Name: profiling thiol redox proteome using isotope tagging mass spectrometry
Uploaded: 2012-03-24T14:00:00
Duration: 12 min 7 s
Description: Watch this Scientific Journal Video about Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry at JoVE.com

فإن الكتاب أود أن أشكر الدكتور غريغ مارتن (جامعة كورنيل) وجماعته لتوفير سلالة DC3000، وبذور الطماطم، وتقديم المشورة. وهم يودون أيضا أن أشكر الدكتور تشونغ لين مذكرة تفاهم للمساعدة في بروتوكول DAB وشعبة البروتيوميات في مركز الجبهة المتحدة المتعدد التخصصات للبحوث التكنولوجيا الحيوية للحصول على المساعدة في تطوير أسلوب. تم تعديل بروتوكول لاستخراج البروتين من Hurkman وتاناكا 16. تم تعديل بروتوكول بشأن وضع العلامات cysTMT، الخطوات من 4 إلى 6 على أساس المنتج الأصلي بيرس الحرارية العلمية فيشر دليل 17. وقد تم تمويل هذا العمل من قبل المؤسسة الوطنية للعلوم (MCB 0818051 لتشن S).

<ol>
	<li>Almeida, N. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+draft+genome+sequence+of+Pseudomonas+syringae+pv.+tomato+T1+reveals+a+type+III+effector+repertoire+significantly+divergent+from+that+of+Pseudomonas+syringae+pv.+tomato+DC3000.">A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.</a> Mol. Plant Microbe Interact. 22, 52-62 (2009).</li><li>Preiter, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Novel+virulence+gene+of+Pseudomonas+syringae+pv.+tomato+strain+DC3000.">Novel virulence gene of Pseudomonas syringae pv. tomato strain DC3000.</a> J. Bacteriol. 187, 7805-7814 (2005).</li><li>Apostol, I., Heinstein, P. F., Low, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+stimulation+of+an+oxidative+burst+during+elicitation+of+cultured+plant+cells:+role+in+defense+and+signal+transduction.">Rapid stimulation of an oxidative burst during elicitation of cultured plant cells: role in defense and signal transduction.</a> Plant Physiol. 90, 109-116 (1989).</li><li>Orozco-Cardenas, M., Ryan, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydrogen+peroxide+is+generated+systemically+in+plant+leaves+by+wounding+and+systemin+via+the+octadecanoid+pathway.">Hydrogen peroxide is generated systemically in plant leaves by wounding and systemin via the octadecanoid pathway.</a> Proc. Natl. Acad. Sci. U.S.A. 96, 6553-6557 (1999).</li><li>Tonks, N. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redox+redux:+revisiting+PTPs+and+the+control+of+cell+signaling.">Redox redux: revisiting PTPs and the control of cell signaling.</a> Cell. 121, 667-670 (2005).</li><li>Alvarez, S., Wilson, G. H., Chen, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+in+vivo+disulfide-bonded+proteins+in+Arabidopsis.">Determination of in vivo disulfide-bonded proteins in Arabidopsis.</a> J. Chromatogr. B. 877, 101-104 (2009).</li><li>Apel, K., Hirt, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reactive+oxygen+species:+metabolism,+oxidative+stress,+and+signal+transduction.">Reactive oxygen species: metabolism, oxidative stress, and signal transduction.</a> Annu. Rev. Plant Biol. 55, 373-399 (2004).</li><li>Dayon, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relative+quantification+of+proteins+in+human+cerebrospinal+fluids+by+MS/MS+using+6-+plex+isobaric+tags.">Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6- plex isobaric tags.</a> Anal. Chem. 80, 2921-2931 (2008).</li><li>Thompson, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tandem+mass+tags:+a+novel+quantification+strategy+for+comparative+analysis+of+complex+protein+mixtures+by+MS/MS.">Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS.</a> Anal. Chem. 75, 1895-1904 (2003).</li><li>Rosenblatt, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+cysteine-reactive+tandem+mass+tag+reagent+for+subproteome+labeling,+enrichment+and+quantitation.">A novel cysteine-reactive tandem mass tag reagent for subproteome labeling, enrichment and quantitation.</a> , TP169 (2010).</li><li>Clark, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phenotypic+analysis+of+Arabidopsis+mutants:+diaminobenzidine+stain+for+hydrogen+peroxide.">Phenotypic analysis of Arabidopsis mutants: diaminobenzidine stain for hydrogen peroxide.</a> Cold Spring Harb. Protoc. , (2009).</li><li>Sethuraman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isotope-Coded+affinity+tag+(ICAT)+approach+to+redox+proteomics:+identification+and+quantification+of+oxidant-sensitive+cysteine+thiols+in+complex+protein+mixtures.">Isotope-Coded affinity tag (ICAT) approach to redox proteomics: identification and quantification of oxidant-sensitive cysteine thiols in complex protein mixtures.</a> J. Proteome Res. 3, 1228-1233 (2004).</li><li>Asso, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=EPR+and+redox+characterization+of+ferredoxins+I+and+II+from+Desulfovibrio+vulgaris+Miyazaki.">EPR and redox characterization of ferredoxins I and II from Desulfovibrio vulgaris Miyazaki.</a> Biochem. Biophys. Res. Commun. 211, 198-204 (1995).</li><li>Huang, H. e. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Disease+resistance+to+bacterial+pathogens+affected+by+the+amount+of+ferredoxin-I+proteins+in+plants.">Disease resistance to bacterial pathogens affected by the amount of ferredoxin-I proteins in plants.</a> Mol. Plant Pathol. 8, 129-137 (2007).</li><li>Hurkman, W., Tanaka, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Solubilization+of+plant+membrane+proteins+for+analysis+by+two-dimensional+gel+electrophoresis.">Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis.</a> Plant Physiol. 81, 802-806 (1986).</li></ol>

