Name: optimal preparation of formalin fixed samples for peptide based matrix assisted laser desorption/ionization mass spectrometry imaging workflows
Uploaded: 2018-01-16T14:00:00
Description: Watch this Scientific Journal Video about Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows at JoVE.com

Forfatterne vil gerne anerkende den Sydney Medical School Foundation og Blues og fundament til finansiering af en del af dette arbejde gennem deres ph.d.-stipendium program for Alzheimers sygdom forskning og en ARC Discovery tilskud (DP160102063) tildeles ULRIKS.

Advarsel: Alle gældende sikkerhedsforanstaltninger bør følges, når du udfører denne procedure, herunder anvendelse af passende personlige værnemidler (PPE) (fx lab frakker, nitrilhandsker, sikkerhedsbriller, osv.)
1. forberedelse af reagenser og udstyr
<ol><li>
Forberedelse af løsninger
	<ol>
<li>For at forberede 500 mL Carnoys væske, blandes 100% ethanol (EtOH), kloroform og iseddike i en 6:3:1 v/v/v forhold i et rent glas Schott flaske.</li>
		<li...

<ol>
	<li>Schwartz, S. A., Reyzer, M. L., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+tissue+analysis+using+matrix-assisted+laser+desorption/ionization+mass+spectrometry:+practical+aspects+of+sample+preparation.">Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation.</a> J Mass Spectrom. 38 (7), 699-708 (2003).</li><li>Caprioli, R. M., Farmer, T. B., Gile, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+Imaging+of+Biological+Samples:+Localization+of+Peptides+and+Proteins+Using+MALDI-TOF+MS.">Molecular Imaging of Biological Samples: Localization of Peptides and Proteins Using MALDI-TOF MS.</a> Anal Chem. 69 (23), 4751-4760 (1997).</li><li>Jackson, S. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI-Ion+Mobility+Mass+Spectrometry+of+Lipids+in+Negative+Ion+Mode.">MALDI-Ion Mobility Mass Spectrometry of Lipids in Negative Ion Mode.</a> Analytical methods : advancing methods and applications. 6 (14), 5001-5007 (2014).</li><li>O'Rourke, M. B., Djordjevic, S. P., Padula, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+non-instrument-based+method+for+the+analysis+of+formalin-fixed+paraffin-embedded+human+spinal+cord+via+matrix-assisted+laser+desorption/ionisation+imaging+mass+spectrometry.">A non-instrument-based method for the analysis of formalin-fixed paraffin-embedded human spinal cord via matrix-assisted laser desorption/ionisation imaging mass spectrometry.</a> Rapid Commun Mass Spectrom. 29 (19), 1836-1840 (2015).</li><li>O'Rourke, M. B., Raymond, B. B. A., Djordjevic, S. P., Padula, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+versatile+cost-effective+method+for+the+analysis+of+fresh+frozen+tissue+sections+via+matrix-assisted+laser+desorption/ionisation+imaging+mass+spectrometry.">A versatile cost-effective method for the analysis of fresh frozen tissue sections via matrix-assisted laser desorption/ionisation imaging mass spectrometry.</a> Rapid Commun Mass Spectrom. 29 (7), 637-644 (2015).</li><li>Chughtai, K., Heeren, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+spectrometric+imaging+for+biomedical+tissue+analysis.">Mass spectrometric imaging for biomedical tissue analysis.</a> Chem Rev. 110 (5), 3237-3277 (2010).</li><li>Ye, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI+mass+spectrometry-assisted+molecular+imaging+of+metabolites+during+nitrogen+fixation+in+the+Medicago+truncatula-Sinorhizobium+meliloti+symbiosis.">MALDI mass spectrometry-assisted molecular imaging of metabolites during nitrogen fixation in the Medicago truncatula-Sinorhizobium meliloti symbiosis.</a> Plant J. 75 (1), 130-145 (2013).</li><li>Powers, T. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI+imaging+mass+spectrometry+profiling+of+N-glycans+in+formalin-fixed+paraffin+embedded+clinical+tissue+blocks+and+tissue+microarrays.">MALDI imaging mass spectrometry profiling of N-glycans in formalin-fixed paraffin embedded clinical tissue blocks and tissue microarrays.</a> PLoS One. 9 (9), 10655 (2014).</li><li>Rompp, A., Spengler, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+spectrometry+imaging+with+high+resolution+in+mass+and+space.">Mass spectrometry imaging with high resolution in mass and space.</a> Histochem Cell Biol. 139 (6), 759-783 (2013).</li><li>Shariatgorji, M., Svenningsson, P., Andren, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+spectrometry+imaging,+an+emerging+technology+in+neuropsychopharmacology.">Mass spectrometry imaging, an emerging technology in neuropsychopharmacology.</a> Neuropsychopharmacology. 39 (1), 34-49 (2014).</li><li>Alexandrov, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI+imaging+mass+spectrometry:+statistical+data+analysis+and+current+computational+challenges.">MALDI imaging mass spectrometry: statistical data analysis and current computational challenges.</a> BMC Bioinformatics. 13, 11 (2012).</li><li>Weaver, E. M., Hummon, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+mass+spectrometry:+From+tissue+sections+to+cell+cultures.">Imaging mass spectrometry: From tissue sections to cell cultures.</a> Adv Drug Deliv Rev. 65 (8), 1039-1055 (2013).</li><li>Watrous, J. D., Dorrestein, P. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+mass+spectrometry+in+microbiology.">Imaging mass spectrometry in microbiology.