysis predicted that the observed changes may be linked to a central metabolic pathway, transforming growth factor beta 1. Canonical pathway analysis focused our attention to two different pathways, namely nicotinamide adenine dinucleotide repair pathway and non-oxidative branch of pentose phosphate pathway. CONCLUSION Our results shed some light onto the molecular mechanisms affected by alkali injury and adjuvant treatments. Further research is needed to propose medically significant target molecules that may be used for novel drug developments for alkali injury.
Collapse
Affiliation(s)
- Sevgi Subasi
- Department of Ophthalmology, Körfez State Hospital, Kocaeli, Turkey.
| | - Ozgul Altintas
- Department of Ophthalmology, Medical Faculty, Acıbadem University, Istanbul, Turkey
| | - Murat Kasap
- Department of Medical Biology, Medical Faculty, Kocaeli University, Kocaeli, Turkey
| | - Nil Guzel
- Department of Medical Biology, Medical Faculty, Kocaeli University, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical Faculty, Kocaeli University, Kocaeli, Turkey
| | - Suleyman Karaman
- Department of Ophthalmology, Talya Medical Center, Antalya, Turkey
| |
Collapse
|
10
|
Arentz G, Mittal P, Zhang C, Ho YY, Briggs M, Winderbaum L, Hoffmann MK, Hoffmann P. Applications of Mass Spectrometry Imaging to Cancer. Adv Cancer Res 2017; 134:27-66. [PMID: 28110654 DOI: 10.1016/bs.acr.2016.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.
Collapse
Affiliation(s)
- G Arentz
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - C Zhang
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - Y-Y Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia; ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA, Australia
| | - L Winderbaum
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M K Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia.
| |
Collapse
|
11
|
Duncan MW, Hunsucker SW. Proteomics as a Tool for Clinically Relevant Biomarker Discovery and Validation. Exp Biol Med (Maywood) 2016; 230:808-17. [PMID: 16339745 DOI: 10.1177/153537020523001105] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The excitement associated with clinical applications of proteomics was initially focused on its potential to serve as a vehicle for both biomarker discovery and drug discovery and routine clinical sample analysis. Some approaches were thought to be able to “identify” mass spectral characteristics that distinguished between control and disease samples, and thereafter it was believed that the same tool could be employed to screen samples in a high-throughput clinical setting. However, this has been difficult to achieve, and the early promise is yet to be fully realized. While we see an important place for mass spectrometry in drug and biomarker discovery, we believe that alternative strategies will prove more fruitful for routine analysis. Here we discuss the power and versatility of 2D gels and mass spectrometry in the discovery phase of biomarker work but argue that it is better to rely on immunochemical methods for high-throughput validation and routine assay applications.
Collapse
Affiliation(s)
- Mark W Duncan
- Department of Pediatrics, Section of Pulmonary Medicine, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.
| | | |
Collapse
|
12
|
Longuespée R, Casadonte R, Kriegsmann M, Pottier C, Picard de Muller G, Delvenne P, Kriegsmann J, De Pauw E. MALDI mass spectrometry imaging: A cutting-edge tool for fundamental and clinical histopathology. Proteomics Clin Appl 2016; 10:701-19. [PMID: 27188927 DOI: 10.1002/prca.201500140] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/07/2016] [Accepted: 05/13/2016] [Indexed: 01/16/2023]
Abstract
Histopathological diagnoses have been done in the last century based on hematoxylin and eosin staining. These methods were complemented by histochemistry, electron microscopy, immunohistochemistry (IHC), and molecular techniques. Mass spectrometry (MS) methods allow the thorough examination of various biocompounds in extracts and tissue sections. Today, mass spectrometry imaging (MSI), and especially matrix-assisted laser desorption ionization (MALDI) imaging links classical histology and molecular analyses. Direct mapping is a major advantage of the combination of molecular profiling and imaging. MSI can be considered as a cutting edge approach for molecular detection of proteins, peptides, carbohydrates, lipids, and small molecules in tissues. This review covers the detection of various biomolecules in histopathological sections by MSI. Proteomic methods will be introduced into clinical histopathology within the next few years.
