This research was supported by the Intramural Research Program of the NIH, National Institute of Allergy and Infectious Diseases.

The authors have nothing to disclose.

Absolute quantification de protéine est essentielle pour une gamme très diversifiée d&#39;applications biomédicales telles que la validation de biomarqueurs et la transduction du signal de modélisation de la voie. Récemment, la protéomique ciblées utilisant LC-SRM a bénéficié des améliorations apportées à de nombreuses technologies, y compris peptide préparation standard, HPLC, QQQ-MS et LC-SRM analyse des données. Par conséquent, il est devenu une alternative puissante aux immunoessais. Immunoessais pe...

Expériences protéomiques qui utilisent la spectrométrie de masse (MS) peuvent être conçus pour utiliser soit non ciblée (fusil de chasse) ou des méthodes ciblées. protéomique de découverte repose généralement sur ​​shotgun bottom-up MS, soit en utilisant un mode d&#39;acquisition traditionnelle dépendant des données, ou en utilisant l&#39;une des techniques de données indépendante récemment développés (par exemple, MS E, COULOIR) 1,2. Protéomique fusil de chasse est un outil puissant pour l&#39;identification à haut débit de peptide et la quantification relative, mais il est généralement impropre à la quantification absolue ou pour cibler les petits ensembles définis (~ RTE) de protéines. La méthode de MS le plus souvent utilisé pour la protéomique ciblées est sélectionné surveillance de réaction (SRM) en raison de sa haute sensibilité, la vitesse, et la gamme dynamique 3-5. Alternatives à SRM comprennent la surveillance de réaction parallèle, qui tire parti de haute résolution, MS balayage complet 6. SRM est habituellement effectuée en utilisant un rever nano-débitChromatographie sed phase liquide à haute performance (nano-RP-LC) couplée à un instrument ionisation nano-électrospray (nano-ESI) source d&#39;ions attaché à un spectromètre de masse triple quadripôle (QQQ-MS). Dans une expérience typique, les protéines de l&#39;échantillon sont digérés par protéolyse, et les peptides obtenus sont séparés par chromatographie, désorbés, et ionisés. Les ions précurseurs qui en résultent sont m / z filtré par le premier quadrupôle (Q1) et fragmentée dans le deuxième quadrupôle (Q2) par les collisions avec un gaz de collision. Les ions fragments résultant sont m / z-filtré dans le troisième quadrupôle (Q3) et quantifié par une dynode. Chaque paire de précurseur et ion de fragment est considéré comme une transition, et chaque transition est surveillée pour une période déterminée de temps (le temps de séjour; typiquement 2-50 msec). Pendant LC-SRM, les cycles QQQ-MS à travers une liste prédéfinie de transitions (le cycle de service est généralement ≤3 sec), et un chromatogramme de chaque transition est produite. Alternative stratégs pour la quantification des protéines utilisent généralement des dosages immunologiques tels que des transferts de points, des transferts de Western, ELISA, anticorps, puces inverse des puces à protéines de phase, immunoessais microfluidiques, ELISA numériques et immunoessais base microsphères-7. Les meilleurs dosages immunologiques peuvent être beaucoup plus sensibles que les LC-SRM, et le débit de l&#39;échantillon des immunodosages peuvent être significativement supérieur à celui de LC-SRM 5. Cependant, immunoessais