الإعلان عن أي تضارب في المصالح.

هذا البروتوكول يوفر معلومات عن أداء تلطيخ DAB، فضلا عن cysTMT المسمى الكمي السيستين الأكسدة. هذه الإجراءات هي مفيدة في دراسة إنتاج ريوس، فضلا عن تأثير ذلك على تنظيم البروتينات عندما يتم تلقيح مغد lycopersicum مع syringae الزائفة. الطرق الواردة في هذا البروتوكول توفير وسيلة لفحص عينات ريوس في ورقة كاملة في الطريقة التي تسبب أقل قدر من الضرر على الأنسجة ورقة. الإجراء وضع العلامات يوفر وسيلة لفحص الأكسدة يحتمل البروتينات تنظم من خلال استخدام أسلوب وضع العلامات السيستين. هذا مفيد عند النظر في مرحلة مبكرة من الاستجابة للضغط النفسي. ويمكن استخدام أساليب مثل علامة تقارب النظائر تلوينها (ICAT) وcysTMT في دراسة إمكانية تنظيم الأكسدة البروتينات في عينات بيولوجية. ICAT يسمح وضع العلامات والمقارنة بين عينتين 12. كلا أساليب تسمية cysteines حرة ويمكن استخدامها لبروتين quantificأوجه 10،12. ومع ذلك، فإن طريقة cysTMT يسمح للانخفاض في اختلاف التجارب وكذلك الإرسال المتعدد 10. عدد العلامات المتاحة يسمح للباحثين لتشمل مكررات أو عينات متعددة في تصميمها التجريبية. وجود المزيد من عينات يوفر احتمال وجود عدد أكبر من البروتينات التي تم تحديدها. ومن المآخذ الرئيسية لتقنية cysTMT هو أنه ينال من الجودة الشاملة لتحديد بروتين بسبب الخطوات تخصيب انتقائية لcysTMT المسمى-الببتيدات (6،5-6،6). عدد الببتيدات لتحديد بروتين يعتمد بشكل كبير على عدد من بقايا السيستين في تسلسل البروتين. ويمكن التغلب على هذه المشكلة عن طريق تقديم جزء من العينة تريبسيني قبل التخصيب لقياس الطيف الكتلي تحديد بروتين. نظرا لطبيعة التصميم التجريبي، وكذلك آلية وضع العلامات التي تستخدم أسلوب cysTMT، خطوات معينة حاسمة. أثناء أداء preci بروتينpitation وبيليه الغسيل (3.9) من المهم للحفاظ على عينات من الفتور على الجليد للحد من تدهور البروتين. خلال وضع العلامات cysTMT، إزالة كاشف الحد من (4.6) مهم جدا لأنه قد يتعرض لوضع العلامات عينات عكس ذلك. وضع العلامات العكس هو ممكن إذا خفض كاشف لا يزال في العينة. إذا خفضت عينات بعد وضع العلامات، يمكن إزالة العلامة cysTMT. مرة واحدة يتم إضافة تسميات للعينات، لا بد من التحقق من مستوى الرقم الهيدروجيني (4.7) من أجل الحصول على أفضل كفاءة وضع العلامات. وبالإضافة إلى ذلك، وتحليل البيانات تعتمد على ما هو مطلوب من الباحث والهدف النهائي في استخدام بروتوكول. كما أنها تعتمد على البرمجيات المستخدمة في كل برنامج لديه خوارزميات مختلفة. هذه التجربة تستخدم الممرض بوصفه elicitor لزيادة الإنتاج من الأنواع المؤكسدة رد الفعل في الطماطم، ومع ذلك، يمكن قياس غيرها من الاستجابات للوائح الأكسدة وفقا لذلك. هذا التصميم التجريبي غير قابلة للتكيف مع النباتية الأخرى والنظم الحيوانية. </P&gt;

