增强组织样品使用组合前体同位素标记和标记等压的复用（cPILOT）
Summary
合并前体同位素标记和等压标记（cPILOT）是定量蛋白质组学战略，增强同量异位标记的样品复用能力。这个协议描述cPILOT的对组织从阿尔茨海默氏病小鼠模型中和野生型对照的应用。
Abstract
有日益增加的需求，分析了大量生物标本用于疾病的理解和生物标志物发现。定量蛋白质组学策略，允许多个样品的同时测量已经普及，大大降低实验成本和时间。我们实验室开发了一种称为合并的前体同位素标记和同量异位素标记（cPILOT）技术，这增强了传统的同位素标记或同量异位的标记方法中的样品的复用。全球cPILOT可以应用于从细胞，组织，体液，或整个生物体始发样品和给出了关于在不同的样品条件相对蛋白质丰度的信息。 cPILOT使用低pH值的缓冲液条件的工作方式是1），以选择性地dimethylate肽的N-末端，并使用高pH缓冲液条件2）标记的赖氨酸残基的伯胺与市售的同量异序的试剂（参见材料/试剂的表 ）。度可用的样本复用取决于所使用的前体的标签的数量和同量异序标记试剂。这里，我们提出使用轻和重的二甲基六-PLEX等压试剂组合以分析来自小鼠组织的12个样品在一次分析中一个12-PLEX分析。增强的复用是用于减少实验时间和成本，并且更重要的是，允许在许多样品条件（生物学重复，疾病阶段，药物治疗，基因型，或纵向的时间点）相比具有较少实验偏差和误差有帮助的。在这项工作中，全球cPILOT方法来分析大脑，心脏和跨越生物学重复肝组织从阿尔茨海默氏症小鼠模型和野生型对照。全球cPILOT可应用于研究其他生物过程和适于增加样本复用大于20个样本。
Introduction
蛋白质组学通常涉及用于更好地了解疾病过程许多样品，酶动力学，翻译后修饰，响应于环境刺激，响应于治疗性治疗，生物标志物发现，或药物机制的分析。可以使用定量方法测量通过样品中的蛋白质水平的相对差异，并且可以是无标记的，或涉及同位素标记（代谢，化学或酶）。稳定同位素标记方法已越来越流行，因为它们允许多个样品同时分析，并且适用于从不同的细胞，组织，体液，或整个生物体的样本。同位素标记方法1，2，3，4，5，6，7增加实验的吞吐量，同时减少了采集时间，成本和实验误差。这些方法使用前体的质谱测量从肽峰的蛋白质的相对丰度。相反，同量异序标记试剂8，9，10生成在MS / MS或MS检测任一报告物离子3 11光谱和这些峰被用于对蛋白的相对丰度的报告。
当前状态的最先进的蛋白质组学复用或者是一个10-PLEX 12或12-PLEX同量异位的标签的分析13。增强样品复用（ 即，> 10个样品）的方法已被开发出由我们的实验室组织14，15，16，17，和由他人细胞18的分析</SUP>，19，20，组织21，或靶向肽22。我们开发了所谓的组合的前体同位素标记与同量异序标记（cPILOT）增强的多路复用技术。全球cPILOT是用于获取有关在不同的样品条件（≥12）14的所有蛋白质的相对浓度信息是有用的。 图1示出了一般cPILOT工作流程。胰蛋白酶或Lys-C肽在使用低pH值2的N末端与二甲基化，并在使用高pH 6-PLEX试剂赖氨酸残基选择性地标记。这种策略双打可以与等压试剂，这有助于降低成本实验，另外分析样品的数量，减少实验步骤和时间。
cPILOT是灵活的，我们已经开发了其他的方法来研究氧化翻译后作案fications，包括3-硝基酪氨酸修饰的蛋白质14和与S-亚硝基化（oxcyscPILOT）23含半胱氨酸的肽。我们还开发了一种氨基酸选择性的方法，半胱氨酸cPILOT（cyscPILOT）17。 MS 3获取具有顶离子11或选择性-Y 1 -离子方法15可以帮助减少报告物离子干扰，提高cPILOT的定量精度。在采集方法中使用的MS 3的要求与轨道阱质量分析仪高分辨率仪器虽然低分辨率离子阱仪器也可工作24。
此前，cPILOT已被用于从阿尔茨海默氏症小鼠模型研究肝蛋白16。在这里，我们将介绍如何使用大脑，心脏和肝匀浆研究periphe的角色来执行全球cPILOT分析RY阿尔茨海默病。本实验采用了生物复制。由于cPILOT的多功能性，有兴趣的用户可以使用该技术来研究其他组织为一系列的生物学问题和系统。
Protocol
伦理声明：小鼠从一个独立的，非盈利性的生物医学研究机构购买和放置在实验室动物资源在匹兹堡大学的分部。所有动物方案都得到了机构动物护理和使用委员会在美国匹兹堡大学获得批准。 1.蛋白提取和多肽的产生化学标记 从组织，细胞，或体液中提取的蛋白质。 与使用机械均化器8M尿素（500μL）匀化60-90毫克在磷酸盐缓冲盐水组织（ 例如<…
Representative Results
cPILOT使用基于胺的化学化学键在N-末端和赖氨酸残基的肽标签和增强样品复用能力。 图2示出了从从阿尔茨海默氏病小鼠模型中和野生型对照脑，心脏和肝组织中的12-plex的cPILOT分析所获得的代表性MS数据。如表1所示，对于阿尔茨海默氏病和野生型小鼠的两个生物学重复被包括在这12个复合体的分析。 图2A示出了一个双电荷峰值对由指?…
Discussion
cPILOT允许多于12个独特的样品的同时测量。为了确保在肽的两个N-末端和赖氨酸残基的成功标记，就必须有正确的pH为每个组反应和首先执行二甲基化反应的肽标记。在N-末端选择性二甲基化是通过在〜2.5的pH（±0.2）中进行。这是通过利用氨基基团的pKa的对赖氨酸和差的N-末端来实现。在pH 2.5，赖氨酸是不活动的（PKA〜10.5）;然而，如果pH在温和的酸性（ 即 pH为5-7）或碱性的，这两个N端和赖?…
Declarações
The authors have nothing to disclose.
Acknowledgements
作者承认匹兹堡启动经费的大学和美国国立卫生研究院，NIGMS R01补助（GM 117191-01）到RASR。