en développement peuvent être coûteux et / ou de temps, et les dosages en résultent peuvent être vulnérables à la réactivité croisée et / ou des interférences, incompatible avec la cellule / lyse des tissus / méthodes d&#39;homogénéisation et / ou ne se prêtent pas au multiplexage 5,8. Certains de ces problèmes peuvent être résolus par couplage techniques anticorps-et MS. Par exemple, les protéines cibles peuvent être enrichies en utilisant une immunoprécipitation préalable à la protéolyse et LC-SRM 12/09. En variante, la technique d&#39;immunoprécipitation SISCAPA emploie ultérieure à la protéolyse à la leve peptidiquel 13,14. En plus des stratégies immunoenrichment, immunodéplétion de protéines de grande abondance peut être utilisé pour augmenter la sensibilité LC-SRM en réduisant les interférences par coélution analytes 15,16. Quantification des protéines MS peut être divisé en quantification relative et absolue, et aussi dans et stable sans marqueur isotopique étiquetage (par exemple, l&#39;étiquetage métabolique, l&#39;étiquetage des produits chimiques, et de protéines lourde marqué et peptidiques normes internes). Techniques sans étiquette peut être utile pour la quantification des protéines rapport, mais ne conviennent pas pour la quantification absolue précision. Par comparaison, les techniques de marquage ont réduit erreur associée à la préparation de l&#39;échantillon et la variance MS, et sont souvent utilisés pour la protéine par rapport quantification 17. Par exemple, les normes (Silap) des isotopes stables du protéome marqué préparés en utilisant une lignée cellulaire humaine cultivées permis quantification relative de biomarqueurs potentiels via LC-SRM de sérum humain 18. Absolue précise la quantification des protéines par MS exige que les normes internes purifiée, quantifiés, protéines ou peptides marqués par des isotopes être dopés-en échantillons biologiques avant MS. L&#39;incorporation des normes internes marqués d&#39;isotopes lourd dans un flux de travail LC-SRM permet une quantification absolue qui a été montré pour être hautement reproductible et transférable entre les laboratoires 16,19. Isotopes stables étiquetés normes internes pour la protéine absolue quantification par MS comprennent des normes peptidiques préparés en utilisant la synthèse en phase solide 20, composées de protéines normes peptidiques de la protéase clivable concaténés 21, et 22 normes protéines pleine longueur. Cible de modification covalente de protéines et de préparation de l&#39;échantillon incomplet (c.-à-lyse incomplète de l&#39;échantillon et l&#39;homogénéisation, et incomplète solubilisation de la protéine, dénaturation, alkylation, et la protéolyse) peut nuire à une quantification précise. P internerotein normes sont les moins susceptibles d&#39;être affectés par la plupart de ces problèmes potentiels, mais ils sont généralement les plus difficiles à préparer. Une alternative consiste à analyser chaque protéine cible à l&#39;aide de multiples normes de peptides internes qui sont conçues pour inclure des résidus flanquant natifs amino et du carboxy terminal. Indépendamment du type de l&#39;étalon interne est utilisé, il doit être enrichi dans les échantillons-biologiques au plus tôt un point lors de la préparation de l&#39;échantillon que possible. En outre, les techniques de préparation d&#39;échantillons