<table border="1" style=";text-align:right;direction:rtl"><tbody><tr><td> اسم كاشف </td><td> شركة </td><td> فهرس العدد </td></tr><tr><td> MetroMix 500 </td><td> شركات مؤسسات بريتون وودز </td><td> TX-500 </td></tr><tr><td> 3،3 &#39;-Diaminobenzidine </td><td> سيغما الدريخ </td><td> D8001 </td></tr><tr><td> ReadyPrep عدة استخراج متسلسل الكاشف 3 </td><td> الحيوي راد </td><td> 163-2104 </td></tr><tr><td> CB-X بروتين مقايسة </td><td> التوالد التكنولوجيا </td><td> 786-12X </td></tr><tr><td> cysTMT الكواشف </td><td> الحرارية البروتين المنتجات بيرس البحث العلمي </td><td> 90071 </td></tr><tr><td> Laemmli عينة الواق </td><td> الحيوي راد </td><td> 161-0737 </td></tr><tr><td> الحيوي الآمن Comassie (G-250 وصمة عار) </td><td> الحيوي راد </td><td> 161-0786 </td></tr><tr><td> Microcon 3KD عمود </td><td> ميليبور </td><td> 42403 </td></tr><tr><td> يجمد مكافحة TMT الراتنج </td><td> الحرارية البروتين المنتجات بيرس البحث العلمي </td><td> 90076 </td></tr><tr><td> عمود الطرد المركزي </td><td> الحرارية البروتين المنتجات بيرس البحث العلمي </td><td> 89896 </td></tr><tr><td> Proteopep العمود الثاني C18 </td><td> جديد الهدف </td><td> PFC7515-PP2-10 </td></tr><tr><td> NanoLC-1D HPLC </td><td> AB Sciex </td><td> 90389 </td></tr><tr><td> LTQ Orbitrap XL </td><td> الحرارية العلمية </td><td> 0020137580 </td></tr><tr><td> SpeedVac </td><td> Labconco </td><td> 7812013 </td></tr><tr><td> بروتيوم مكتشف 1،2 البرمجيات </td><td> الحرارية البروتين المنتجات بيرس البحث العلمي </td><td></td></tr><tr><td> التربسين </td><td> Promega </td><td> V5111 </td></tr><tr><td> Oakridge أنبوب جهاز طرد مركزي </td><td> الحرارية العلمية Nalgeشركة الشرق الأدنى </td><td> 3139-0050 </td></tr><tr><td> أنبوب Microcentrifuge (2ml) </td><td> الولايات المتحدة الأمريكية والعلم </td><td> 1620-2700 </td></tr><tr><td> 12٪ مصغرة متلون TGX سابقة الصب جل </td><td> الحيوي راد </td><td> 456-1043 </td></tr><tr><td> أعلى النموذج &gt; الحيوي الآمن Coomassie StainBottom من نموذج </td><td> الحيوي راد </td><td> 161-0786 </td></tr><tr><td> TMT تخصيب عدة </td><td> الحرارية البروتين المنتجات بيرس البحث العلمي </td><td> 90077 </td></tr></tbody></table>