Collapse
Affiliation(s)
- Rémi Longuespée
- Proteopath GmbH, Trier, Germany.,Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | | | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany.,MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| |
Collapse
|
13
|
Direct analysis of ethylenediaminetetraacetic acid (EDTA) on concrete by reactive-desorption electrospray ionization mass spectrometry. Talanta 2015; 132:877-83. [DOI: 10.1016/j.talanta.2014.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/10/2014] [Accepted: 10/14/2014] [Indexed: 11/19/2022]
|
14
|
Three-dimensional imaging of lipids and metabolites in tissues by nanospray desorption electrospray ionization mass spectrometry. Anal Bioanal Chem 2014; 407:2063-71. [PMID: 25395201 DOI: 10.1007/s00216-014-8174-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 10/24/2022]
Abstract
Three-dimensional (3D) imaging of tissue sections is a new frontier in mass spectrometry imaging (MSI). Here, we report on fast 3D imaging of lipids and metabolites associated with mouse uterine decidual cells and embryo at the implantation site on day 6 of pregnancy. 2D imaging of 16-20 serial tissue sections deposited on the same glass slide was performed using nanospray desorption electrospray ionization (nano-DESI)-an ambient ionization technique that enables sensitive localized analysis of analytes on surfaces without special sample pretreatment. In this proof-of-principle study, nano-DESI was coupled to a high-resolution Q-Exactive instrument operated at high repetition rate of >5 Hz with moderate mass resolution of 35,000 (m/Δm at m/z 200), which enabled acquisition of the entire 3D image with a spatial resolution of ∼150 μm in less than 4.5 h. The results demonstrate localization of acetylcholine in the primary decidual zone (PDZ) of the implantation site throughout the depth of the tissue examined, indicating an important role of this signaling molecule in decidualization. Choline and phosphocholine-metabolites associated with cell growth-are enhanced in the PDZ and abundant in other cellular regions of the implantation site. Very different 3D distributions were obtained for fatty acids (FA), oleic acid and linoleic acid (FA 18:1 and FA 18:2), differing only by one double bond. Localization of FA 18:2 in the PDZ indicates its important role in decidualization while FA 18:1 is distributed more evenly throughout the tissue. In contrast, several lysophosphatidylcholines (LPC) observed in this study show donut-like distributions with localization around the PDZ. Complementary distributions with minimal overlap were observed for LPC 18:0 and FA 18:2 while the 3D image of the potential precursor phosphatidylcholine 36:2 (PC 36:2) showed a significant overlap with both LPC 18:0 and FA 18:2.
Collapse
|
15
|
Norris JL, Caprioli RM. Imaging mass spectrometry: a new tool for pathology in a molecular age. Proteomics Clin Appl 2014; 7:733-8. [PMID: 24178781 DOI: 10.1002/prca.201300055] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/15/2013] [Accepted: 08/21/2013] [Indexed: 12/28/2022]
Abstract
Mass spectrometry (MS) provides unique advantages for the analysis of clinical specimens, and these capabilities have been critical to the advancement of diagnostic medicine. To date, LC-MS is the MS platform most commonly used for diagnostics; however, LC-MS based proteomics is very labor intensive and costly to implement for high volume assays. Furthermore, when analyzing tissue samples, additional laborious sample preparation steps must be employed (e.g. extraction methods or laser microdissection). The direct analysis of cells and tissues by MALDI imaging MS has developed significant momentum for applications that have diagnostic potential. MALDI imaging MS provides molecular information from specific cell types within tissue sections; however, this laser-based approach significantly reduces the analysis time for each location sampled. This Viewpoint discusses the technologies for direct analysis of tissues, the potential for diagnostic applications using MALDI imaging MS, and the challenges faced in the transfer of the technology to the clinical laboratory.
Collapse
Affiliation(s)
- Jeremy L Norris
- Department of Biochemistry, National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | | |
Collapse
|
16
|
Minerva L, Ceulemans A, Baggerman G, Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin Appl 2014; 6:581-95. [PMID: 23090913 DOI: 10.1002/prca.201200033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/12/2022]
Abstract
MALDI MS imaging (MSI) is an analytical tool capable of providing spatial distribution and relative abundance of biomolecules directly in tissue. After 15 years of intense efforts to improve the acquisition and quality of molecular images, MSI has matured into an asset of the proteomic toolbox. The power of MSI lies in the ability to differentiate tissue regions that are not histologically distinct but are characterized by different MS profiles. Recently, MSI has been gaining momentum in biomedical research and has found applications in disease diagnosis and prognosis, biomarker discovery, and drug therapy. Although the technology holds great promise, MSI is still faced with a set of methodological challenges presented by the clinical setting. There is a growing awareness regarding this topic and efforts are being taken to develop clear and practical standards to overcome these challenges. This review presents an overview of MALDI MSI as a biomarker discovery tool and recent methodological progress in the field.
Collapse
Affiliation(s)
- Laurens Minerva
- Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | |
Collapse
|
17
|
Skandarajah AR, Moritz RL, Tjandra JJ, Simpson RJ. Proteomic analysis of colorectal cancer: discovering novel biomarkers. Expert Rev Proteomics 2014; 2:681-92. [PMID: 16209648 DOI: 10.1586/14789450.2.5.681] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Colorectal cancer is one of the most common cancers in the Western world. When detected at an early stage, the majority of cancers can be cured with current treatment modalities. However, most cancers present at an intermediate stage. The discovery of sensitive and specific biomarkers has the potential to improve preclinical diagnosis of primary and recurrent colorectal cancer, and holds the promise of prognostic and therapeutic application. Current biomarkers such as carcinoembryonic antigen lack sensitivity and specificity for general population screening. This review aims to highlight the role of current proteomic technologies in the discovery and validation of potential biomarkers with a view to translation to the clinic.