multiples (par exemple, différentes conditions de dénaturation) doivent être testés. L&#39;utilisation de plusieurs techniques expérimentales orthogonales (cross-validation expérimentale) est une stratégie viable pour surmonter les plus quantification potentiel défis 23-25. LC-SRM quantification de protéines est une technique très souple qui a été utilisée dans une grande variété d&#39;applications. Notamment, il a été utilisé pour étudier peptides et de protéines à l&#39;intérieur de biomarqueurséchantillons cliniques tels que le sérum, les biopsies de base, et des aspirations à l&#39;aiguille fine 5. LC-SRM a également été utilisée pour mesurer la stoechiométrie des complexes protéiques 5,26, pour détecter des neurotoxines botuliniques 27, pour quantifier la dynamique de phosphorylation de protéine à l&#39;intérieur des voies de signalisation 5, et à quantifier des changements dans la conformation des protéines 28. Notre laboratoire utilise LC-SRM pour quantifier les protéines de signalisation qui interviennent dans le chimiotactisme des macrophages pour soutenir le développement de simulations de la voie de la chimiotaxie. Le schéma global du protocole (Figure 1) commence avec le classement des peptides cibles provisoires. Par la suite, les normes peptidiques externes bruts sont synthétisés et utilisés pour développer des tests LC-SRM pour des analyses qualitatives des échantillons biologiques. Si le peptide cible biologique de l&#39;échantillon dérivé est détectée, les normes lourds marqué purifiés peptidiques internes sont préparés pour quantitative LC-SRM. Ce protocole peut être utilisé pour acquantifier curately protéines à partir d&#39;une grande variété d&#39;échantillons biologiques, et d&#39;appuyer les enquêtes d&#39;une grande variété de protéines cibles.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Acetonitrile (ACN), LC-MS grade</td>
			<td>Fisher</td>
			<td>A955-1</td>
			<td></td>
		</tr>
		<tr>
			<td>BCA (bicinchoninic acid) protein assay kit</td>
			<td>Fisher</td>
			<td>23235</td>
			<td></td>
		</tr>
		<tr>
			<td>Beads for bead beating, zirconia-silica, 0.1mm</td>
			<td>BioSpec Products</td>
			<td>11079101z</td>
			<td></td>
		</tr>
		<tr>
			<td>Bestatin hydrochloride</td>
			<td>Sigma</td>
			<td>B8385-10MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture DMEM (with glucose, without L-glutamine)</td>
			<td>Lonza</td>
			<td>12-614F</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture EDTA, 500mM, pH8</td>
			<td>Gibco</td>
			<td>15575</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture fetal bovine serum (FBS)</td>
			<td>Atlanta Biologicals</td>
			<td>S11550</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture L-glutamine</td>
			<td>Sigma</td>
			<td>G8540-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture phosphate buffered saline (PBS) pH 7.4</td>
			<td>Gibco</td>
			<td>10010-049</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture Trypan Blue viability stain, 0.4% w/v</td>
			<td>Lonza</td>
			<td>17-942E</td>
			<td></td>
		</tr>
		<tr>
			<td>Cellometer Auto T4 cell counter</td>
			<td>Nexcelom Bioscience</td>
			<td>Cellometer Auto T4</td>
			<td></td>
		</tr>
		<tr>
			<td>Cellometer Auto T4 disposable counting chambers</td>
			<td>Nexcelom Bioscience</td>
			<td>CHT4-SD100-014</td>
			<td></td>
		</tr>
		<tr>