</a> Nat Rev Microbiol. 9 (9), 683-694 (2011).</li><li>O'Rourke, M., Padula, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Non-Instrument+Based+Preparation+of+Tissue+Samples+Destined+for+Imaging+Mass+Spectrometry+(IMS)+Analysis.">The Non-Instrument Based Preparation of Tissue Samples Destined for Imaging Mass Spectrometry (IMS) Analysis.</a> Protocol Exchange. , (2017).</li><li>O'Rourke, M. B., Padula, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+standard+of+visual+data+representation+for+imaging+mass+spectrometry.">A new standard of visual data representation for imaging mass spectrometry.</a> Proteomics Clin Appl. 11 (3-4), (2017).</li><li>O'Rourke, M. B., Padula, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+formalin-fixed,+paraffin-embedded+(FFPE)+tissue+via+proteomic+techniques+and+misconceptions+of+antigen+retrieval.">Analysis of formalin-fixed, paraffin-embedded (FFPE) tissue via proteomic techniques and misconceptions of antigen retrieval.</a> Biotechniques. 60 (5), 229-238 (2016).</li><li>Casadonte, R., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+analysis+of+formalin-fixed+paraffin-embedded+tissue+by+MALDI+imaging+mass+spectrometry.">Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry.</a> Nat. Protocols. 6 (11), 1695-1709 (2011).</li><li>Ong, T. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+Spectrometry+Imaging+and+Identification+of+Peptides+Associated+with+Cephalic+Ganglia+Regeneration+in+Schmidtea+mediterranea.">Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea.</a> J Biol Chem. 291 (15), 8109-8120 (2016).</li><li>Seeley, E. H., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+imaging+of+proteins+in+tissues+by+mass+spectrometry.">Molecular imaging of proteins in tissues by mass spectrometry.</a> Proc Natl Acad Sci U S A. 105 (47), 18126-18131 (2008).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Blood-smear+showing+Experimental+Infection+with+Herpetomonas.">Blood-smear showing Experimental Infection with Herpetomonas.</a> Proc R Soc Med. 18, 55 (1925).</li><li>Gorrie, C. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+human+OEC-derived+cell+transplants+in+rodent+spinal+cord+contusion+injury.">Effects of human OEC-derived cell transplants in rodent spinal cord contusion injury.</a> Brain Res. 1337, 8-20 (2010).</li><li>Wu, Q., Comi, T. J., Li, B., Rubakhin, S. S., Sweedler, J. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On-Tissue+Derivatization+via+Electrospray+Deposition+for+Matrix-Assisted+Laser+Desorption/Ionization+Mass+Spectrometry+Imaging+of+Endogenous+Fatty+Acids+in+Rat+Brain+Tissues.">On-Tissue Derivatization via Electrospray Deposition for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Endogenous Fatty Acids in Rat Brain Tissues.</a> Anal Chem. 88 (11), 5988-5995 (2016).</li><li>Sturm, R. M., Greer, T., Chen, R., Hensen, B., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+NIMS+and+MALDI+platforms+for+neuropeptide+and+lipid+mass+spectrometric+imaging+in+C.+borealis+brain+tissue.">Comparison of NIMS and MALDI platforms for neuropeptide and lipid mass spectrometric imaging in C. borealis brain tissue.</a> Anal Methods. 5 (6), 1623-1628 (2013).</li><li>Kompauer, M., Heiles, S., Spengler, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atmospheric+pressure+MALDI+mass+spectrometry+imaging+of+tissues+and+cells+at+1.4-mum+lateral+resolution.">Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-mum lateral resolution.</a> Nat Methods. 14 (1), 90-96 (2017).</li><li>Yang, J., Caprioli, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Matrix+sublimation/recrystallization+for+imaging+proteins+by+mass+spectrometry+at+high+spatial+resolution.">Matrix sublimation/recrystallization for imaging proteins by mass spectrometry at high spatial resolution.</a> Anal Chem. 83 (14), 5728-5734 (2011).</li><li>Rohner, T. C., Staab, D., Stoeckli, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MALDI+mass+spectrometric+imaging+of+biological+tissue+sections.">MALDI mass spectrometric imaging of biological tissue sections.</a> Mech Ageing Dev. 126 (1), 177-185 (2005).</li><li>Li, B., Bhandari, D. R., Rompp, A., Spengler, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+MALDI+mass+spectrometry+imaging+of+gallotannins+and+monoterpene+glucosides+in+the+root+of+Paeonia+lactiflora.">High-resolution MALDI mass spectrometry imaging of gallotannins and monoterpene glucosides in the root of Paeonia lactiflora.</a> Sci Rep. 6, 36074 (2016).</li><li>Spengler, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+spectrometry+imaging+of+biomolecular+information.">Mass spectrometry imaging of biomolecular information.</a> Anal Chem. 87 (1), 64-82 (2015).</li><li>Widlak, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+molecular+signatures+of+oral+squamous+cell+carcinoma+and+normal+epithelium+-+application+of+a+novel+methodology+for+unsupervised+segmentation+of+imaging+mass+spectrometry+data.">Detection of molecular signatures of oral squamous cell carcinoma and normal epithelium - application of a novel methodology for unsupervised segmentation of imaging mass spectrometry data.</a> Proteomics. 16 (11-12), 1613-1621 (2016).</li></ol>