Collapse
Affiliation(s)
- Anita R Skandarajah
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Grattan Street, Parkville 3050, Victoria, Australia.
| | | | | | | |
Collapse
|
18
|
Trimpin S, Wang B, Lietz CB, Marshall DD, Richards AL, Inutan ED. New ionization processes and applications for use in mass spectrometry. Crit Rev Biochem Mol Biol 2013; 48:409-29. [DOI: 10.3109/10409238.2013.806887] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
19
|
|
20
|
Inutan ED, Wager-Miller J, Mackie K, Trimpin S. Laserspray ionization imaging of multiply charged ions using a commercial vacuum MALDI ion source. Anal Chem 2012; 84:9079-84. [PMID: 23009673 PMCID: PMC3703845 DOI: 10.1021/ac301665h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This is the first report of imaging mass spectrometry (MS) from multiply charged ions at vacuum. Laserspray ionization (LSI) was recently extended to applications at vacuum producing electrospray ionization-like multiply charged ions directly from surfaces using a commercial intermediate pressure matrix-assisted laser desorption/ionization ion mobility spectrometry (IMS) MS instrument. Here, we developed a strategy to image multiply charged peptide ions. This is achieved by the use of 2-nitrophloroglucinol as matrix for spray deposition onto the tissue section and implementation of "soft" acquisition conditions including lower laser power and ion accelerating voltages similar to electrospray ionization-like conditions. Sufficient ion abundance is generated by the vacuum LSI method to employ IMS separation in imaging multiply charged ions obtained on a commercial mass spectrometer ion source without physical instrument modifications using the laser in the commercially available reflection geometry alignment. IMS gas-phase separation reduces the complexity of the ion signal from the tissue, especially for multiply charged relative to abundant singly charged ions from tissue lipids. We show examples of LSI tissue imaging from charge state +2 of three endogenous peptides consisting of between 1 and 16 amino acid residues from the acetylated N-terminal end of myelin basic protein: mass-to-charge (m/z) 795.81 (+2) molecular weight (MW) 1589.6, m/z 831.35 (+2) MW 1660.7, and m/z 917.40 (+2) MW 1832.8.
Collapse
Affiliation(s)
- Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | | | | | | |
Collapse
|
21
|
TARGETED MASS spectrometry Imaging: Specific Targeting Mass Spectrometry imaging technologies from history to perspective. ACTA ACUST UNITED AC 2012; 47:133-74. [DOI: 10.1016/j.proghi.2012.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2012] [Indexed: 12/28/2022]
|
22
|
Nanostructure Initiator Mass Spectrometry for tissue imaging in metabolomics: Future prospects and perspectives. J Proteomics 2012; 75:5061-5068. [DOI: 10.1016/j.jprot.2012.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 04/29/2012] [Accepted: 05/02/2012] [Indexed: 01/01/2023]
|
23
|
Flanigan PM, Radell LL, Brady JJ, Levis RJ. Differentiation of Eight Phenotypes and Discovery of Potential Biomarkers for a Single Plant Organ Class Using Laser Electrospray Mass Spectrometry and Multivariate Statistical Analysis. Anal Chem 2012; 84:6225-32. [DOI: 10.1021/ac3012335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paul M. Flanigan
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia,
Pennsylvania 19122, United States
| | - Laine L. Radell
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia,
Pennsylvania 19122, United States
| | - John J. Brady
- U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, Maryland
20783, United States
| | - Robert J. Levis
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia,
Pennsylvania 19122, United States
| |
Collapse
|
24
|
Imaging mass spectrometry of thin tissue sections: a decade of collective efforts. J Proteomics 2012; 75:4883-4892. [PMID: 22525544 DOI: 10.1016/j.jprot.2012.04.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 12/21/2022]
Abstract
Imaging mass spectrometry (MS) allows to monitor the spatial distribution and abundance of endogenous and administered compounds present within tissue specimens. Several different but complementary imaging MS technologies have been developed allowing the analysis of a wide variety of compounds including inorganic elementals, metabolites, lipids, peptides, proteins and xenobiotics with spatial resolutions from micrometer to nanometer scales. In the past decade, an enormous collective body of work has been done to develop and improve the imaging MS technology. This article gives a historical perspective, an overview of the principle and status of the technology and lists the main fields of applications. It also enumerates some of the critical challenges we need to collectively address for imaging MS to be considered a mainstream analytical method.
Collapse
|
25
|
Abstract
Lipidomics, a major part of metabolomics, constitutes the detailed analysis and global characterization, both spatial and temporal, of the structure and function of lipids (the lipidome) within a living system. As with proteomics, mass spectrometry has earned a central analytical role in lipidomics, and this role will continue to grow with technological developments. Currently, there exist two mass spectrometry-based lipidomics approaches, one based on a division of lipids into categories and classes prior to analysis, the "comprehensive lipidomics analysis by separation simplification" (CLASS), and the other in which all lipid species are analyzed together without prior separation, shotgun. In exploring the lipidome of various living systems, novel lipids are being discovered, and mass spectrometry is helping characterize their chemical structure. Deuterium exchange mass spectrometry (DXMS) is being used to investigate the association of lipids and membranes with proteins and enzymes, and imaging mass spectrometry (IMS) is being applied to the in situ analysis of lipids in tissues.