profiling thiol redox proteome using isotope tagging mass spectrometry

الزائفة syringae الكهروضوئية DC3000 السلالة. الطماطم ليس فقط يسبب مرض جرثومي بقعة في lycopersicum مغد ولكن أيضا على أنواع الكرنب، وكذلك على thaliana Arabidopsis، وهو نبات المضيف لين العريكة وراثيا 1،2. تراكم أنواع الاكسجين التفاعلية (ريوس) في النبتات تلقيح مع DC3000 يشير إلى وجود دور للروس في تحوير موت الخلايا نخرية خلال مرض جرثومي بقعة من الطماطم 3. ويتم إنتاج بيروكسيد الهيدروجين، وهو مكون من روس، بعد تلقيح نباتات الطماطم مع الزائفة 3. ويمكن الكشف عن بيروكسيد الهيدروجين باستخدام وصمة عار 3&#39;-3 النسيجية &quot;diaminobenzidine (DAB) 4. DAB تلطيخ يتفاعل مع بيروكسيد الهيدروجين لإنتاج البني وصمة عار على ورقة 4 الأنسجة. ROS بدور تنظيمي للبيئة الأكسدة الخلوية، والتي يمكن تغيير حالة الأكسدة من بروتينات معينة 5. السيستين هو حمض أميني مهم حساسة للالأكسدة التغييرات. تحت أكسدة خفيفة، وأكسدة عكسها الجماعات السيستين سلفهيدريل بمثابة المجسات الأكسدة ومحولات الطاقة إشارة إلى أن تنظيم مجموعة متنوعة من العمليات الفيزيولوجية 6،7. جنبا إلى جنب كتلة علامة (TMT) الكواشف تمكين المتزامنة وتحديد الكميات المضاعفة من البروتينات في عينات مختلفة باستخدام جنبا إلى جنب قياس الطيف الكتلي 8،9. والسيستين التفاعل TMT (cysTMT) الكواشف تمكين وضع العلامات انتقائية والكميات النسبية للالسيستين التي تحتوي على الببتيدات من ما يصل الى ستة العينات البيولوجية. كل علامة cysTMT إسوي الضغط له نفس كتلة الأم الاسمي، وتتكون من مجموعة سلفهيدريل التفاعل، وهي ذراع هل MS-محايدة وافاد مراسل MS / MS 10. بعد وضع العلامات، وكانت العينات التي تخضع لعملية الهضم البروتيني. وقد أثرى الببتيدات السيستين المسمى باستخدام الراتنج التي تحتوي على المضادة للTMT الأجسام المضادة. خلال MS / MS تحليل، سلسلة من الأيونات مراسل (أي 126-131 دا) تنشأ في المنطقة كتلة منخفضة، وتوفير المعلومات عن الكميات النسبية.سير العمل غير فعالة للحد من تعقيد العينة، وتحسين المدى الديناميكي ودراسة التعديلات السيستين. هنا نقدم تحليل البروتين الأكسدة من الطماطم DC3000 الباسيفيكي المعالجة (ريو غراندي) يترك باستخدام تكنولوجيا cysTMT. هذا أسلوب الإنتاجية العالية لديه القدرة على أن تطبق على دراسة أخرى الأكسدة التنظيم العمليات الفيزيولوجية.

Watch this Scientific Journal Video about Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry at JoVE.com

Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry

ورفع مستوى رد الفعل أنواع الاكسجين عندما تواجه الخلايا ظروف الإجهاد. هنا نعرض على سبيل المثال من تلطيخ diaminobenzidine 3&#39;-3 &quot;فضلا عن cysTMT وضع العلامات وقياس الطيف الكتلي لمحة عن بروتيوم الأكسدة في<em&gt; الزائفة syringae</em&gt; تعامل أوراق الطماطم.

التنميط بروتيوم الأكسدة والاختزال ثيول استخدام الطيف النظائر كتلة توصيف

Pseudomonas syringae pv. tomato strain DC3000 not only causes bacterial speck disease in Solanum lycopersicum but also on Brassica species, as well as on ...

profiling-thiol-redox-proteome-using-isotope-tagging-mass-spectrometry

Research

JoVE Journal

Biology

MALDI Sample Preparation: the Ultra Thin Layer Method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) 1,2. The ultra-thin layer method involves the production of a substrate layer of matrix crystals (alpha-cyano-4-hydroxycinnamic acid) on the sample plate, which serves as a seeding ground for subsequent crystallization of a matrix/analyte mixture. Advantages of the ultra-thin layer method over other sample deposition approaches (e.g. dried droplet) are that it provides (i) greater tolerance to impurities such as salts and detergents, (ii) better resolution, and (iii) higher spatial uniformity. This method is especially useful for the accurate mass determination of proteins. The protocol was initially developed and optimized for the analysis of membrane proteins and used to successfully analyze ion channels, metabolite transporters, and receptors, containing between 2 and 12 transmembrane domains 2. Since the original publication, it has also shown to be equally useful for the analysis of soluble proteins. Indeed, we have used it for a large number of proteins having a wide range of properties, including those with molecular masses as high as 380 kDa 3. It is currently our method of choice for the molecular mass analysis of all proteins. The described procedure consistently produces high-quality spectra, and it is sensitive, robust, and easy to implement.

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS).

MALDI تحضير العينة : الترا أسلوب طبقة رقيقة

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption ...

