The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate‐washed membrane standard

Peng, Lifeng; Kapp, Eugene A.; Fenyö, David; Kwon, Min Seok; Pin, Jiang; Wu, Songfeng; Jiang, Ying; Aguilar, Marie Isabel; Ahmed, Nikhat; Baker, Mark S.; Cai, Zongwei; Chen, Yu‐Ju; Van, Phan; Chung, Maxey C. M.; He, Fuchu; Len, Alice C. L.; Liao, Pao Chi; Nakamura, Kazuyuki; Ngai, Sai Ming; Paik, Young Ki; Pan, Tai‐Long; Poon, Terence Chuen Wai; Salekdeh, Ghasem Hosseini; Simpson, Richard J.; Sirdeshmukh, Ravi; Srisomsap, Chantragan; Svasti, Jisnuson; Tyan, Yu‐Chang; Dreyer, Florian S.; McLauchlan, Danyl; Rawson, Pisana; Jordan, T. William

doi:10.1002/pmic.201000126

Cited by 24 publications

(36 citation statements)

References 25 publications

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“…Peng’s group recommended the use of a similar method for enrichment of membranes from the liver microsomal fraction, to be followed by SDS-PAGE, tryptic digestion of excised proteins and identification by LC-MS/MS [15]. The Peng’s group protocol was also discussed by the Asia Oceania Proteome Organization Membrane Proteomics Initiative as a standard protocol for sample preparation for further proteomic analysis of membrane proteins [16, 17]. …”

Section: Introductionmentioning

confidence: 99%

Mass Spectrometry-Based Analysis of Rat Liver and Hepatocellular Carcinoma Morris Hepatoma 7777 Plasma Membrane Proteome

et al. 2013

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The gel-based proteomic analysis of plasma membranes from rat liver and chemically induced, malignant hepatocellular carcinoma Morris hepatoma 7777 was systematically optimized to yield the maximum number of proteins containing transmembrane domains (TMDs). Incorporation of plasma membrane proteins into polyacrylamide “tube gel” followed by in-gel digestion of “tube gel” pieces significantly improved detection by ESI-LC-MS/MS. Removal of less hydrophobic proteins by washing isolated plasma membranes with 0.1 M sodium carbonate enables detection of hydrophobic proteins with one or more TMDs in both tissues. Subsequent treatment of plasma membranes by a proteolytic enzyme (trypsin) causes the loss of some of the proteins that are detected after washing with sodium carbonate, but it enables the detection of other hydrophobic proteins containing TMDs. Introduction of mass spectrometers with higher sensitivity, higher mass resolution and mass accuracy, and a faster scan rate significantly improved detection of membrane proteins, but the improved sample preparation is still useful, and enables detection of additional hydrophobic proteins. Proteolytic pre-digestion of plasma membranes enables detection of additional hydrophobic proteins and better sequence coverage of TMD-containing proteins in plasma membranes from both tissues.

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Section: Introductionmentioning

confidence: 99%

Mass Spectrometry-Based Analysis of Rat Liver and Hepatocellular Carcinoma Morris Hepatoma 7777 Plasma Membrane Proteome

et al. 2013

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“…In addition, SDS‐PAGE separation and in‐gel digestion were used in reference , which led to higher labor and time consumed. For number of CYPs and UGTs, our protocol generated slightly higher number of CYPs (27 versus 25) and UGTs (12 versus 9) than that in reference , and lower number of CYPs (27 versus 35) than that in reference . Considering the differences of mass spectrometer and sample preparation method used in our protocol and reference (LTQ versus LTQ‐Orbitrap, in‐solution digestion versus SDS‐PAGE separation and in‐gel digestion) and also the difference of analyzed sample (human liver microsome versus mouse liver microsome), the results indicate that our protocol is valuable for comprehensive membrane proteome analysis of liver microsome, especially CYPs and UGTs analysis.…”

Section: Cyps and Ugts Identified With Sds‐page‐free Protocolmentioning

confidence: 89%

“…These results demonstrated that the SDS-PAGE-free protocol could obtain comprehensive and accurate information about the relative abundance of CYPs and UGTs in HLMs. We also compared the results from our protocol with that from references [29] and [30] for liver microsome membrane proteome analysis. Peng et al [29] applied sodium carbonate (pH 11.5) washing step for enrichment of integral and lipid-anchored membrane proteins from mouse liver microsome, followed by in-solution trypsin digestion and LC-ESI-MS/MS (LTQ) analysis.…”

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confidence: 99%

SDS-PAGE-free protocol for comprehensive identification of cytochrome P450 enzymes and uridine diphosphoglucuronosyl transferases in human liver microsomes

et al. 2012

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Comprehensive identification of cytochrome P450 enzymes (CYPs) and uridine diphosphoglucuronosyl transferases (UGTs) in human liver microsomes (HLMs) was performed with an SDS-PAGE-free protocol. HLMs were solubilized with 5% v/v ionic liquid, 1-butyl-3-methyl imidazolium tetrafluoroborate, followed by tryptic digestion, and 2D-SCX-RPLC-ESI-MS/MS (LTQ XL) analysis in triplicate. In total, 27 CYPs and 12 UGTs were confidently identified with average sequence coverage as 30.99 and 25.07%, average peptide number as 14 and 13, and average unique peptide number as 7 and 4, respectively. The highly similar isoforms of CYP3A, CYP2C, and CYP4F subfamilies could be unambiguously differentiated from each other, despite the fact that the sequence similarity of CYP2C9 and CYP2C19 is 91%. In addition, protein spectral count was used to approximately evaluate the relative abundance of identified CYPs and UGTs, and the results agreed with previous immunochemistry reports. Keywords:1-Butyl-3-methyl imidazolium tetrafluoroborate / 2D-LC-ESI-MS/MS / Cytochrome P450 enzyme / Protein spectral count / Uridine diphosphoglucuronosyl transferase Additional supporting information may be found in the online version of this article at the publisher's web-site Liver is the main organ of metabolism in humans, through which both endogenous and exogenous substances might be converted into more polar metabolites that could be easily excreted from the body. Cytochrome P450 enzymes (CYPs) are the most important drug-metabolizing enzymes in mammals

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“…Several previously published reports have described the analysis of plasma membrane (47,49,50) and microsomal membrane proteins (49, 51, 52) of mouse or rat liver origin. Two observations are noteworthy when the current data are compared with those reported previously.…”

Section: Development Of Centrifugal Proteomicmentioning

confidence: 99%

Improved Recovery and Identification of Membrane Proteins from Rat Hepatic Cells using a Centrifugal Proteomic Reactor

Zhou

Wang

et al. 2011

Molecular & Cellular Proteomics

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Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with >2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism.

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The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate‐washed membrane standard

Cited by 24 publications

References 25 publications

Mass Spectrometry-Based Analysis of Rat Liver and Hepatocellular Carcinoma Morris Hepatoma 7777 Plasma Membrane Proteome

Mass Spectrometry-Based Analysis of Rat Liver and Hepatocellular Carcinoma Morris Hepatoma 7777 Plasma Membrane Proteome

SDS-PAGE-free protocol for comprehensive identification of cytochrome P450 enzymes and uridine diphosphoglucuronosyl transferases in human liver microsomes

Improved Recovery and Identification of Membrane Proteins from Rat Hepatic Cells using a Centrifugal Proteomic Reactor

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