Collapse
Affiliation(s)
- Richard Harkewicz
- Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California at San Diego, La Jolla, California 92093-0601, USA.
| | | |
Collapse
|
26
|
Outcome prediction in pneumonia induced ALI/ARDS by clinical features and peptide patterns of BALF determined by mass spectrometry. PLoS One 2011; 6:e25544. [PMID: 21991318 PMCID: PMC3184998 DOI: 10.1371/journal.pone.0025544] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 09/05/2011] [Indexed: 01/11/2023] Open
Abstract
Background Peptide patterns of bronchoalveolar lavage fluid (BALF) were assumed to reflect the complex pathology of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) better than clinical and inflammatory parameters and may be superior for outcome prediction. Methodology/Principal Findings A training group of patients suffering from ALI/ARDS was compiled from equal numbers of survivors and nonsurvivors. Clinical history, ventilation parameters, Murray's lung injury severity score (Murray's LISS) and interleukins in BALF were gathered. In addition, samples of bronchoalveolar lavage fluid were analyzed by means of hydrophobic chromatography and MALDI-ToF mass spectrometry (MALDI-ToF MS). Receiver operating characteristic (ROC) analysis for each clinical and cytokine parameter revealed interleukin-6>interleukin-8>diabetes mellitus>Murray's LISS as the best outcome predictors. Outcome predicted on the basis of BALF levels of interleukin-6 resulted in 79.4% accuracy, 82.7% sensitivity and 76.1% specificity (area under the ROC curve, AUC, 0.853). Both clinical parameters and cytokines as well as peptide patterns determined by MALDI-ToF MS were analyzed by classification and regression tree (CART) analysis and support vector machine (SVM) algorithms. CART analysis including Murray's LISS, interleukin-6 and interleukin-8 in combination was correct in 78.0%. MALDI-ToF MS of BALF peptides did not reveal a single identifiable biomarker for ARDS. However, classification of patients was successfully achieved based on the entire peptide pattern analyzed using SVM. This method resulted in 90% accuracy, 93.3% sensitivity and 86.7% specificity following a 10-fold cross validation (AUC = 0.953). Subsequent validation of the optimized SVM algorithm with a test group of patients with unknown prognosis yielded 87.5% accuracy, 83.3% sensitivity and 90.0% specificity. Conclusions/Significance MALDI-ToF MS peptide patterns of BALF, evaluated by appropriate mathematical methods can be of value in predicting outcome in pneumonia induced ALI/ARDS.
Collapse
|
27
|
Agar NYR, Golby AJ, Ligon KL, Norton I, Mohan V, Wiseman JM, Tannenbaum A, Jolesz FA. Development of stereotactic mass spectrometry for brain tumor surgery. Neurosurgery 2011; 68:280-89; discussion 290. [PMID: 21135749 DOI: 10.1227/neu.0b013e3181ff9cbb] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Surgery remains the first and most important treatment modality for the majority of solid tumors. Across a range of brain tumor types and grades, postoperative residual tumor has a great impact on prognosis. The principal challenge and objective of neurosurgical intervention is therefore to maximize tumor resection while minimizing the potential for neurological deficit by preserving critical tissue. OBJECTIVE To introduce the integration of desorption electrospray ionization mass spectrometry into surgery for in vivo molecular tissue characterization and intraoperative definition of tumor boundaries without systemic injection of contrast agents. METHODS Using a frameless stereotactic sampling approach and by integrating a 3-dimensional navigation system with an ultrasonic surgical probe, we obtained image-registered surgical specimens. The samples were analyzed with ambient desorption/ionization mass spectrometry and validated against standard histopathology. This new approach will enable neurosurgeons to detect tumor infiltration of the normal brain intraoperatively with mass spectrometry and to obtain spatially resolved molecular tissue characterization without any exogenous agent and with high sensitivity and specificity. RESULTS Proof of concept is presented in using mass spectrometry intraoperatively for real-time measurement of molecular structure and using that tissue characterization method to detect tumor boundaries. Multiple sampling sites within the tumor mass were defined for a patient with a recurrent left frontal oligodendroglioma, World Health Organization grade II with chromosome 1p/19q codeletion, and mass spectrometry data indicated a correlation between lipid constitution and tumor cell prevalence. CONCLUSION The mass spectrometry measurements reflect a complex molecular structure and are integrated with frameless stereotaxy and imaging, providing 3-dimensional molecular imaging without systemic injection of any agents, which can be implemented for surgical margins delineation of any organ and with a rapidity that allows real-time analysis.
Collapse
Affiliation(s)
- Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Green-Mitchell SM, Cazares LH, Semmes OJ, Nadler JL, Nyalwidhe JO. On-tissue identification of insulin: in situ reduction coupled with mass spectrometry imaging. Proteomics Clin Appl 2011; 5:448-53. [PMID: 21656913 DOI: 10.1002/prca.201000152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/22/2011] [Accepted: 03/03/2011] [Indexed: 11/10/2022]
Abstract
PURPOSE The aim of this study was to use on-tissue reduction followed by MALDI-MS imaging (MSI) to identify an m/z 5812.85 peak, which is over-expressed in healthy human pancreatic tissue compared with type one Diabetes (T1D) tissue. EXPERIMENTAL DESIGN A major constraint of MALDI-MSI is identification of compounds with m/z ≥4000. On-tissue reduction using tris (2-carboxyethyl) phosphine (TCEP) breaks the inter-domain disulphide bonds generating low-molecular-weight peptides amenable to direct MS/MS analysis. Pancreatic tissues from healthy (n=4) and diabetic subjects (n=4) were profiled by MALDI-MSI with/without reduction. RESULTS On-tissue reduction resulted in the loss of the over-expressed 5812.85 m/z peak and the simultaneous appearance of a 3430.664 m/z peak in healthy tissues. The latter peak presumably derived from the 5812.85 m/z peak was identified as the insulin B chain by MS/MS. MALDI-MSI images show that both the 5812.85 insulin peak before reduction and the 3430.664 peak after reduction co-localized with the healthy pancreatic islets. CONCLUSION AND CLINICAL RELEVANCE On-tissue reduction followed by MALDI-MSI resulted in the identification of insulin and localization of pancreatic islets of langerhans. The approach will be useful in the future identification of novel therapeutic molecular targets to β-cells lost during type one diabetes.