A Quantitative Assessment of The Yeast Lipidome using Electrospray Ionization Mass Spectrometry

Lipids are one of the major classes of biomolecules and play important roles membrane dynamics, energy storage, and signalling1-4. The budding yeast Saccharomyces cerevisiae, a genetically and biochemically manipulable unicellular eukaryote with annotated genome and very simple lipidome, is a valuable model for studying biological functions of various lipid species in multicellular eukaryotes2,3,5. S. cerevisiae has 10 major classes of lipids with chain lengths mainly of 16 or 18 carbon atoms and either zero or one degree of unsaturation6,7. Existing methods for lipid identification and quantification - such as high performance liquid chromatography, thin-layer chromatography, fluorescence microscopy, and gas chromatography followed by MS - are well established but have low sensitivity, insufficiently separate various molecular forms of lipids, require lipid derivitization prior to analysis, or can be quite time consuming. Here we present a detailed description of our experimental approach to solve these inherent limitations by using survey-scan ESI/MS for the identification and quantification of the entire complement of lipids in yeast cells. The described method does not require chromatographic separation of complex lipid mixtures recovered from yeast cells, thereby greatly accelerating the process of data acquisition. This method enables lipid identification and quantification at the concentrations as low as g/ml and has been successfully applied to assessing lipidomes of whole yeast cells and their purified organelles. Lipids extraction from whole yeast cells for using this method of lipid analysis takes two to three hours. It takes only five to ten minutes to run each sample of extracted and dried lipids on a Q-TOF mass spectrometer equipped with a nano-electrospray source.

We describe a new quantitative lipidomics method for identifying numerous lipid species in yeast using survey-scan electrospray ionization mass spectrometry (ESI/MS). This method exceeds currently available methods for lipid identification and quantification in the ability to resolve various molecular forms of lipids, sensitivity, and speed.

والتقييم الكمي لاستخدام الطيف Lipidome الخميرة Electrospray قداس التأين

Lipids are one of the major classes of biomolecules and play important roles membrane dynamics, energy storage, and signalling1-4. The budding yeast ...

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Living cells control and regulate their biological processes through the coordinated action of a large number of proteins that assemble themselves into an array of dynamic, multi-protein complexes1. To gain a mechanistic understanding of the various cellular processes, it is crucial to determine the structure of such protein complexes, and reveal how their structural organization dictates their function. Many aspects of multi-protein complexes are, however, difficult to characterize, due to their heterogeneous nature, asymmetric structure, and dynamics. Therefore, new approaches are required for the study of the tertiary levels of protein organization.
One of the emerging structural biology tools for analyzing macromolecular complexes is mass spectrometry (MS)2-5. This method yields information on the complex protein composition, subunit stoichiometry, and structural topology. The power of MS derives from its high sensitivity and, as a consequence, low sample requirement, which enables examination of protein complexes expressed at endogenous levels. Another advantage is the speed of analysis, which allows monitoring of reactions in real time. Moreover, the technique can simultaneously measure the characteristics of separate populations co-existing in a mixture. 
Here, we describe a detailed protocol for the application of structural MS to the analysis of large protein assemblies. The procedure begins with the preparation of gold-coated capillaries for nanoflow electrospray ionization (nESI). It then continues with sample preparation, emphasizing the buffer conditions which should be compatible with nESI on the one hand, and enable to maintain complexes intact on the other. We then explain, step-by-step, how to optimize the experimental conditions for high mass measurements and acquire MS and tandem MS spectra. Finally, we chart the data processing and analyses that follow. Rather than attempting to characterize every aspect of protein assemblies, this protocol introduces basic MS procedures, enabling the performance of MS and MS/MS experiments on non-covalent complexes. Overall, our goal is to provide researchers unacquainted with the field of structural MS, with knowledge of the principal experimental tools.

Mass spectrometry has proven to be a valuable tool for analyzing large protein complexes. This method enables insights into the composition, stoichiometry and overall architecture of multi-subunit assemblies. Here, we describe, step-by-step, how to perform a structural mass spectrometry analysis, and characterize macromolecular structures.

تحليل البروتين المجمعات الكبيرة التي الطيف الكتلي الإنشائية

Living cells control and regulate their biological processes through the coordinated action of a large number of proteins that assemble themselves into an ...