Denne protokol blev designet til at maksimere generation af ionizable molekylære arter samtidig fjerne delokaliseringen af analysander. Nøglefaktorerne inddrage ved hjælp af den samme overordnede princip, når du anvender matrix, fordøje prøven, eller recrystallizing efter sublimering24; nemlig, at en selv aflejring af dampe, matrix eller andet, der skal oprettes og vedligeholdes. Pipettering opløsningsmiddel vasker for omkrystallisering og fordøjelse, jævnt under prøven, forhindrer enhve...

Matrix assisted laser desorption/Ionisation massespektrometri imaging (MALDI MSI) har været ansat som et billede baseret teknik for to årtier1,2, analysere en række biomolekyler herunder: lipider3, peptider2 ,4, proteiner2,5, metabolitter6,7, N-glycans8og syntetiske molekyler såsom terapeutiske lægemidler9,10. Antallet af publikationer påvise nytten af denne teknik er vokset betydeligt i det sidste årti6,11,12,13. Visse molekyler, såsom lipider, er relativt nemme at analysere via MALDI MSI, som de ionisere let på grund af deres kemiske karakter og dermed kræver lidt forudgående forberedelse3. Men for mere vanskelige mål såsom peptider, de nødvendige skridt til at effektivt ionisere disse molekyler er omfattende og generelt komplicerede14. Der er i øjeblikket meget få publikationer, der har til formål at adresse eller påvise reproducerbarhed i de metoder, der er ansat til at forberede denne unikke visuelle teknik15væv. Derfor har vi udarbejdet observationer og gennemført optimeringer i en enkelt, let at gennemføre, metode, der bør kræver lidt at ingen ændring, til analyse af peptider fra en formaldehyd tværbunden væv kilde14.
I dette manuskript har vi beskrevet en valideret, lave omkostninger reproducerbar metode til påvisning og geografisk kortlægning af peptider, genereret fra formalin-fast frosset (FFF) og formalin-fast paraffin-embedded (FFPE) væv sektioner. Denne metode kræver eller stole på nogen specialiserede instrumentation3. Specifikt, vi tager fat på de mange aspekter af specialiserede prøveforberedelse nødvendigt at analysere peptider; trin som antigen hentning16 og matrix belægning. Vores protokol udnytter også billigt materiel og reagenser, hvilket gør denne metode tilgængelig for et bredere samfund, der ellers ville være afskåret fra råd til alternative robot apparater17.
Ræsonnementet bag udviklingen af præparationsmetode manuel prøve var to gange: for det første brug af en sublimator skaber en konsekvent og ensartet belægning af matrix krystaller, der er ~ 1 µm i længde18, noget uopnåeligt med mere fælles sprøjtning teknikker. For det andet, den relativt lille nedsat omkostninger: de samlede omkostninger af den brugerdefinerede apparater var <$ 1500 AUD. Vi bemærker med hensyn til omkostningseffektivitet, pris pr. prøve er langt billigere, når der er ingen robot maskiner involveret. Brugen af sublimation er blevet rapporteret tidligere, dog at bedste af vores viden, trinvise metoder, der beskriver denne proces og prøve forberedelse ikke har været rapporteret eller beskrevet i litteraturen.
Denne protokol er beregnet til at hjælpe forskere, der har adgang til en MALDI massespektrometer og der er opsat på at skabe geografisk information i forbindelse med en bio-molekyle af interesse19. I det væsentlige er MALDI MSI en form for histologiske screening at ikke stole på antistoffer eller pletter2.