Collapse
|
29
|
The application of SELDI-TOF-MS in clinical diagnosis of cancers. J Biomed Biotechnol 2011; 2011:245821. [PMID: 21687541 PMCID: PMC3114543 DOI: 10.1155/2011/245821] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/30/2011] [Indexed: 12/24/2022] Open
Abstract
Cancer diagnosis is important, and the early diagnosis of cancers could predict a more successful treatment. The proteomic studies emerged to be useful in combined analyses of samples from patients and provide more accurate diagnosis when compared to the single-factor-based diagnosis. In recent years, cancer detection with surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS) is flourishing and brought significant progress in this area. This paper summarizes some recent results with this technique for cancer diagnosis.
Collapse
|
30
|
Taverna D, Nanney LB, Pollins AC, Sindona G, Caprioli R. Spatial mapping by imaging mass spectrometry offers advancements for rapid definition of human skin proteomic signatures. Exp Dermatol 2011; 20:642-7. [PMID: 21545539 DOI: 10.1111/j.1600-0625.2011.01289.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigations into the human skin proteome by classical analytical procedures have not addressed spatial molecular distributions in whole-skin biopsies. The aim of this study was to develop methods for the detection of protein signatures and their spatial disposition in human skin using advanced molecular imaging technology based on mass spectrometry technologies. This technology allows for the generation of protein images at specific molecular weight values without the use of antibody while maintaining tissue architecture. Two experimental approaches were employed: MALDI-MS profiling, where mass spectra were taken from discrete locations based on histology, and MALDI-IMS imaging, where complete molecular images were obtained at various MW values. In addition, proteins were identified by in situ tryptic digestion, sequence analysis of the fragment peptides and protein database searching. We have detected patterns of protein differences that exist between epidermis and dermis as well as subtle regional differences between the papillary and reticular dermis. Furthermore, we were able to detect proteins that are constitutive features of human skin as well as those associated with unique markers of individual variability.
Collapse
Affiliation(s)
- Domenico Taverna
- Department of Chemistry, Universita' della Calabria, Arcavacata di Rende, Cs, Italy
| | | | | | | | | |
Collapse
|
31
|
Aizikov K, Smith DF, Chargin DA, Ivanov S, Lin TY, Heeren RMA, O'Connor PB. Vacuum compatible sample positioning device for matrix assisted laser desorption∕ionization Fourier transform ion cyclotron resonance mass spectrometry imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:054102. [PMID: 21639522 PMCID: PMC3117896 DOI: 10.1063/1.3594099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 05/03/2011] [Indexed: 05/19/2023]
Abstract
The high mass accuracy and resolving power of Fourier transform ion cyclotron resonance mass spectrometers (FT-ICR MS) make them ideal mass detectors for mass spectrometry imaging (MSI), promising to provide unmatched molecular resolution capabilities. The intrinsic low tolerance of FT-ICR MS to RF interference, however, along with typically vertical positioning of the sample, and MSI acquisition speed requirements present numerous engineering challenges in creating robotics capable of achieving the spatial resolution to match. This work discusses a two-dimensional positioning stage designed to address these issues. The stage is capable of operating in ∼1 × 10(-8) mbar vacuum. The range of motion is set to 100 mm × 100 mm to accommodate large samples, while the positioning accuracy is demonstrated to be less than 0.4 micron in both directions under vertical load over the entire range. This device was integrated into three different matrix assisted laser desorption∕ionization (MALDI) FT-ICR instruments and showed no detectable RF noise. The "oversampling" MALDI-MSI experiments, under which the sample is completely ablated at each position, followed by the target movement of the distance smaller than the laser beam, conducted on the custom-built 7T FT-ICR MS demonstrate the stability and positional accuracy of the stage robotics which delivers high spatial resolution mass spectral images at a fraction of the laser spot diameter.
Collapse
Affiliation(s)
- Konstantin Aizikov
- Cardiovascular Proteomics Center, Boston University School of Medicine, 670 Albany Street, Room 504 Boston, Massachusetts 02118, USA
| | | | | | | | | | | | | |
Collapse
|
32
|
Richards AL, Lietz CB, Wager-Miller JB, Mackie K, Trimpin S. Imaging mass spectrometry in transmission geometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:815-20. [PMID: 21337644 PMCID: PMC3677958 DOI: 10.1002/rcm.4927] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Affiliation(s)
| | | | - James B. Wager-Miller
- Gill Center for Biomolecular Science and the Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Ken Mackie
- Gill Center for Biomolecular Science and the Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA
| | - Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Correspondence to: S. Trimpin, Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
| |
Collapse
|
33
|
Watrous JD, Alexandrov T, Dorrestein PC. The evolving field of imaging mass spectrometry and its impact on future biological research. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:209-22. [PMID: 21322093 PMCID: PMC3303182 DOI: 10.1002/jms.1876] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 11/30/2010] [Indexed: 05/20/2023]
Abstract
Within the past decade, imaging mass spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its rapid evolution has resulted in an impressive array of instrument variations and sample applications, yet the tools and data are largely confined to specialists. It is therefore important that at this junction the IMS community begin to establish IMS as a permanent fixture in life science research thereby making the technology and/or the data approachable by non-mass spectrometrists, leading to further integration into biological and clinical research. In this perspective article, we provide insight into the evolution and current state of IMS and propose some of the directions that IMS could develop in order to stay on course to become one of the most promising new tools in life science research.
