Detergent addition to tryptic digests and ion mobility separation prior to MS/MS improves peptide yield and protein identification for <i>in situ</i> proteomic investigation of frozen and formalin‐fixed paraffin‐embedded adenocarcinoma tissue sections

Djidja, Marie Claude; Francese, Simona; Loadman, Paul M.; Sutton, Chris W.; Scriven, Peter; Claude, Emmanuelle; Snel, Marten F.; Franck, Julien; Clench, Malcolm R.

doi:10.1002/pmic.200800624

Cited by 105 publications

(107 citation statements)

References 34 publications

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“…The detection of histone types in the stroma with acini seems to indicate mitotic and apoptotic indices for these cells, which reflects the possibility that their phenotype is more similar to benign than to healthy cells. These data are consistent with the results obtained for other cancers, such as breast [50] or ovarian [18] cancers. Interestingly, we showed that based on the 150 m/z detection using PCA-SDA in the tumor region, only four were related to actin.…”

Section: In-source Decay Approachsupporting

confidence: 83%

“…Consequently, many efforts by others and by our group [35,37] have been implemented to find a strategy to analyze tissues using MALDI-MSI [37,[48][49][50]. Most of the libraries are builds of FFPE tissues because this preservation protocol produces well-conserved morphology and high stability along time avoiding degradation of molecules.…”

Section: In-source Decay Approachmentioning

confidence: 99%

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Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer

Bonnel

Longuespée

Franck³

et al. 2011

Anal Bioanal Chem

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The large amount of data generated using matrixassisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) poses a challenge for data analysis. In fact, generally about 1.10 8 -1.10 9 values (m/z, I) are stored after a single MALDI-MSI experiment. This imposes processing techniques using dedicated informatics tools to be used since manual data interpretation is excluded. This work proposes and summarizes an approach that utilizes a multivariable analysis of MSI data. The multivariate analysis, such as principal component analysis-symbolic discriminant analysis, can remove and highlight specific m/z from the spectra in a specific region of interest. This approach facilitates data processing and provides better reproducibility, and thus, broadband acquisition for MALDI-MSI should be considered an effective tool to highlight biomarkers of interest. Additionally, we demonstrate the importance of the hierarchical classification of biomarkers by analyzing studies of clusters obtained either from digested or undigested tissues and using bottom-up and in-source decay strategies for in-tissue protein identification. This provides the possibility for the rapid identification of specific markers from different histological samples and their direct localization in tissues. We present an example from a prostate cancer study using formalinfixed paraffin-embedded tissue.

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Section: In-source Decay Approachsupporting

confidence: 83%

Section: In-source Decay Approachmentioning

confidence: 99%

Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer

Bonnel

Longuespée

Franck³

et al. 2011

Anal Bioanal Chem

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“…Recently, this approach has also been applied to endogenous proteins and peptides for localization of cancerous tissue and tumors. In 1 such study, the proteins histone H3, H4, and Grp75 were identified in situ in the tumor region of breast cancer tissue sections (50 ). Similarly, MALDI-IM-MSI was shown capable of improving selectivity for identification of protein biomarkers in pancreatic cancer tissue sections (51 ).…”

Section: Applications Of Ion Mobility In Proteomics Metabolomics Anmentioning

confidence: 95%

Ion Mobility in Clinical Analysis: Current Progress and Future Perspectives

et al. 2016

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BACKGROUND Ion mobility spectrometry (IMS) is a rapid separation tool that can be coupled with several sampling/ionization methods, other separation techniques (e.g., chromatography), and various detectors (e.g., mass spectrometry). This technique has become increasingly used in the last 2 decades for applications ranging from illicit drug and chemical warfare agent detection to structural characterization of biological macromolecules such as proteins. Because of its rapid speed of analysis, IMS has recently been investigated for its potential use in clinical laboratories. CONTENT This review article first provides a brief introduction to ion mobility operating principles and instrumentation. Several current applications will then be detailed, including investigation of rapid ambient sampling from exhaled breath and other volatile compounds and mass spectrometric imaging for localization of target compounds. Additionally, current ion mobility research in relevant fields (i.e., metabolomics) will be discussed as it pertains to potential future application in clinical settings. SUMMARY This review article provides the authors' perspective on the future of ion mobility implementation in the clinical setting, with a focus on ambient sampling methods that allow IMS to be used as a “bedside” standalone technique for rapid disease screening and methods for improving the analysis of complex biological samples such as blood plasma and urine.

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“…However, many medical samples are routinely formaldehyde-fixed and paraffin-embedded (FFPE) just after dissection. To address this problem, the on-tissue proteolytic digestion method, in which proteins are denatured and digested by enzymes, has been developed (Djidja et al, 2009;Groseclose et al, 2007;Lemaire et al, 2007;Morita et al, 2010). The ontissue proteolytic digestion method includes a paraffin removal step using xylene and ethanol.…”

Section: Fixation and Embeddingmentioning

confidence: 99%

Application of Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry

Zaima¹

2012

Pharmacology

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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

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Cited by 105 publications

References 34 publications

Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer

Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer

Ion Mobility in Clinical Analysis: Current Progress and Future Perspectives

Application of Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry

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