			<td>Dithiothreitol (DTT)</td>
			<td>Sigma</td>
			<td>D5545-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>Formic acid, LC-MS grade, ampules</td>
			<td>Fisher</td>
			<td>A117-10X1AMP</td>
			<td></td>
		</tr>
		<tr>
			<td>Hemocytometer, Neubauer-improved, 0.1mm deep</td>
			<td>Marienfeld-Superior</td>
			<td>0640030</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES, 1M, pH 7.2</td>
			<td>Mediatech</td>
			<td>25-060-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid, 37% w/w</td>
			<td>VWR</td>
			<td>BDH3028-2.5LG</td>
			<td></td>
		</tr>
		<tr>
			<td>Iodoacetamide</td>
			<td>Sigma</td>
			<td>I1149-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>Laser Based Micropipette Puller</td>
			<td>Sutter Instrument Co.</td>
			<td>P-2000</td>
			<td></td>
		</tr>
		<tr>
			<td>LC Magic C18AQ, 5&#181;m, 200&#8491;, loose media</td>
			<td>Michrom Bioresources</td>
			<td>PM5/61200/00</td>
			<td></td>
		</tr>
		<tr>
			<td>LC Halo ES-C18, 2.7&#181;m, 160&#8491;, loose media</td>
			<td>Michrom Bioresources</td>
			<td>PM3/93100/00</td>
			<td></td>
		</tr>
		<tr>
			<td>LC coated silica capillary, 50&#181;m id</td>
			<td>Polymicro Technologies</td>
			<td>1068150017</td>
			<td></td>
		</tr>
		<tr>
			<td>LC vial, autosampler, 12x32mm polypropylene</td>
			<td>SUN SRI</td>
			<td>200-268</td>
			<td></td>
		</tr>
		<tr>
			<td>LC vial screw cap, autosampler, pre-slit PTFE/silicone</td>
			<td>SUN SRI</td>
			<td>500-061</td>
			<td></td>
		</tr>
		<tr>
			<td>Luciferase, from Photinus pyralis</td>
			<td>Sigma</td>
			<td>L9506-1MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Pepstatin A</td>
			<td>EMD Millipore</td>
			<td>516481-25MG</td>
			<td></td>
		</tr>
		<tr>
			<td>pH strips colorpHast (pH 0.0-6.0)</td>
			<td>EMD Chemicals</td>
			<td>9586-1</td>
			<td></td>
		</tr>
		<tr>
			<td>PhosStop phosphatase inhibitor cocktail</td>
			<td>Roche</td>
			<td>04906837001</td>
			<td></td>
		</tr>
		<tr>
			<td>RapiGest SF</td>
			<td>Waters</td>
			<td>186001861</td>
			<td></td>
		</tr>
		<tr>
			<td>Sep-Pak SPE, C18 1ml 100mg cartridge</td>
			<td>Waters</td>
			<td>WAT023590</td>
			<td></td>
		</tr>
		<tr>
			<td>Sep-Pak SPE, extraction manifold, 20 position</td>
			<td>Waters</td>
			<td>WAT200609</td>
			<td></td>
		</tr>
		<tr>
			<td>Sep-Pak SPE, flat-surfaced rubber bulb</td>
			<td>Fisher</td>
			<td>03-448-25</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydroxide (NaOH)</td>
			<td>Fisher</td>
			<td>S318-500</td>
			<td></td>
		</tr>
		<tr>
			<td>SpeedVac vacuum concentrator</td>
			<td>Fisher</td>
			<td>SPD111V</td>
			<td></td>
		</tr>
		<tr>
			<td>Trifluoroacetic acid (TFA), LC-MS grade</td>
			<td>Fisher</td>
			<td>A116-50</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin, sequencing grade, modified</td>
			<td>Promega</td>
			<td>V5113</td>
			<td></td>
		</tr>
		<tr>
			<td>Tube decapper for Micronic tubes</td>
			<td>USA Scientific</td>
			<td>1765-4000</td>
			<td></td>
		</tr>
		<tr>
			<td>Tubes, 2ml microcentrifuge, o-ring screw-cap, sterile</td>
			<td>Sarstedt</td>
			<td>72.694.006</td>
			<td></td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Sigma</td>
			<td>U0631-500g</td>
			<td></td>
		</tr>
		<tr>
			<td>Water, LC-MS grade</td>
			<td>Fisher</td>
			<td>W6-1</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