Materials
| Water – MS Grade | Fisher Scientific | W6-4 | 4 L quantity is not necessary |
| Acetonitrile – MS Grade | Fisher Scientific | A955-4 | 4 L quantity is not necessary |
| Acetic Acid | J.T. Baker | 9508-01 | |
| Ammonium hydroxide solution (28 – 30%) | Sigma Aldrich | 320145-500ML | |
| Ammonium formate | Acros Organics | 208-753-9 | |
| Formic Acid | Fluka Analytical | 94318-250ML-F | |
| BCA protein assay kit | Pierce Thermo Fisher Scientific | 23227 | |
| Urea | Biorad | 161-0731 | |
| Tris | Biorad | 161-0716 | |
| Dithiothreiotol (DTT) | Fisher Scientific | BP172-5 | |
| Iodoacetamide (IAM) | Acros Organics | 144-48-9 | |
| L-Cysteine | Sigma Aldrich, Chemistry | 168149-25G | |
| L-1-tosylamido-2 phenylethyl cholormethyl ketone (TPCK)-treated Trypsin from bovine pancreas | Sigma Aldrich, Life Science | T1426-100MG | |
| Formaldehyde (CH2O) solution; 36.5 – 38% in H2O | Sigma Aldrich, Life Science | F8775-25ML | |
| Formaldehyde (13CD2O) solution; 20 wt % in D2O, 98 atom % D, 99 atom % 13 C | Sigma Aldrich, Chemistry | 596388-1G | |
| Sodium Cyanoborohydride; reagent grade, 95% | Sigma Aldrich | 156159-10G | |
| Sodium Cyanoborodeuteride; 96 atom % D, 98% CP | Sigma Aldrich, Chemistry | 190020-1G | |
| Strong Cation Exchange (SCX) spin tips sample prep kit | Protea BioSciences | SP-155-24kit | |
| Triethyl ammonium bicarbonate (TEAB) buffer | Sigma Aldrich, Life Science | T7408-100ML | |
| Isobaric Tagging Kit (TMT 6 plex) – 6 reactions (1 x 0.8 mg) | Thermo Fisher Scientific | 90061 | |
| Hydroxylamine hydrochloride | Sigma Aldrich, Chemistry | 255580-100G | |
| Standard vortex mixer | Fisher Scientific | 2215365 | any mixer can be used |
| Oasis HLB 1cc (10 mg) extraction cartridges | Waters | 186000383 | These are C18 cartridges |
| Visiprep SPE vacuum manifold, DL (disposable liner), 24 port model | Sigma Aldrich | 57265 | A 12 port model is also sufficient |
| Speed-vac | Thermo Scientific | SPD1010 | any brand of speed vac is sufficient |
| Water bath chamber | Thermo Scientific | 2825/2826 | Any brand of a water bath chamber with controlled temperatures is sufficient. |
| Mechanical Homogenizer (i.e. FastPrep-24 5G) | MP Biomedicals | 116005500 | |
| Eksigent Nano LC – Ultra 2D with Nano LC AS-2 autosampler | Sciex | – | This model is no longer available. Any nano LC with an autosampler is sufficient. |
| LTQ Orbitrap Velos Mass Spectrometer | Thermo Scientific | – | This model is no longer available. Other high resolution instruments (e.g. Orbitrap Elite, Orbitrap Fusion, or Orbitrap Fusion Lumos) can be used. |