Collapse
Affiliation(s)
- Jeramie D. Watrous
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | | | - Pieter C. Dorrestein
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Center For Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography
| |
Collapse
|
34
|
Beatty KE. Chemical strategies for tagging and imaging the proteome. MOLECULAR BIOSYSTEMS 2011; 7:2360-7. [DOI: 10.1039/c1mb05040k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
35
|
Zhang FZ, Hong D. Elastic net-based framework for imaging mass spectrometry data biomarker selection and classification. Stat Med 2010; 30:753-68. [DOI: 10.1002/sim.4147] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 10/22/2010] [Indexed: 12/20/2022]
|
36
|
Perdian DC, Lee YJ. Imaging MS Methodology for More Chemical Information in Less Data Acquisition Time Utilizing a Hybrid Linear Ion Trap−Orbitrap Mass Spectrometer. Anal Chem 2010; 82:9393-400. [DOI: 10.1021/ac102017q] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. C. Perdian
- Ames Laboratory, U.S. Department of Energy, and Department of Chemistry, Iowa State University of Science and Technology, Ames, Iowa 50011, United States
| | - Young Jin Lee
- Ames Laboratory, U.S. Department of Energy, and Department of Chemistry, Iowa State University of Science and Technology, Ames, Iowa 50011, United States
| |
Collapse
|
37
|
Inutan ED, Richards AL, Wager-Miller J, Mackie K, McEwen CN, Trimpin S. Laserspray ionization, a new method for protein analysis directly from tissue at atmospheric pressure with ultrahigh mass resolution and electron transfer dissociation. Mol Cell Proteomics 2010; 10:M110.000760. [PMID: 20855542 PMCID: PMC3033668 DOI: 10.1074/mcp.m110.000760] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Laserspray ionization (LSI) mass spectrometry (MS) allows, for the first time, the analysis of proteins directly from tissue using high performance atmospheric pressure ionization mass spectrometers. Several abundant and numerous lower abundant protein ions with molecular masses up to ∼20,000 Da were detected as highly charged ions from delipified mouse brain tissue mounted on a common microscope slide and coated with 2,5-dihydroxyacetophenone as matrix. The ability of LSI to produce multiply charged ions by laser ablation at atmospheric pressure allowed protein analysis at 100,000 mass resolution on an Orbitrap Exactive Fourier transform mass spectrometer. A single acquisition was sufficient to identify the myelin basic protein N-terminal fragment directly from tissue using electron transfer dissociation on a linear trap quadrupole (LTQ) Velos. The high mass resolution and mass accuracy, also obtained with a single acquisition, are useful in determining protein molecular weights and from the electron transfer dissociation data in confirming database-generated sequences. Furthermore, microscopy images of the ablated areas show matrix ablation of ∼15 μm-diameter spots in this study. The results suggest that LSI-MS at atmospheric pressure potentially combines speed of analysis and imaging capability common to matrix-assisted laser desorption/ionization and soft ionization, multiple charging, improved fragmentation, and cross-section analysis common to electrospray ionization.
Collapse
Affiliation(s)
- Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | | | | | | | | | | |
Collapse
|
38
|
Streckfus CF, Brown RE, Bull JM. Proteomics, morphoproteomics, saliva and breast cancer: An emerging approach to guide the delivery of individualised thermal therapy, thermochemotherapy and monitor therapy response. Int J Hyperthermia 2010; 26:649-61. [DOI: 10.3109/02656736.2010.506470] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
39
|
Chaurand P, Cornett DS, Angel PM, Caprioli RM. From whole-body sections down to cellular level, multiscale imaging of phospholipids by MALDI mass spectrometry. Mol Cell Proteomics 2010; 10:O110.004259. [PMID: 20736411 DOI: 10.1074/mcp.o110.004259] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Significant progress in instrumentation and sample preparation approaches have recently expanded the potential of MALDI imaging mass spectrometry to the analysis of phospholipids and other endogenous metabolites naturally occurring in tissue specimens. Here we explore some of the requirements necessary for the successful analysis and imaging of phospholipids from thin tissue sections of various dimensions by MALDI time-of-flight mass spectrometry. We address methodology issues relative to the imaging of whole-body sections such as those cut from model laboratory animals, sections of intermediate dimensions typically prepared from individual organs, as well as the requirements for imaging areas of interests from these sections at a cellular scale spatial resolution. We also review existing limitations of MALDI imaging MS technology relative to compound identification. Finally, we conclude with a perspective on important issues relative to data exploitation and management that need to be solved to maximize biological understanding of the tissue specimen investigated.