Le développement de modèles informatiques de prévision de voies de signalisation est l&#39;un des objectifs fondamentaux de la biologie des systèmes 53. Malheureusement, même pour les voies qui ont été largement étudiés et ont une haute signification clinique de signalisation, il est encore généralement pas possible de prédire quantitativement le comportement voie en réponse à des perturbations (par exemple, cela est vrai pour le / ERK MAPK 54). Récemment, une enquête emplo...

Watch this Scientific Journal Video about Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification at JoVE.com

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

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.

Selected Reaction Monitoring spectrométrie de masse pour Absolute quantification des protéines

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

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16.9K vues.  National Institutes of Health. 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.

Vidéo: Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

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).

Préparation des échantillons MALDI: la méthode de la couche ultra mince

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

Recherche

Biologie

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.

L&#39;analyse des complexes protéiques par spectrométrie de masse Grande structurels

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

T-wave Ion Mobility-mass Spectrometry: Basic Experimental Procedures for Protein Complex Analysis

Ion mobility (IM) is a method that measures the time taken for an ion to travel through a pressurized cell under the influence of a weak electric field. The speed by which the ions traverse the drift region depends on their size: large ions will experience a greater number of collisions with the background inert gas (usually N2) and thus travel more slowly through the IM device than those ions that comprise a smaller cross-section. In general, the time it takes for the ions to migrate though the dense gas phase separates them, according to their collision cross-section (&Omega;). 
Recently, IM spectrometry was coupled with mass spectrometry and a traveling-wave (T-wave) Synapt ion mobility mass spectrometer (IM-MS) was released. Integrating mass spectrometry with ion mobility enables an extra dimension of sample separation and definition, yielding a three-dimensional spectrum (mass to charge, intensity, and drift time). This separation technique allows the spectral overlap to decrease, and enables resolution of heterogeneous complexes with very similar mass, or mass-to-charge ratios, but different drift times. Moreover, the drift time measurements provide an important layer of structural information, as &Omega; is related to the overall shape and topology of the ion. The correlation between the measured drift time values and &Omega; is calculated using a calibration curve generated from calibrant proteins with defined cross-sections1.
The power of the IM-MS approach lies in its ability to define the subunit packing and overall shape of protein assemblies at micromolar concentrations, and near-physiological conditions1. Several recent IM studies of both individual proteins2,3 and non-covalent protein complexes4-9, successfully demonstrated that protein quaternary structure is maintained in the gas phase, and highlighted the potential of this approach in the study of protein assemblies of unknown geometry. Here, we provide a detailed description of IMS-MS analysis of protein complexes using the Synapt (Quadrupole-Ion Mobility-Time-of-Flight) HDMS instrument (Waters Ltd; the only commercial IM-MS instrument currently available)10. We describe the basic optimization steps, the calibration of collision cross-sections, and methods for data processing and interpretation. The final step of the protocol discusses methods for calculating theoretical &Omega; values. Overall, the protocol does not attempt to cover every aspect of IM-MS characterization of protein assemblies; rather, its goal is to introduce the practical aspects of the method to new researchers in the field.

Ion mobility-mass spectrometry is an emerging gas-phase technology that separates ions, based on their collision cross-section and mass. The method provides three-dimensional information on the overall topology and shape of protein complexes. Here, we outline a basic procedure for instrument setting and optimization, calibration of drift times, and data interpretation.

L&#39;onde T de mobilité ionique et spectrométrie de masse: Procédures de base expérimentale pour l&#39;analyse de protéines complexes

Ion mobility (IM) is a method that measures the time taken for an ion to travel through a pressurized cell under the influence of a weak electric field. ...

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.

La quantification des protéines à l&#39;aide d&#39;enrichissement d&#39;immunoaffinité peptide couplé à la spectrométrie de masse

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

Profiling Thiol Redox Proteome Using Isotope Tagging Mass Spectrometry

Pseudomonas syringae pv. tomato strain DC3000 not only causes bacterial speck disease in Solanum lycopersicum but also on Brassica species, as well as on Arabidopsis thaliana, a genetically tractable host plant1,2. The accumulation of reactive oxygen species (ROS) in cotyledons inoculated with DC3000 indicates a role of ROS in modulating necrotic cell death during bacterial speck disease of tomato3. Hydrogen peroxide, a component of ROS, is produced after inoculation of tomato plants with Pseudomonas3. Hydrogen peroxide can be detected using a histochemical stain 3'-3' diaminobenzidine (DAB)4. DAB staining reacts with hydrogen peroxide to produce a brown stain on the leaf tissue4. ROS has a regulatory role of the cellular redox environment, which can change the redox status of certain proteins5. Cysteine is an important amino acid sensitive to redox changes. Under mild oxidation, reversible oxidation of cysteine sulfhydryl groups serves as redox sensors and signal transducers that regulate a variety of physiological processes6,7. Tandem mass tag (TMT) reagents enable concurrent identification and multiplexed quantitation of proteins in different samples using tandem mass spectrometry8,9. The cysteine-reactive TMT (cysTMT) reagents enable selective labeling and relative quantitation of cysteine-containing peptides from up to six biological samples. Each isobaric cysTMT tag has the same nominal parent mass and is composed of a sulfhydryl-reactive group, a MS-neutral spacer arm and an MS/MS reporter10. After labeling, the samples were subject to protease digestion. The cysteine-labeled peptides were enriched using a resin containing anti-TMT antibody. During MS/MS analysis, a series of reporter ions (i.e., 126-131 Da) emerge in the low mass region, providing information on relative quantitation. The workflow is effective for reducing sample complexity, improving dynamic range and studying cysteine modifications. Here we present redox proteomic analysis of the Pst DC3000 treated tomato (Rio Grande) leaves using cysTMT technology. This high-throughput method has the potential to be applied to studying other redox-regulated physiological processes.

