1
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Danko K, Lukasheva E, Zhukov VA, Zgoda V, Frolov A. Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics. Int J Mol Sci 2022; 23:13903. [PMID: 36430380 PMCID: PMC9695859 DOI: 10.3390/ijms232213903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022] Open
Abstract
Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.
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Affiliation(s)
- Katerina Danko
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin, 196608 St. Petersburg, Russia
| | - Viktor Zgoda
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Andrej Frolov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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2
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Li Y, Wang Y, Yao Y, Lyu J, Qiao Q, Mao J, Xu Z, Ye M. Rapid Enzyme-Mediated Biotinylation for Cell Surface Proteome Profiling. Anal Chem 2021; 93:4542-4551. [PMID: 33660993 DOI: 10.1021/acs.analchem.0c04970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell surface is the primary site for sensing extracellular stimuli. The knowledge of the transient changes on the surfaceome upon a perturbation is very important as the initial changed proteins could be driving molecules for some phenotype. In this study, we report a fast cell surface labeling strategy based on peroxidase-mediated oxidative tyrosine coupling strategy, enabling efficient and selective cell surface labeling within seconds. With a labeling time of 1 min, 2684 proteins, including 1370 (51%) cell surface-annotated proteins (cell surface/plasma membrane/extracellular), 732 transmembrane proteins, and 81 cluster of differentiation antigens, were identified from HeLa cells. By comparison with the negative control experiment using quantitative proteomics, 500 (68%) out of the 731 significantly enriched proteins (p-value < 0.05, ≥2-fold) in positive experimental samples were cell surface-annotated proteins. Finally, this technology was applied to track the dynamic changes of the surfaceome upon insulin stimulation at two time points (5 min and 2 h) in HepG2 cells. Thirty-two proteins, including INSR, CTNNB1, TFRC, IGF2R, and SORT1, were found to be significantly regulated (p-value < 0.01, ≥1.5-fold) after insulin exposure by different mechanisms. We envision that this technique could be a powerful tool to analyze the transient changes of the surfaceome with a good time resolution and to delineate the temporal and spatial regulation of cellular signaling.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yating Yao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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3
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Achour B, Al-Majdoub ZM, Rostami-Hodjegan A, Barber J. Mass Spectrometry of Human Transporters. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:223-247. [PMID: 32084322 DOI: 10.1146/annurev-anchem-091719-024553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transporters are key to understanding how an individual will respond to a particular dose of a drug. Two patients with similar systemic concentrations may have quite different local concentrations of a drug at the required site. The transporter profile of any individual depends upon a variety of genetic and environmental factors, including genotype, age, and diet status. Robust models (virtual patients) are therefore required and these models are data hungry. Necessary data include quantitative transporter profiles at the relevant organ. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is currently the most powerful method available for obtaining this information. Challenges include sourcing the tissue, isolating the hydrophobic membrane-embedded transporter proteins, preparing the samples for MS (including proteolytic digestion), choosing appropriate quantification methodology, and optimizing the LC-MS/MS conditions. Great progress has been made with all of these, especially within the last few years, and is discussed here.
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Affiliation(s)
- Brahim Achour
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Zubida M Al-Majdoub
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
- Certara, Princeton, New Jersey 08540, USA
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
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4
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Schultzhaus JN, Dean SN, Leary DH, Hervey WJ, Fears KP, Wahl KJ, Spillmann CM. Pressure cycling technology for challenging proteomic sample processing: application to barnacle adhesive. Integr Biol (Camb) 2019; 11:235-247. [DOI: 10.1093/intbio/zyz020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/08/2019] [Accepted: 05/29/2019] [Indexed: 12/23/2022]
Abstract
AbstractSuccessful proteomic characterization of biological material depends on the development of robust sample processing methods. The acorn barnacle Amphibalanus amphitrite is a biofouling model for adhesive processes, but the identification of causative proteins involved has been hindered by their insoluble nature. Although effective, existing sample processing methods are labor and time intensive, slowing progress in this field. Here, a more efficient sample processing method is described which exploits pressure cycling technology (PCT) in combination with protein solvents. PCT aids in protein extraction and digestion for proteomics analysis. Barnacle adhesive proteins can be extracted and digested in the same tube using PCT, minimizing sample loss, increasing throughput to 16 concurrently processed samples, and decreasing sample processing time to under 8 hours. PCT methods produced similar proteomes in comparison to previous methods. Two solvents which were ineffective at extracting proteins from the adhesive at ambient pressure (urea and methanol) produced more protein identifications under pressure than highly polar hexafluoroisopropanol, leading to the identification and description of >40 novel proteins at the interface. Some of these have homology to proteins with elastomeric properties or domains involved with protein-protein interactions, while many have no sequence similarity to proteins in publicly available databases, highlighting the unique adherent processes evolved by barnacles. The methods described here can not only be used to further characterize barnacle adhesive to combat fouling, but may also be applied to other recalcitrant biological samples, including aggregative or fibrillar protein matrices produced during disease, where a lack of efficient sample processing methods has impeded advancement. Data are available via ProteomeXchange with identifier PXD012730.