OLIgo Mass Profiling (OLIMP) of Extracellular Polysaccharides

The direct contact of cells to the environment is mediated in many organisms by an extracellular matrix. One common aspect of extracellular matrices is that they contain complex sugar moieties in form of glycoproteins, proteoglycans, and/or polysaccharides. Examples include the extracellular matrix of humans and animal cells consisting mainly of fibrillar proteins and proteoglycans or the polysaccharide based cell walls of plants and fungi, and the proteoglycan/glycolipid based cell walls of bacteria. All these glycostructures play vital roles in cell-to-cell and cell-to-environment communication and signalling.
An extraordinary complex example of an extracellular matrix is present in the walls of higher plant cells. Their wall is made almost entirely of sugars, up to 75% dry weight, and consists of the most abundant biopolymers present on this planet. Therefore, research is conducted how to utilize these materials best as a carbon-neutral renewable resource to replace petrochemicals derived from fossil fuel. The main challenge for fuel conversion remains the recalcitrance of walls to enzymatic or chemical degradation due to the unique glycostructures present in this unique biocomposite.
Here, we present a method for the rapid and sensitive analysis of plant cell wall glycostructures. This method OLIgo Mass Profiling (OLIMP) is based the enzymatic release of oligosaccharides from wall materials facilitating specific glycosylhydrolases and subsequent analysis of the solubilized oligosaccharide mixtures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS)1 (Figure 1). OLIMP requires walls of only 5000 cells for a complete analysis, can be performed on the tissue itself2, and is amenable to high-throughput analyses3. While the absolute amount of the solubilized oligosaccharides cannot be determined by OLIMP the relative abundance of the various oligosaccharide ions can be delineated from the mass spectra giving insights about the substitution-pattern of the native polysaccharide present in the wall.
OLIMP can be used to analyze a wide variety of wall polymers, limited only by the availability of specific enzymes4. For example, for the analysis of polymers present in the plant cell wall enzymes are available to analyse the hemicelluloses xyloglucan using a xyloglucanase5, 11, 12, 13, xylan using an endo-&beta;-(1-4)-xylanase 6,7, or for pectic polysaccharides using a combination of a polygalacturonase and a methylesterase 8. Furthermore, using the same principles of OLIMP glycosylhydrolase and even glycosyltransferase activities can be monitored and determined 9.

OLIgo Mass Profiling OLIMP of Extracellular Polysaccharides

A rapid way is described to gain insights into the structure of polysaccharides in an extracellular matrix. The method takes advantage of the specificity of glycosylhydrolases and the sensitivity of mass spectrometry allowing minute amounts of materials to be analyzed. This technique is adaptable to be used directly on tissue itself.

أليغو التنميط قداس (OLIMP) من السكريات خارج الخلية

The direct contact of cells to the environment is mediated in many organisms by an extracellular matrix. One common aspect of extracellular matrices is ...

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS)

There is a variety of approaches to reduce the complexity of the proteome on the basis of functional small molecule-protein interactions such as affinity chromatography 1 or Activity Based Protein Profiling 2. Trifunctional Capture Compounds (CCs, Figure 1A) 3 are the basis for a generic approach, in which the initial equilibrium-driven interaction between a small molecule probe (the selectivity function, here S-adenosyl-L-homocysteine, SAH, Figure 1A) and target proteins is irreversibly fixed upon photo-crosslinking between an independent photo-activable reactivity function (here a phenylazide) of the CC and the surface of the target proteins. The sorting function (here biotin) serves to isolate the CC - protein conjugates from complex biological mixtures with the help of a solid phase (here streptavidin magnetic beads). Two configurations of the experiments are possible: "off-bead" 4 or the presently described "on-bead" configuration (Figure 1B). The selectivity function may be virtually any small molecule of interest (substrates, inhibitors, drug molecules).
S-Adenosyl-L-methionine (SAM, Figure 1A) is probably, second to ATP, the most widely used cofactor in nature 5, 6. It is used as the major methyl group donor in all living organisms with the chemical reaction being catalyzed by SAM-dependent methyltransferases (MTases), which methylate DNA 7, RNA 8, proteins 9, or small molecules 10. Given the crucial role of methylation reactions in diverse physiological scenarios (gene regulation, epigenetics, metabolism), the profiling of MTases can be expected to become of similar importance in functional proteomics as the profiling of kinases. Analytical tools for their profiling, however, have not been available. We recently introduced a CC with SAH as selectivity group to fill this technological gap (Figure 1A).
SAH, the product of SAM after methyl transfer, is a known general MTase product inhibitor 11. For this reason and because the natural cofactor SAM is used by further enzymes transferring other parts of the cofactor or initiating radical reactions as well as because of its chemical instability 12, SAH is an ideal selectivity function for a CC to target MTases. Here, we report the utility of the SAH-CC and CCMS by profiling MTases and other SAH-binding proteins from the strain DH5&alpha; of Escherichia coli (E. coli), one of the best-characterized prokaryotes, which has served as the preferred model organism in countless biochemical, biological, and biotechnological studies. Photo-activated crosslinking enhances yield and sensitivity of the experiment, and the specificity can be readily tested for in competition experiments using an excess of free SAH.

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

Capture Compounds are trifunctional small molecules to reduce the complexity of the proteome by functional reversible small molecule-protein interaction followed by photo-crosslinking and purification. Here we use a Capture Compound with S-adenosyl-L-homocysteine-binding as selectivity function to isolate methyltransferases from an Escherichia coli whole cell lysate and identify them by MS.