Reactive oxygen species level is elevated when cells encounter stress conditions. Here we show the example of 3'-3' diaminobenzidine staining as well as cysTMT labeling and mass spectrometry to profile the redox proteome in Pseudomonas syringae treated tomato leaves.

Profilage thiol redox du protéome par spectrométrie de masse isotopique de l&#39;étiquetage

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

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.

Identification des complexes protéiques dans<em&gt; Escherichia coli</em&gt; En utilisant séquentielle Purification par affinité peptide en combinaison avec la spectrométrie de masse en tandem

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

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in current research and a plethora of methods for their investigation is available1. Protein-protein interactions often are highly dynamic and may depend on subcellular localization, post-translational modifications and the local protein environment2. Therefore, they should be investigated in their natural environment, for which co-immunoprecipitation approaches are the method of choice3. Co-precipitated interaction partners are identified either by immunoblotting in a targeted approach, or by mass spectrometry (LC-MS/MS) in an untargeted way. The latter strategy often is adversely affected by a large number of false positive discoveries, mainly derived from the high sensitivity of modern mass spectrometers that confidently detect traces of unspecifically precipitating proteins. A recent approach to overcome this problem is based on the idea that reduced amounts of specific interaction partners will co-precipitate with a given target protein whose cellular concentration is reduced by RNAi, while the amounts of unspecifically precipitating proteins should be unaffected. This approach, termed QUICK for QUantitative Immunoprecipitation Combined with Knockdown4, employs Stable Isotope Labeling of Amino acids in Cell culture (SILAC)5 and MS to quantify the amounts of proteins immunoprecipitated from wild-type and knock-down strains. Proteins found in a 1:1 ratio can be considered as contaminants, those enriched in precipitates from the wild type as specific interaction partners of the target protein. Although innovative, QUICK bears some limitations: first, SILAC is cost-intensive and limited to organisms that ideally are auxotrophic for arginine and/or lysine. Moreover, when heavy arginine is fed, arginine-to-proline interconversion results in additional mass shifts for each proline in a peptide and slightly dilutes heavy with light arginine, which makes quantification more tedious and less accurate5,6. Second, QUICK requires that antibodies are titrated such that they do not become saturated with target protein in extracts from knock-down mutants.
Here we introduce a modified QUICK protocol which overcomes the abovementioned limitations of QUICK by replacing SILAC for 15N metabolic labeling and by replacing RNAi-mediated knock-down for affinity modulation of protein-protein interactions. We demonstrate the applicability of this protocol using the unicellular green alga Chlamydomonas reinhardtii as model organism and the chloroplast HSP70B chaperone as target protein7 (Figure 1). HSP70s are known to interact with specific co-chaperones and substrates only in the ADP state8. We exploit this property as a means to verify the specific interaction of HSP70B with its nucleotide exchange factor CGE19.

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on 15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.

Un protocole pour l&#39;identification des interactions protéine-protéine Basé sur<sup&gt; 15</sup&gt; N marquage métabolique, immunoprécipitation, la spectrométrie de masse quantitative et d&#39;affinité de modulation

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in ...

