Name: lerlic-ms/ms for in-depth characterization and quantification of glutamine and asparagine deamidation in shotgun proteomics
Uploaded: 2017-04-09T15:00:00
Description: Watch this Scientific Journal Video about LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics at JoVE.com

Singapur (NMRC-OF-IRG-0003-2016) ve NTU-NHG Araştırma Grant Yaşlanma Ulusal Tıbbi Araştırma Konseyi (: Bu çalışma kısmen Eğitim Singapur Bakanlığının (Grant ARC9 / 15 Tier 2) hibe ile desteklenmiştir Grant ARG / 14017). Biz nazik bu çalışma mümkün kılan ambalaj materyalleri sağlayan Dr. Andrew Alpert ve PolyLC ekibine şükranlarımızı ve en içten teşekkürlerimi ifade etmek istiyorum.

1. Uzun uzunlukta Anyon değişim ambalaj (lax) Kılcal Sütun (Not: lax kolon evde bu protokolde tarif olarak paketlenmiş, lax sütunlar da ticari olarak temin edilebilir olmasına rağmen, daha fazla ayrıntı için Materyaller ve Reaktifler: İçindekiler&#39;i bakınız). <ol><li> Bulamaç hazırlamak üzere tamponu (Tablo 1) ambalaj 3.5 mL zayıf anyon değiştirme ambalaj malzemesi, 50 mg süspanse edin. </li><li> bir dişi-dişi b...

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Bu video yazıda LERLIC-MS / MS 3&#39;ün bir adım adım protokol sunmak için bir yöntem derinlemesine karakterizasyonunun ve doğru bir şekilde, protein deamidasyonu ve bu protein modifikasyonu ilgili enzimatik işlemlerin kapsamını tespit etmek. LERLIC-MS / MS elektrostatik itme-hidrofilik interaksiyon kromatografisi (ERLIC) 27 ilkesi altında uzun bir uzunlukta (50 sm) lax kullanımına dayanmaktadır. Çalışmamızda 3&#39;te gösterildi?...

Deamidasyonu bir protein dönüşüm sonrası modifikasyonu asparagin (Asn) ve / veya glutamin (Gln) kalıntıları 1 modifikasyonu yoluyla protein omurgasına bir negatif yük getirmektedir (PTM) &#39;dir. 2: 1 oranında Asn kalıntısının etki ederken bu değişiklik, bir ortak 3 de izomerik ürünleri isoaspartic asit (IsoAsp) ve n -aspartic asit (Asp) oluşturur. Rağmen, bu oran tamir enzimi, L-isoaspartyl metiltransferaz (PIMT) 3, 4 müdahalesi ile değiştirilebilir. Benzer şekilde, Gln kalıntısının deamidasyon beklenen 1 de izomer gama-glutamik asit (γ-Glu) ve alfa-glutamik asit izoformu (α-Glu) oluşturur: 7 oranında 3, 5, bu oran aksiyonu ile kaydırılabilir her yerde enzim transglutaminaz 2 ve diğer transglütaminazlar da dahil olmak üzere transglütaminaz 1, ebeyin 6 hücre dışı veziküller ile ilişkili olarak nzyme yakın zamanda tespit edilmiş. Deamidasyon kökeni (birkaç kronik de Gln transamidasyon ile ilgili detaylar ve Etkileri 3 bakınız önceki transglütaminazlar ve diğer enzimler, transamidasyon yoluyla arası / molekül içi çapraz bağlanma aracılık ettiği Gln kalıntıları özellikle yaygındır, kendiliğinden veya enzimatik olarak mevcut olabilir ve ölümcül insan hastalıkları). Bu nedenle, deamidasyon etkilenen moleküller 4, 7, 8, önemli bir yapı üzerinde yankı ve işlevi vardır ve 9 yaşlanma, hizmet olarak moleküler saat dahil olmak üzere çeşitli biyokimyasal sonuçları ışığında derinlemesine bir kimyasal karakterizasyonu 3 gerektiren bir PTM olan . Asn kalıntılarına deamidasyonunun olmasına rağmen<html> nispeten aşağıdan yukarı tüfek proteomik ile iyi karakterize edilmiş 1, 10, Gln kalıntısının deamidasyon yine elektron esaslı radikal parçalanma 11 model bileşimlerinin zor analizi ötesinde, uygun bir karakterizasyon yöntemi bulunmamaktadır. Son zamanlarda, tek bir analizde karmaşık biyolojik numunelerin ve model bileşiklerinden Gln ve Asn deamidasyon izoformlarının ayrılmasını sağlayan yeni bir tek boyutlu tüfek proteomik stratejisi (LERLIC-MS / MS) 3 geliştirdik. LERLIC-MS / MS, uzun uzunlukta (50 sm) elektrostatik itme-hidrofilik interaksiyon kromatografisi (ERLIC) modunda çalışan iyon değişim kolonu (lax) kullanılarak triptik sindirilmiş peptidlerin ayrılması göre ve tandem kütle spektrometrisi ile birleştirilir (LC MS / MS). Bu yeni analitik strateji karakterize ve nispeten insan beyin dokularında her deamide kalıntısının ölçüde ölçmek için kullanılmıştırf &quot;&gt; 3. Yine de burada özetlenen protokol ilgi biyokimyasal bağlamında protein deamidasyon özelliklerini incelemek amaçlanmıştır LERLIC-MS / MS video görüntüleme sağlayacaktır. ETİK TABLOSU Bu protokolün tüm işlemler Singapur Nanyang Teknoloji Üniversitesi kurumsal inceleme kurulu tarafından onaylanmış ve kurumsal kurallarına uygun olarak yapılmıştır.