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Affiliation(s)
- Janna N Schultzhaus
- National Research Council Research Associateship Programs Fellow, Washington, D.C., USA
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, D.C., USA
| | - Scott N Dean
- National Research Council Research Associateship Programs Fellow, Washington, D.C., USA
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, D.C., USA
| | - Dagmar H Leary
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, D.C., USA
| | - W Judson Hervey
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, D.C., USA
| | - Kenan P Fears
- Chemistry Division, Naval Research Laboratory, Washington, D.C., USA
| | - Kathryn J Wahl
- Chemistry Division, Naval Research Laboratory, Washington, D.C., USA
| | - Christopher M Spillmann
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, D.C., USA
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5
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An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
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Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
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6
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Shekari F, Baharvand H, Salekdeh GH. Organellar proteomics of embryonic stem cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:215-30. [PMID: 24985774 DOI: 10.1016/b978-0-12-800453-1.00007-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Embryonic stem cells (ESCs) are undifferentiated cells with two common remarkable features known as self-renewal and differentiation. Proteomics plays an increasingly important role in understanding molecular mechanisms underlying self-renewal and pluripotency of ESCs and their applications in cell therapy and developmental biology studies. As the function of a protein is strongly associated with its localization in cell, a complete and accurate picture of the proteome of ESCs cannot be achieved without knowing the subcellular locations of proteins. Subcellular fractionation allows enrichment of low abundant proteins and signaling complexes and reduces the complexity of the sample. It also provided insight into tracking proteins that shuttle between different compartments. Despite the substantial interest and efforts in ESC subcellular proteomics area, progress has been relatively limited. In this review, we present an overview on current status of ESCs organelle proteomics research and discuss challenges in subcellular proteomics.
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Affiliation(s)
- Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran; Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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7
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Debelyy MO, Waridel P, Quadroni M, Schneiter R, Conzelmann A. Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins. PLoS One 2017; 12:e0186840. [PMID: 29073188 PMCID: PMC5658093 DOI: 10.1371/journal.pone.0186840] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022] Open
Abstract
Here we made an attempt to obtain partial structural information on the topology of multispan integral membrane proteins of yeast by isolating organellar membranes, removing peripheral membrane proteins at pH 11.5 and introducing chemical crosslinks between vicinal amino acids either using homo- or hetero-bifunctional crosslinkers. Proteins were digested with specific proteases and the products analysed by mass spectrometry. Dedicated software tools were used together with filtering steps optimized to remove false positive crosslinks. In proteins of known structure, crosslinks were found only between loops residing on the same side of the membrane. As may be expected, crosslinks were mainly found in very abundant proteins. Our approach seems to hold to promise to yield low resolution topological information for naturally very abundant or strongly overexpressed proteins with relatively little effort. Here, we report novel XL-MS-based topology data for 17 integral membrane proteins (Akr1p, Fks1p, Gas1p, Ggc1p, Gpt2p, Ifa38p, Ist2p, Lag1p, Pet9p, Pma1p, Por1p, Sct1p, Sec61p, Slc1p, Spf1p, Vph1p, Ybt1p).
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Affiliation(s)
- Mykhaylo O. Debelyy
- Division of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (MD); (AC)
| | - Patrice Waridel
- Protein Analysis Facility, Center of Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center of Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Roger Schneiter
- Division of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Andreas Conzelmann
- Division of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (MD); (AC)
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8
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Peng W, Zhang Y, Zhu R, Mechref Y. Comparative membrane proteomics analyses of breast cancer cell lines to understand the molecular mechanism of breast cancer brain metastasis. Electrophoresis 2017; 38:2124-2134. [PMID: 28523741 DOI: 10.1002/elps.201700027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/04/2017] [Accepted: 04/19/2017] [Indexed: 12/22/2022]
Abstract
Breast cancer is the leading type of cancer in women. Breast cancer brain metastasis is currently considered an issue of concern among breast cancer patients. Membrane proteins play important roles in breast cancer brain metastasis, involving cell adhesion and penetration of blood-brain barrier. To understand the mechanism of breast cancer brain metastasis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed in conjunction with enrichment of membrane proteins to analyze the proteomes from five different breast cancer and a brain cancer cell lines. Quantitative proteomic data of all cell lines were compared with MDA-MB-231BR which is a brain seeking breast cancer cell line, thus representing brain metastasis characteristics. Label-free proteomics of the six cell lines facilitates the identification of 1238 proteins and the quantification of 899 proteins of which more than 70% were membrane proteins. Unsupervised principal component analysis (PCA) of the label-free proteomics data resulted in a distinct clustering of cell lines, suggesting quantitative differences in the expression of several proteins among the different cell lines. Unique protein expressions in 231BR were observed for 28 proteins. The up-regulation of STAU1, AT1B3, NPM1, hnRNP Q, and hnRNP K and the down-regulation of TUBB4B and TUBB5 were noted in 231BR relative to 231 (precursor cell lines from which 231BR is derived). These proteins might contribute to the breast cancer brain metastasis. Ingenuity pathway analysis (IPA) supported the great brain metastatic propensity of 231BR and suggested the importance of the up-regulation of integrin proteins and down-regulation of EPHA2 in brain metastasis.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Yu Zhang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
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9
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Abdelmoez A, Coraça-Huber DC, Thurner GC, Debbage P, Lukas P, Skvortsov S, Skvortsova II. Screening and identification of molecular targets for cancer therapy. Cancer Lett 2017; 387:3-9. [DOI: 10.1016/j.canlet.2016.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 12/18/2022]
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10
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Zhang X. Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine. Proteomics 2016; 17. [PMID: 27633951 DOI: 10.1002/pmic.201600209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023]
Abstract
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine.