| Protein software (e.g. Proteome Discoverer) | Thermo Scientific | IQLAAEGABSFAKJMAUH | |
| Analytical balance | Mettler Toledo | AL54 | |
| Stir plate | VWR | 12365-382 | Any brand of stir plates are sufficient. |
| pH meter (Tris compatiable) | Fisher Scientific (Accumet) | 13-620-183 | Any brand of a ph meter is sufficient |
| pH 10 buffer | Fisher Scientific | 06-664-261 | Any brand of ph buffer 10 is sufficient |
| pH 7 buffer | Fisher Scientific | 06-664-260 | Any brand ph buffer 7 is sufficient |
| 1.5 mL eppendorf tubes, 500pk | Fisher Scientific | 05-408-129 | Any brand of 1.5 mL eppendorf tubes are sufficient |
| 0.6 mL eppendorf tubes, 500pk | Fisher Scientific | 04-408-120 | Any brand of 0.6 mL eppendorf tubes are sufficient |
| 0.65µm Ultrafree MC DV centrifugal filter units | EMD Millipore | UFC30DV00 | |
| 2 mL microcentrifuge tubes, 72 units | Thermo Scientific | 69720 | |
| C18 packing material (5 µm, 100 Å) | Bruker | PM5/61100/000 | This item is no longer available from Bruker. Alternative packing material with listed specifications will be sufficient. |
| C18 packing material (5 µm, 200 Å) | Bruker | PM5/61200/000 | This item is no longer available from Bruker. Alternative packing material with listed specifications will be sufficient. |
Referências
- Ong, S. -. E., et al. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics. Mol Cell Proteomics. 1 (5), 376-386 (2002).
- Koehler, C. J., Arntzen, M. &. #. 2. 1. 6. ;., de Souza, G. A., Thiede, B. An Approach for Triplex-Isobaric Peptide Termini Labeling (Triplex-IPTL). Anal. Chem. 85 (4), 2478-2485 (2013).
- Langen, H. F., Evers, M., Wipf, S., Berndt, B., P, . From Genome to Proteome 3rd Siena 2D Electrophoresis Meeting. , (1998).
- Yao, X., Freas, A., Ramirez, J., Demirev, P. A., Fenselau, C. Proteolytic 18O Labeling for Comparative Proteomics: Model Studies with Two Serotypes of Adenovirus. Anal. Chem. 73 (13), 2836-2842 (2001).
- Reynolds, K. J., Yao, X., Fenselau, C. Proteolytic 18O Labeling for Comparative Proteomics: Evaluation of Endoprotease Glu-C as the Catalytic Agent. J. Proteome Res. 1 (1), 27-33 (2002).
- Gygi, S. P., et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotech. 17 (10), 994-999 (1999).
- Schmidt, A., Kellermann, J., Lottspeich, F. A novel strategy for quantitative proteomics using isotope-coded protein labels. PROTEOMICS. 5 (1), 4-15 (2005).