التنميط وغيره من Methyltransferases S - adenosyl - L - الهموسيستين ملزم البروتينات المركبة من قبل التقاط الطيف الكتلي (CCMS)

There is a variety of approaches to reduce the complexity of the proteome on the basis of functional small molecule-protein interactions such as affinity ...

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

There is a great need for quantitative assays in measuring proteins. Traditional sandwich immunoassays, largely considered the gold standard in quantitation, are associated with a high cost, long lead time, and are fraught with drawbacks (e.g. heterophilic antibodies, autoantibody interference, 'hook-effect').1 An alternative technique is affinity enrichment of peptides coupled with quantitative mass spectrometry, commonly referred to as SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies).2 In this technique, affinity enrichment of peptides with stable isotope dilution and detection by selected/multiple reaction monitoring mass spectrometry (SRM/MRM-MS) provides quantitative measurement of peptides as surrogates for their respective proteins. SRM/MRM-MS is well established for accurate quantitation of small molecules 3, 4 and more recently has been adapted to measure the concentrations of proteins in plasma and cell lysates.5-7 To achieve quantitation of proteins, these larger molecules are digested to component peptides using an enzyme such as trypsin. One or more selected peptides whose sequence is unique to the target protein in that species (i.e. "proteotypic" peptides) are then enriched from the sample using anti-peptide antibodies and measured as quantitative stoichiometric surrogates for protein concentration in the sample. Hence, coupled to stable isotope dilution (SID) methods (i.e. a spiked-in stable isotope labeled peptide standard), SRM/MRM can be used to measure concentrations of proteotypic peptides as surrogates for quantification of proteins in complex biological matrices. The assays have several advantages compared to traditional immunoassays. The reagents are relatively less expensive to generate, the specificity for the analyte is excellent, the assays can be highly multiplexed, enrichment can be performed from neat plasma (no depletion required), and the technique is amenable to a wide array of proteins or modifications of interest.8-13 In this video we demonstrate the basic protocol as adapted to a magnetic bead platform.

Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) couples affinity enrichment of peptides with stable isotope dilution mass spectrometry (MRM-MS) to provide quantitative measurement of peptides as surrogates for their respective proteins. Here we describe the protocol using magnetic particles in a partially automated format.

الكمي من البروتينات عن طريق التخصيب الببتيد Immunoaffinity اقترن الطيف الكتلي

There is a great need for quantitative assays in measuring proteins. Traditional sandwich immunoassays, largely considered the gold standard in ...

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems1, 2. Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria1-6. In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes1, 2, 7. Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast8, 9, and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system10. Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits).
Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking.

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Affinity purification of tagged proteins in combination with mass spectrometry (APMS) is a powerful method for the systematic mapping of protein interaction networks and for investigating the mechanistic basis of biological processes. Here, we describe an optimized sequential peptide affinity (SPA) APMS procedure developed for the bacterium Escherichia coli that can be used to isolate and characterize stable multi-protein complexes to near homogeneity even starting from low copy numbers per cell.

تحديد بروتين في مجمعات<em&gt; كولاي</em&gt; استخدام المتعاقبة تنقية تقارب الببتيد في تركيبة مع جنبا إلى جنب الطيف الكتلي

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the ...

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Absolute quantification of target proteins within complex biological samples is critical to a wide range of research and clinical applications. This protocol provides step-by-step instructions for the development and application of quantitative assays using selected reaction monitoring (SRM) mass spectrometry (MS). First, likely quantotypic target peptides are identified based on numerous criteria. This includes identifying proteotypic peptides, avoiding sites of posttranslational modification, and analyzing the uniqueness of the target peptide to the target protein. Next, crude external peptide standards are synthesized and used to develop SRM assays, and the resulting assays are used to perform qualitative analyses of the biological samples. Finally, purified, quantified, heavy isotope labeled internal peptide standards are prepared and used to perform isotope dilution series SRM assays. Analysis of all of the resulting MS data is presented. This protocol was used to accurately assay the absolute abundance of proteins of the chemotaxis signaling pathway within RAW 264.7 cells (a mouse monocyte/macrophage cell line). The quantification of Gi2 (a heterotrimeric G-protein &#945;-subunit) is described in detail.

This protocol describes how to perform absolute quantification assays of target proteins within complex biological samples using selected reaction monitoring. It was used to accurately quantify proteins of the mouse macrophage chemotaxis signaling pathway. Target peptide selection, assay development, and qualitative and quantitative assays are described in detail.