Collapse
Affiliation(s)
- Pierre Chaurand
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-8575, USA
| | | | | | | |
Collapse
|
40
|
Agar NYR, Malcolm JG, Mohan V, Yang HW, Johnson MD, Tannenbaum A, Agar JN, Black PM. Imaging of meningioma progression by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal Chem 2010; 82:2621-5. [PMID: 20196536 DOI: 10.1021/ac100113w] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Often considered benign, meningiomas represent 32% of intracranial tumors with three grades of malignancy defined by the World Health Organization (WHO) histology based classification. Malignant meningiomas are associated with less than 2 years median survival. The inability to predict recurrence and progression of meningiomas induces significant anxiety for patients and limits physicians in implementing prophylactic treatment approaches. This report presents an analytical approach to tissue characterization based on matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry imaging (MSI) which is introduced in an attempt to develop a reference database for predictive classification of brain tumors. This pilot study was designed to evaluate the potential of such an approach and to begin to address limitations of the current methodology. Five recurrent and progressive meningiomas for which surgical specimens were available from the original and progressed grades were selected and tested against nonprogressive high-grade meningiomas, high-grade gliomas, and nontumor brain specimens. The common profiling approach of data acquisition was compared to imaging and revealed significant benefits in spatially resolved acquisition for improved spectral definition. A preliminary classifier based on the support vector machine showed the ability to distinguish meningioma image spectra from the nontumor brain and from gliomas, a different type of brain tumor, and to enable class imaging of surgical tissue. Although the development of classifiers was shown to be sensitive to data preparation parameters such as recalibration and peak picking criteria, it also suggested the potential for maturing into a predictive algorithm if provided with a larger series of well-defined cases.
Collapse
Affiliation(s)
- Nathalie Y R Agar
- Surgical Molecular Imaging Laboratory, Department of Neurosurgery, 221, Longwood Avenue, BLI-137, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
McDonnell LA, Corthals GL, Willems SM, van Remoortere A, van Zeijl RJM, Deelder AM. Peptide and protein imaging mass spectrometry in cancer research. J Proteomics 2010; 73:1921-44. [PMID: 20510389 DOI: 10.1016/j.jprot.2010.05.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 04/28/2010] [Accepted: 05/16/2010] [Indexed: 12/12/2022]
Abstract
MALDI mass spectrometry is able to acquire protein profiles directly from tissue that can describe the levels of hundreds of distinct proteins. MALDI imaging MS can simultaneously reveal how each of these proteins varies in heterogeneous tissues. Numerous studies have now demonstrated how MALDI imaging MS can generate different protein profiles from the different cell types in a tumor, which can act as biomarker profiles or enable specific candidate protein biomarkers to be identified. MALDI imaging MS can be directly applied to patient samples where its utility is to accomplish untargeted multiplex analysis of the tissue's protein content, enabling the different regions of the tissue to be differentiated on the basis of previously unknown protein profiles/biomarkers. The technique continues to rapidly develop and is now approaching the cusp whereby its potential to provide new diagnostic/prognostic tools for cancer patients can be routinely investigated. Here the latest methodological developments are summarized and its application to a range of tumors is reported in detail. The prospects of MALDI imaging MS are then described from the perspectives of modern pathological practice and MS-based proteomics, to ensure the outlook addresses real clinical needs and reflects the real capabilities of MS-based proteomics of complex tissue samples.
Collapse
Affiliation(s)
- Liam A McDonnell
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands.
| | | | | | | | | | | |
Collapse
|
42
|
Liu X, Wen F, Yang J, Chen L, Wei YQ. A review of current applications of mass spectrometry for neuroproteomics in epilepsy. MASS SPECTROMETRY REVIEWS 2010; 29:197-246. [PMID: 19598206 DOI: 10.1002/mas.20243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.
Collapse
Affiliation(s)
- Xinyu Liu
- National Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | | | | | | | | |
Collapse
|
43
|
Djidja MC, Claude E, Snel MF, Francese S, Scriven P, Carolan V, Clench MR. Novel molecular tumour classification using MALDI-mass spectrometry imaging of tissue micro-array. Anal Bioanal Chem 2010; 397:587-601. [PMID: 20204332 DOI: 10.1007/s00216-010-3554-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 02/05/2010] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
Abstract
The development of tissue micro-array (TMA) technologies provides insights into high-throughput analysis of proteomics patterns from a large number of archived tumour samples. In the work reported here, matrix-assisted laser desorption/ionisation-ion mobility separation-mass spectrometry (MALDI-IMS-MS) profiling and imaging methodology has been used to visualise the distribution of several peptides and identify them directly from TMA sections after on-tissue tryptic digestion. A novel approach that combines MALDI-IMS-MSI and principal component analysis-discriminant analysis (PCA-DA) is described, which has the aim of generating tumour classification models based on protein profile patterns. The molecular classification models obtained by PCA-DA have been validated by applying the same statistical analysis to other tissue cores and patient samples. The ability to correlate proteomic information obtained from samples with known and/or unknown clinical outcome by statistical analysis is of great importance, since it may lead to a better understanding of tumour progression and aggressiveness and hence improve diagnosis, prognosis as well as therapeutic treatments. The selectivity, robustness and current limitations of the methodology are discussed.