<table border="0" cellpadding="0" cellspacing="0" style="width:820px;" width="820">
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	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Cryo Microtome</td>
			<td style="width:121px;">Leica</td>
			<td style="width:160px;">CM3050</td>
			<td style="width:275px;">For preparation and section of tissue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Indium Tin Oxide Microscope slides</td>
			<td style="width:121px;">Bruker</td>
			<td>8237001</td>
			<td>For preparation and section of tissue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Coplin Jars</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>S5516</td>
			<td>For preparation and section of tissue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Pressure Cooker</td>
			<td style="width:121px;">Kambrook</td>
			<td>KPR620BSS</td>
			<td>For preparation and section of tissue.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Sublimator</td>
			<td style="width:121px;">Chem Glass</td>
			<td>NA</td>
			<td>For sublimation procedure. Similar in design to the CG-3038 however it was custom made&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Sand bath</td>
			<td style="width:121px;">NA</td>
			<td>NA</td>
			<td>For sublimation procedure. Fine grade river sand held in folded aluminium foil sourced from outside not from any specific company</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Glass Petri Dish</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>CLS70165100</td>
			<td>For sublimation procedure.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Vacuum Pump</td>
			<td style="width:121px;">NA</td>
			<td>NA</td>
			<td>For sublimation procedure. Sourced as a spare part from an old mass spectrometer&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Cold trap</td>
			<td style="width:121px;">Chem Glass</td>
			<td>CG-4510-02</td>
			<td>For sublimation procedure.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Hot Plate</td>
			<td style="width:121px;">John Morris</td>
			<td>EW-15956-32.&#160;</td>
			<td>For sublimation procedure.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Plastic petri dish</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>Z717223</td>
			<td>For sublimation procedure.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">37 &#176;C incubator</td>
			<td style="width:121px;">NA</td>
			<td>NA</td>
			<td>For sublimation procedure. Not applicable, incubator is non sterile and over 30 years old&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Blotting paper</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>P7796</td>
			<td>For sublimation procedure.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Nitrocellulose&#160;</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>N8395</td>
			<td>For washing of slides.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Acetone</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>650501</td>
			<td>For washing of slides.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Xylene</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>214736</td>
			<td>For washing of slides.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">100% EtOH</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>1.02428</td>
			<td>For washing of slides.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">70% EtOH</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>NA</td>
			<td>For washing of slides. Made in lab from 95% stock ethanol&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Chloroform</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>C2432</td>
			<td>For washing of slides.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Glacial Acetic Acid</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>ARK2183</td>
			<td>For washing of slides.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Tris HCL pH 8.8</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>TRIS-RO</td>
			<td>For proteolytic cleavage. Powder made to 1M followed by equilibration with 32% HCl to PH 8.8</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Milli Q Ultra-Pure Water</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>NA</td>
			<td>For proteolytic cleavage. Purification performed in house by sartorious water purification system</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Ammonium Bircarbonate</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>A6141</td>
			<td>For proteolytic cleavage.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Trypsin</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>T0303</td>
			<td>For proteolytic cleavage.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">CHCA Matrix</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>C2020</td>
			<td>For recrystallisation.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Acetonitrile</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>1.00029</td>
			<td>For recrystallisation.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:264px;">Trifluoroacetic Acid (TFA)&#160;</td>
			<td style="width:121px;">Sigma Aldrich</td>
			<td>302031</td>
			<td>For recrystallisation.</td>
		</tr>
	</tbody>
</table>

optimal preparation of formalin fixed samples for peptide based matrix assisted laser desorption/ionization mass spectrometry imaging workflows

Brug af matrix assisted laser desorption/Ionisation massespektrometri imaging (MALDI MSI) er blevet hurtigt udvidet, da denne teknik analyserer et væld af biomolekyler fra narkotika og lipider til N-glycans. Selvom forskellige prøve forberedelse teknikker findes, forbliver afsløre peptider fra formaldehyd bevaret væv en af de vanskeligste udfordringer for denne type af massespektrometriske analyse. Derfor har vi skabt og optimeret en robust metode, der bevarer den geografisk information indeholdt i prøven, mens fremkalde det største antal ionizable peptider. Vi har også sigtede på at opnå dette på en omkostningseffektiv og enkel måde, hvorved man undgår potentiel bias eller forberedelse fejl, som kan opstå, når du bruger automatiseret instrumentation. Slutresultatet er en reproducerbar og billig protokol.