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must be maintained to avoid deleterious consequences 1. External or internal factors that disrupt this balance can lead to protein aggregation, toxicity and cell death. In humans this is a major contributing factor to the symptoms associated with neurodegenerative disorders such as Huntington's, Parkinson's, and Alzheimer's diseases 10. It is therefore essential that the proteins involved in maintenance of proteostasis be identified in order to develop treatments for these debilitating diseases. This article describes techniques for monitoring in vivo protein folding at near-real time resolution using the model protein firefly luciferase fused to green fluorescent protein (FFL-GFP). FFL-GFP is a unique model chimeric protein as the FFL moiety is extremely sensitive to stress-induced misfolding and aggregation, which inactivates the enzyme 12. Luciferase activity is monitored using an enzymatic assay, and the GFP moiety provides a method of visualizing soluble or aggregated FFL using automated microscopy. These coupled methods incorporate two parallel and technically independent approaches to analyze both refolding and functional reactivation of an enzyme after stress. Activity recovery can be directly correlated with kinetics of disaggregation and re-solubilization to better understand how protein quality control factors such as protein chaperones collaborate to perform these functions. In addition, gene deletions or mutations can be used to test contributions of specific proteins or protein subunits to this process. In this article we examine the contributions of the protein disaggregase Hsp104 13, known to partner with the Hsp40/70/nucleotide exchange factor (NEF) refolding system 5, to protein refolding to validate this approach.

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

This article describes the use of a firefly luciferase-GFP fusion protein to investigate in vivo protein folding in Saccharomyces cerevisiae. Using this reagent, refolding of a model heat-denatured protein can be monitored simultaneously by fluorescence microscopy and an enzymatic assay to probe the roles of proteostasis network components in protein quality control.

Les analyses couplées pour la surveillance protéines repliement<em&gt; Saccharomyces cerevisiae</em

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must ...

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis

The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins that provides biophysical and biochemical cues that are major regulators of cell proliferation, survival, migration, etc. The ECM plays important roles in development and in diverse pathologies including cardio-vascular and musculo-skeletal diseases, fibrosis, and cancer. Thus, characterizing the composition of ECMs of normal and diseased tissues could lead to the identification of novel prognostic and diagnostic biomarkers and potential novel therapeutic targets. However, the very nature of ECM proteins (large in size, cross-linked and covalently bound, heavily glycosylated) has rendered biochemical analyses of ECMs challenging. To overcome this challenge, we developed a method to enrich ECMs from fresh or frozen tissues and tumors that takes advantage of the insolubility of ECM proteins. We describe here in detail the decellularization procedure that consists of sequential incubations in buffers of different pH and salt and detergent concentrations and that results in 1) the extraction of intracellular (cytosolic, nuclear, membrane and cytoskeletal) proteins and 2) the enrichment of ECM proteins. We then describe how to deglycosylate and digest ECM-enriched protein preparations into peptides for subsequent analysis by mass spectrometry.

This protocol describes a procedure for enriching ECM proteins from tissues or tumors and deglycosylating and digesting the ECM-enriched preparations into peptides to analyze their protein composition by mass spectrometry.

Enrichissement de matrice extracellulaire de protéines à partir de tissus et la digestion en peptides pour l&#39;analyse de spectrométrie de masse

The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins that provides biophysical and biochemical cues that are major regulators of ...

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is therefore fundamental for the understanding of cellular processes. However, many protein complexes are dynamic assemblies and are not accessible by conventional structural techniques. Mass spectrometry contributes to the structural investigation of these assemblies, and particularly the combination of various mass spectrometric techniques delivers valuable insights into their structural arrangement.
In this article, we describe the application and combination of two complementary mass spectrometric techniques, namely chemical cross-linking coupled with mass spectrometry and native mass spectrometry. Chemical cross-linking involves the covalent linkage of amino acids in close proximity by using chemical reagents. After digestion with proteases, cross-linked di-peptides are identified by mass spectrometry and protein interactions sites are uncovered. Native mass spectrometry on the other hand is the analysis of intact protein assemblies in the gas phase of a mass spectrometer. It reveals protein stoichiometries as well as protein and ligand interactions. Both techniques therefore deliver complementary information on the structure of protein-ligand assemblies and their combination proved powerful in previous studies.

The architecture of protein complexes is essential for their function. Combining various mass spectrometric techniques proved powerful to study their assembly. We provide protocols for chemical cross-linking and native mass spectrometry and show how these complementary techniques help to elucidate the architecture of multi-subunit protein assemblies.

Combinant la réticulation chimique et spectrométrie de masse des Complexes de protéine intacte pour étudier l’Architecture des assemblées de plusieurs sous-unités protéiques

Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is ...