Collapse
Affiliation(s)
- Marie-Claude Djidja
- Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield, S1 1WB, UK
| | | | | | | | | | | | | |
Collapse
|
44
|
Genji T, Fukuzawa S, Tachibana K. Distribution and possible function of the marine alkaloid, norzoanthamine, in the zoanthid Zoanthus sp. using MALDI imaging mass spectrometry. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:81-87. [PMID: 19575264 DOI: 10.1007/s10126-009-9202-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 06/10/2009] [Indexed: 05/28/2023]
Abstract
The role of the marine alkaloid, norzoanthamine, in the colonial zoanthid Zoanthus sp. was previously unknown. High concentrations of norzoanthamine are present in the epidermal tissue of Zoanthus sp., as determined using protonated molecular ion peak mapping of norzoanthamine by matrix-assisted laser desorption/ionization mass spectrometry and high-performance liquid chromatography quantification. Sodium dodecylsulfate polyacrylamide gel electrophoresis experiments indicate that norzoanthamine increases the resistance of collagen to damage from UV light, probably not via UV light absorption, but by strengthening collagen itself, thus suggesting that collagen strengthening may be the function of norzoanthamine in Zoanthus sp.
Collapse
Affiliation(s)
- Takahisa Genji
- Department of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | |
Collapse
|
45
|
Hsieh Y, Li F, Korfmacher WA. Mapping pharmaceuticals in rat brain sections using MALDI imaging mass spectrometry. Methods Mol Biol 2010; 656:147-158. [PMID: 20680589 DOI: 10.1007/978-1-60761-746-4_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Matrix-assisted laser desorption/ionization-tandem mass spectrometric method (MALDI-MS/MS) has proven to be a reliable tool for direct measurement of the disposition of small molecules in animal tissue sections. As example, MALDI-MS/MS imaging system was employed for visualizing the spatial distribution of astemizole and its primary metabolite in rat brain tissues. Astemizole is a second-generation antihistamine, a block peripheral H1 receptor, which was introduced to provide comparable therapeutic benefit but was withdrawn in most countries due to toxicity risks. Astemizole was observed to be heterogeneously distributed to most parts of brain tissue slices including cortex, hippocampus, hypothalamic, thalamus, and ventricle regions while its major metabolite, desmethylastemizole, was only found around ventricle sites. We have shown that astemizole alone is likely to be responsible for the central nervous system (CNS) side effects when its exposures became elevated.
Collapse
Affiliation(s)
- Yunsheng Hsieh
- Department of Drug Metabolism and Pharmacokinetics, Merck Research Laboratories, Kenilworth, NJ, USA
| | | | | |
Collapse
|
46
|
Xu BJ. Combining laser capture microdissection and proteomics: Methodologies and clinical applications. Proteomics Clin Appl 2009; 4:116-23. [DOI: 10.1002/prca.200900138] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/28/2009] [Accepted: 10/19/2009] [Indexed: 12/26/2022]
|
47
|
Franck J, El Ayed M, Wisztorski M, Salzet M, Fournier I. On-Tissue N-Terminal Peptide Derivatizations for Enhancing Protein Identification in MALDI Mass Spectrometric Imaging Strategies. Anal Chem 2009; 81:8305-17. [DOI: 10.1021/ac901043n] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Franck
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. El Ayed
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. Wisztorski
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - M. Salzet
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| | - I. Fournier
- MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, CNRS-FRE 2933, Université de Lille1, IFR 147, Bâtiment SN3, 1er étage, F-59655 Villeneuve d’Ascq Cedex, France
| |
Collapse
|
48
|
Djidja MC, Francese S, Loadman PM, Sutton CW, Scriven P, Claude E, Snel MF, Franck J, Salzet M, Clench MR. Detergent addition to tryptic digests and ion mobility separation prior to MS/MS improves peptide yield and protein identification for in situ proteomic investigation of frozen and formalin-fixed paraffin-embedded adenocarcinoma tissue sections. Proteomics 2009; 9:2750-63. [PMID: 19405023 DOI: 10.1002/pmic.200800624] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The identification of proteins involved in tumour progression or which permit enhanced or novel therapeutic targeting is essential for cancer research. Direct MALDI analysis of tissue sections is rapidly demonstrating its potential for protein imaging and profiling in the investigation of a range of disease states including cancer. MALDI-mass spectrometry imaging (MALDI-MSI) has been used here for direct visualisation and in situ characterisation of proteins in breast tumour tissue section samples. Frozen MCF7 breast tumour xenograft and human formalin-fixed paraffin-embedded breast cancer tissue sections were used. An improved protocol for on-tissue trypsin digestion is described incorporating the use of a detergent, which increases the yield of tryptic peptides for both fresh frozen and formalin-fixed paraffin-embedded tumour tissue sections. A novel approach combining MALDI-MSI and ion mobility separation MALDI-tandem mass spectrometry imaging for improving the detection of low-abundance proteins that are difficult to detect by direct MALDI-MSI analysis is described. In situ protein identification was carried out directly from the tissue section by MALDI-MSI. Numerous protein signals were detected and some proteins including histone H3, H4 and Grp75 that were abundant in the tumour region were identified.
Collapse
Affiliation(s)
- Marie-Claude Djidja
- Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Malmström J, Malmström L, Marko-Varga G. Proteomics: A new research area for the biomedical field. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/17471060500223910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
50
|
Abstract
The analysis of insoluble proteins represents a major technical challenge for the field of proteomics. For example, membrane proteins are often insoluble in common solvents and represent 20-30% of the proteins encoded by the human genome. Chemical analysis on an individual basis is often required and is laborious and time consuming. This review presents an overview of methods for purification of expressed proteins using fusion tags as well as methods for analysis of insoluble proteins by mass spectrometry with a goal of achieving high-throughput analysis.
Collapse
Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Department of Chemistry, Detroit, Michigan, USA
| | | |
Collapse
|