- Thompson, A., et al. Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS. Anal. Chem. 75 (8), 1895-1904 (2003).
- Ross, P. L., et al. Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents. Mol Cell Proteomics. 3 (12), 1154-1169 (2004).
- Xiang, F., Ye, H., Chen, R., Fu, Q., Li, L. N,N-Dimethyl Leucines as Novel Isobaric Tandem Mass Tags for Quantitative Proteomics and Peptidomics. Anal. Chem. 82 (7), 2817-2825 (2010).
- Ting, L., Rad, R., Gygi, S. P., Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Meth. 8 (11), 937-940 (2011).
- McAlister, G. C., et al. Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses. Anal. Chem. 84 (17), 7469-7478 (2012).
- Frost, D. C., Greer, T., Li, L. High-Resolution Enabled 12-Plex DiLeu Isobaric Tags for Quantitative Proteomics. Anal. Chem. 87 (3), 1646-1654 (2015).
- Robinson, R. A. S., Evans, A. R. Enhanced Sample Multiplexing for Nitrotyrosine-Modified Proteins Using Combined Precursor Isotopic Labeling and Isobaric Tagging. Anal. Chem. 84 (11), 4677-4686 (2012).
- Evans, A. R., Robinson, R. A. S. Global combined precursor isotopic labeling and isobaric tagging (cPILOT) approach with selective MS(3) acquisition. Proteomics. 13 (22), 3267-3272 (2013).
- Evans, A. R., Gu, L., Guerrero, R., Robinson, R. A. S. Global cPILOT analysis of the APP/PS-1 mouse liver proteome. PROTEOMICS – Clin Appl. 9 (9-10), 872-884 (2015).
- Gu, L., Evans, A. R., Robinson, R. A. S. Sample Multiplexing with Cysteine-Selective Approaches: cysDML and cPILOT. J. Am. Soc Mass Spectrom. 26 (4), 615-630 (2015).
- Dephoure, N., Gygi, S. P. Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast. Sci Signal. 5 (217), rs2 (2012).
- Hebert, A. S., et al. Neutron-encoded mass signatures for multiplexed proteome quantification. Nat Meth. 10 (4), 332-334 (2013).
- Merrill, A. E., et al. NeuCode Labels for Relative Protein Quantification. Mol Cell Proteomics. 13 (9), 2503-2512 (2014).
- Braun, C. R., et al. Generation of Multiple Reporter Ions from a Single Isobaric Reagent Increases Multiplexing Capacity for Quantitative Proteomics. Analytical Chemistry. 87 (19), 9855-9863 (2015).
- Everley, R. A., Kunz, R. C., McAllister, F. E., Gygi, S. P. Increasing Throughput in Targeted Proteomics Assays: 54-Plex Quantitation in a Single Mass Spectrometry Run. Anal. Chem. 85 (11), 5340-5346 (2013).
- Gu, L., Robinson, R. A. S. High-throughput endogenous measurement of S-nitrosylation in Alzheimer’s disease using oxidized cysteine-selective cPILOT. Analyst. 141 (12), 3904-3915 (2016).
- Cao, Z., Evans, A. R., Robinson, R. A. S. MS3-based quantitative proteomics using pulsed-Q dissociation. Rapid Commun Mass Spectrom. 29 (11), 1025-1030 (2015).
- Swaney, D. L., Wenger, C. D., Coon, J. J. Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics. J. Proteome Res. 9 (3), 1323-1329 (2010).
- McAlister, G. C., et al. MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes. Anal. Chem. 86 (14), 7150-7158 (2014).
Tags
Enhanced Sample MultiplexingCombined Precursor Isotopic LabelingIsobaric TaggingCPILOTAlzheimer’s DiseaseMouse ModelProtein ChangesAgingNeurodegenerative DiseaseCancerPathogenesisDiagnosisPrognosisTherapeutic TargetsAcetylationProtein NitrationBrainHeartLiverBCA AssayProtein ConcentrationDithiothreitolIodoacetamideL-cysteineTrypsin Digestion
Citar este artigo
King, C. D., Dudenhoeffer, J. D., Gu, L., Evans, A. R., Robinson, R. A. S. Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging (cPILOT). J. Vis. Exp. (123), e55406, doi:10.3791/55406 (2017).