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		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Michrom Thermo CaptiveSpray&#160;</td>
			<td style="width:424px;">Michrom-Bruker Inc.</td>
			<td style="width:207px;">TCSI-SS2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Incubator INCUCELL&#160;</td>
			<td style="width:424px;">MMM Group</td>
			<td style="width:207px;">INCUCELL111</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Sequencing-grade modified trypsin</td>
			<td style="width:424px;">Promega</td>
			<td style="width:207px;">V5111</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Protease inhibitor cocktail tablets</td>
			<td style="width:424px;">Roche</td>
			<td style="width:207px;">11836170001 (ROCHE)</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Phosphate buffer solution 10X (diluted to 1x)</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">P5493</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Ammonium acetate</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">A1542</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Sodium deoxycholate</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">D6750</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Dithiothreitol</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">D0632</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Iodoacetamide</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">i6125</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Formic acid</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">F0507 (HONEYWELL)</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Ammonium hydroxide</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">338818 (HONEYWELL)</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Acetonitrile HPLC grade</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">675415</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Isopropanol HPLC grade</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">675431</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:359px;">Water HPLC grade</td>
			<td style="width:424px;">Sigma-Aldrich</td>
			<td style="width:207px;">14263</td>
			<td></td>
		</tr>
	</tbody>
</table>

lerlic-ms/ms for in-depth characterization and quantification of glutamine and asparagine deamidation in shotgun proteomics

Protein deamidasyon Karakterizasyonu İnsan patoloji ve diğer biyokimyasal bağlamlarda bu protein dönüşüm sonrası modifikasyonu (PTM) rolü (ler) i ve potansiyeli deşifre zorunludur. Protein deamidasyon karakterizasyonu gerçekleştirmek için, yakın zamanda glutamin (Gln), ve asparajin (Asn) izoformu ayırabilen yeni bir uzun uzunlukta elektrostatik itme-hidrofilik interaksiyon kromatografisi-tandem kütle spektrometrisi (LERLIC-MS / MS) yöntemi geliştirdik son derece karmaşık biyolojik örnekler model bileşiklerinden deamidasyon ürünleri. LERLIC-MS / MS, bu nedenle, bir, Gln, deamidasyon izoform ayrılması ve ölçümü için, ilk tüfek proteomik stratejisi. Ayrıca burada açıklanan örnek işleme protokolü LERLIC-MS / MS ile karakterizasyonu sağlayan süksinimid ara stabilize olduğu, bir yenilik olarak, göstermektedir. Bu video makalede gösterildiği gibi LERLIC-MS / MS uygulanması halen bilinmeyen aydınlatmak için yardımcı olabilirProtein deamidasyon n moleküler diziler. Buna ek olarak, LERLIC-MS / MS belirgin biyolojik kökenden deamidasyonu kapsayan enzimatik reaksiyonların daha iyi anlaşılmasını sağlar.