Hvis fulgt korrekt, producerer denne protokol billeder, der tydeligt repræsenterer brutto morfologi af væv uden nogen ridser eller andre deformationer (figur 1). Den ideelle validering for et korrekt udført prøveforberedelse, er evnen til at skelne mellem forskellige fysiske strukturer ved at ændre det molekyle, der har set på (figur 2).
En god guide til at bestem...

Watch this Scientific Journal Video about Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows at JoVE.com

Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows

Optimal forberedelse af Formalin fast prøver for peptid baseret Matrix Assisted Laser Desorption/Ionisation massespektrometri Imaging arbejdsprocesser

Denne protokol beskriver en reproducerbar og pålidelig metode til sublimation-baserede fremstilling af formalin faste væv bestemt til billedbehandling massespektrometri.

The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host ...

Research

JoVE Journal

Biochemistry

Sheathless Capillary Electrophoresis&#8211;Mass Spectrometry for Metabolic Profiling of Biological Samples

Sheathless Capillary ElectrophoresisÃƒÆ’Ã‚Â¢ÃƒÂ¢Ã¢â‚¬Å¡Ã‚Â¬ÃƒÂ¢Ã¢â€šÂ¬Ã…â€œMass Spectrometry for Metabolic Profiling of Biological Samples

Sheathless kapillarelektroforese-massespektrometri for Metabolic profilering biologiske prøver

In metabolomics, a wide range of analytical techniques is used for the global profiling of (endogenous) metabolites in complex samples. In this paper, a ...

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Time-løst elektrosprayioniserings Brint-deuterium Exchange-massespektrometri til at studere proteiners struktur og Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Løsning affinitetsrensede proteinkomplekser ved Blå Native PAGE og protein Korrelation Profilering

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological ...

Glycoproteomics of the Extracellular Matrix: A Method for Intact Glycopeptide Analysis Using Mass Spectrometry

Glycoproteomics af den ekstracellulære matrix: En metode til Intakt glycopeptid analyse ved hjælp massespektrometri

Fibrosis is a hallmark of many cardiovascular diseases and is associated with the exacerbated secretion and deposition of the extracellular matrix (ECM). ...

Easy Manipulation of Architectures in Protein-based Hydrogels for Cell Culture Applications

Let Manipulation af arkitekturer i Protein-baseret Hydrogels til celle kultur applikationer

Hydrogels are recognized as promising materials for cell culture applications due to their ability to provide highly hydrated cell environments. The field ...

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Prøveforberedelse til massespektrometri-baseret identifikation af RNA-bindende regioner

Noncoding RNAs play important roles in several nuclear processes, including regulating gene expression, chromatin structure, and DNA repair. In most ...

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Påvisning af proteinubiquitinationssteder ved peptidberigelse og massespektrometri

The posttranslational modification of proteins by the small protein ubiquitin is involved in many cellular events. After tryptic digestion of ...

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

En forberedelse til plasmaprøve til massespektrometri ved hjælp af en automatiseret arbejdsstation

Sample preparation for mass spectrometry analysis in proteomics requires enzymatic cleavage of proteins into a peptide mixture. This process involves ...

Sample Preparation for Probe Electrospray Ionization Mass Spectrometry

Prøve forberedelse til Sonde Elektrospray Ionization Mass Spektrometri

Mass spectrometry (MS) is a powerful tool in analytical chemistry because it provides very accurate information about molecules, such as mass-to-charge ...

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Quantitative Analysis of the Cellular Lipidome of Saccharomyces Cerevisiae Using Liquid Chromatography Coupled with Tandem Mass Spectrometry

Kvantitativ analyse af cellulære lipidom af Saccharomyces Cerevisiae Ved hjælp af flydende kromatografi kombineret med tandem massespektrometri

Lipids are structurally diverse amphipathic molecules that are insoluble in water. Lipids are essential contributors to the organization and function of ...