رد الفعل المحدد رصد الطيف الكتلي لالمطلق البروتين الكمي

Absolute quantification of target proteins within complex biological samples is critical to a wide range of research and clinical applications. This ...

Identification of MyoD Interactome Using Tandem Affinity Purification Coupled to Mass Spectrometry

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ability to proliferate or they can differentiate and fuse into multinucleated myotubes, which maturate further to form myofibers. Skeletal muscle terminal differentiation is orchestrated by the coordinated action of various transcription factors, in particular the members of the Muscle Regulatory Factors or MRFs (MyoD, Myogenin, Myf5, and MRF4), also called the myogenic bHLH transcription factors family. These factors cooperate with chromatin-remodeling complexes within elaborate transcriptional regulatory network to achieve skeletal myogenesis. In this, MyoD is considered the master myogenic transcription factor in triggering muscle terminal differentiation. This notion is strengthened by the ability of MyoD to convert non-muscle cells into skeletal muscle cells. Here we describe an approach used to identify MyoD protein partners in an exhaustive manner in order to elucidate the different factors involved in skeletal muscle terminal differentiation. The long-term aim is to understand the epigenetic mechanisms involved in the regulation of skeletal muscle genes, i.e., MyoD targets. MyoD partners are identified by using Tandem Affinity Purification (TAP-Tag) from a heterologous system coupled to mass spectrometry (MS) characterization, followed by validation of the role of relevant partners during skeletal muscle terminal differentiation. Aberrant forms of myogenic factors, or their aberrant regulation, are associated with a number of muscle disorders: congenital myasthenia, myotonic dystrophy, rhabdomyosarcoma and defects in muscle regeneration. As such, myogenic factors provide a pool of potential therapeutic targets in muscle disorders, both with regard to mechanisms that cause disease itself and regenerative mechanisms that can improve disease treatment. Thus, the detailed understanding of the intermolecular interactions and the genetic programs controlled by the myogenic factors is essential for the rational design of efficient therapies.

MyoD is a myogenic transcription factor with a strong capacity to induce myogenic transdifferentiation of many fully differentiated non-muscle cell lines. The epigenetic mechanisms involved in this transdifferentiation are largely unknown. Here we describe a double-affinity purification method followed by mass spectrometry to exhaustively characterize MyoD partners.

تحديد MyoD Interactome عن طريق جنبا الى جنب الانجذاب تنقية جانب لقياس الطيف الكتلي

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ...

Cellular Redox Profiling Using High-content Microscopy

Reactive oxygen species (ROS) regulate essential cellular processes including gene expression, migration, differentiation and proliferation. However, excessive ROS levels induce a state of oxidative stress, which is accompanied by irreversible oxidative damage to DNA, lipids and proteins. Thus, quantification of ROS provides a direct proxy for cellular health condition. Since mitochondria are among the major cellular sources and targets of ROS, joint analysis of mitochondrial function and ROS production in the same cells is crucial for better understanding the interconnection in pathophysiological conditions. Therefore, a high-content microscopy-based strategy was developed for simultaneous quantification of intracellular ROS levels, mitochondrial membrane potential (&#916;&#936;m) and mitochondrial morphology. It is based on automated widefield fluorescence microscopy and image analysis of living adherent cells, grown in multi-well plates, and stained with the cell-permeable fluorescent reporter molecules CM-H2DCFDA (ROS) and TMRM (&#916;&#936;m and mitochondrial morphology). In contrast with fluorimetry or flow-cytometry, this strategy allows quantification of subcellular parameters at the level of the individual cell with high spatiotemporal resolution, both before and after experimental stimulation. Importantly, the image-based nature of the method allows extracting morphological parameters in addition to signal intensities. The combined feature set is used for explorative and statistical multivariate data analysis to detect differences between subpopulations, cell types and/or treatments. Here, a detailed description of the assay is provided, along with an example experiment that proves its potential for unambiguous discrimination between cellular states after chemical perturbation.

This paper presents a high-content microscopy workflow for simultaneous quantification of intracellular ROS levels, as well as mitochondrial membrane potential and morphology &#8211; jointly referred to as mitochondrial morphofunction &#8211; in living adherent cells using the cell-permeant fluorescent reporter molecules 5-(and-6)-chloromethyl-2&#39;,7&#39;-dichlorodihydrofluorescein diacetate, acetyl ester (CM-H2DCFDA) and tetramethylrhodamine methylester (TMRM).

الخلوية الأكسدة التنميط باستخدام عالية المحتوى المجهري

Reactive oxygen species (ROS) regulate essential cellular processes including gene expression, migration, differentiation and proliferation. However, ...