Gln ve Asn kalıntısının deamidasyonu birçok kronik ve ölümcül hastalıklarda 14 içine dahil edilen bir dejeneratif protein modifikasyonu (DPM) olarak kabul edilir. PTM insan vücudunun ve benzer biyolojik arka 1, 15, antikorlar ve diğer moleküllerin yarı-ömrü ve parçalayıcı durumları tahmin edebilirsiniz gösterilmiştir. Protein deamidasyon önemi, aslında, dolayısıyla bu modifikasyon...

Watch this Scientific Journal Video about LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics at JoVE.com

LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics

Burada uzun uzunlukta elektrostatik itme-hidrofilik interaksiyon kromatografisi-tandem kütle spektrometresi (LERLIC-MS / MS) yöntemi bir adım adım protokol mevcut. Bu av tüfeği proteomik tarafından glutamin ve asparajin deamidasyon izoformlarının ilk kez ölçümü ve karakterizasyonu için sağlayan bir roman yöntemdir.

Av tüfeği Proteomics derinlemesine Karakterizasyonu için LERLIC-MS / MS ve Glutamin ölçümü ve Asparajin deamidasyonu

Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in ...

Research

JoVE Journal

Biochemistry

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Derin Proteom izobarik etiketleme, kapsamlı sıvı Kromatografi, kütle spektrometresi ve yazılım destekli miktar tarafından profil oluşturma

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) ...

Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques

X-ışını kristalografisi ve biyofiziksel teknikleri immünglobulin katlanmış glikoproteinlerin karakterizasyonu

Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of ...

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Hücre dışı Protein Mikroarray teknoloji yüksek işlem hacmi düşük benzeşme reseptör-Ligand etkileşimleri algılanması için

Secreted factors, membrane-tethered receptors, and their interacting partners are main regulators of cellular communication and initiation of signaling ...

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Peptit Zenginleştirme ve Kütle Spektrometresi ile Protein Ubiquitinasyon Sitelerinin Saptanması

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

SUMO-Binding Entities (SUBEs) as Tools for the Enrichment, Isolation, Identification, and Characterization of the SUMO Proteome in Liver Cancer

SUMO-Binding Entities SUBEs as Tools for the Enrichment, Isolation, Identification, and Characterization of the SUMO Proteome in Liver Cancer

Karaciğer Kanserinde SUMO Proteomunun Zenginleştirilmesi, İzolasyon, Tanımlama ve Karakterizasyonu Için Araçlar Olarak SUMO Bağlayıcı Varlıklar (SUBEs)

Post-translational modification is a key mechanism regulating protein homeostasis and function in eukaryotic cells. Among all ubiquitin-like proteins in ...

Quantification of Coenzyme A in Cells and Tissues

Hücre ve Dokularda Koenzim A'nın Sayısallaştırılması

Emerging research has revealed that the cellular coenzyme A (CoA) supply can become limiting with a detrimental impact on growth, metabolism and survival. ...

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis

Proteomik Tesis Gönderimi ve Müteakip Veri Analizi için TMT Örnek Hazırlama

Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view ...

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: Proteomikte Protein Ko-İfade Kümelemesi ve Ağ Analizi için Kolaylaştırılmış Bir Uygulama

With recent advances in mass spectrometry-based proteomics technologies, deep profiling of hundreds of proteomes has become increasingly feasible. ...

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Açık Kaynaklı Bir Laboratuvar Robotu Tarafından Otomatikleştirilmiş Av Tüfeği Proteomik Numune İşleme

Mass spectrometry-based shotgun proteomics experiments require multiple sample preparation steps, including enzymatic protein digestion and clean-up, ...

Shotgun Lipidomics of Rodent Tissues

Kemirgen Dokularının Av Tüfeği Lipidomikleri

Lipids play a vital role as essential components of all prokaryotic and eukaryotic cells. Constant technological improvements in mass spectrometry have ...