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Affiliation(s)
- Xi Zhang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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11
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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12
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Development of a sample preparation method for monitoring correct disulfide linkages of monoclonal antibodies by liquid chromatography–mass spectrometry. Anal Biochem 2016; 495:21-8. [DOI: 10.1016/j.ab.2015.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022]
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13
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Fang X, Qiao L, Yan G, Yang P, Liu B. Multifunctional nanoreactor for comprehensive characterization of membrane proteins based on surface functionalized mesoporous foams. Anal Chem 2015; 87:9360-7. [PMID: 26305297 DOI: 10.1021/acs.analchem.5b02135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An integrated protocol is proposed here for efficient analysis of membrane proteins based on surface functionalized mesoporous graphene foams (MGF). The inherent hydrophobic nature of MGF and surface modification with hydrophilic chitosan (CS) make it highly suitable for the enrichment of hydrophobic membrane proteins from organic solvent, while remaining well-dispersed in aqueous solution for subsequent proteolysis. Therefore, such a multifunctional reactor ensures a facile solvent adjustment route. Furthermore, as a chitosan modified nanoporous reactor, it also provides a biocompatible nanoenvironment that can maintain the stability and activity of enzymes to realize efficient in situ digestion of the enriched membrane proteins. The concept was first proved with a standard hydrophobic membrane protein, bacteriorhodopsin, where a high number of identified peptides and amino acid sequence coverage were achieved even at extremely low protein concentration. The mesoporous reaction system was further applied to the analysis of complex real-case proteome samples, where 931 membrane proteins were identified in triplicate analyses by 2D LC-MS/MS. In contrast, with in-solution proteolysis, only 73 membrane proteins were identified from the same sample by the same 2D LC-MS/MS. The identified membrane proteins by the MGF-CS protocol include many biomarkers of the cell line. These results suggest that the multifunctional MGF-CS protocol is of great value to facilitate the comprehensive characterization of membrane proteins in the proteome research.
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Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
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14
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Gomes-Alves P, Serra M, Brito C, R.-Borlado L, López JA, Vázquez J, Carrondo MJT, Bernad A, Alves PM. Exploring analytical proteomics platforms toward the definition of human cardiac stem cells receptome. Proteomics 2015; 15:1332-7. [DOI: 10.1002/pmic.201400318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/03/2014] [Accepted: 12/08/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Patrícia Gomes-Alves
- iBET; Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Margarida Serra
- iBET; Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Catarina Brito
- iBET; Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | | | - Juan A. López
- Laboratorio de Proteómica Cardiovascular and Unidad de Proteómica; Centro Nacional de Investigaciones Cardiovasculares; Madrid Spain
| | - Jesús Vázquez
- Laboratorio de Proteómica Cardiovascular and Unidad de Proteómica; Centro Nacional de Investigaciones Cardiovasculares; Madrid Spain
| | - Manuel J. T. Carrondo
- iBET; Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
- Faculdade de Ciências e Tecnologia; Universidade Nova de Lisboa; Monte da Caparica Portugal
| | | | - Paula M. Alves
- iBET; Instituto de Biologia Experimental e Tecnológica; Oeiras Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
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15
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Raimondo F, Corbetta S, Savoia A, Chinello C, Cazzaniga M, Rocco F, Bosari S, Grasso M, Bovo G, Magni F, Pitto M. Comparative membrane proteomics: a technical advancement in the search of renal cell carcinoma biomarkers. MOLECULAR BIOSYSTEMS 2015; 11:1708-16. [DOI: 10.1039/c5mb00020c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Set-up of a specific protocol for membrane protein analysis, applied to label free, comparative proteomics of renal cell carcinoma microdomains.
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Affiliation(s)
| | | | - Andrea Savoia
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Clizia Chinello
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Marta Cazzaniga
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Francesco Rocco
- Department of Specialistic Surgical Sciences
- Urology unit
- Ospedale Maggiore Policlinico Foundation
- IRCCS
- Milano
| | - Silvano Bosari
- Department of Medicine
- Surgery and Dental Sciences
- Pathology Unit
- Ospedale Maggiore Policlinico Foundation Milano
- IRCCS
| | - Marco Grasso
- Department of Surgical Pathology
- Cytology
- Medical Genetics and Nephropathology
- Azienda Ospedaliera San Gerardo
- Monza
| | - Giorgio Bovo
- Department of Surgical Pathology
- Cytology
- Medical Genetics and Nephropathology
- Azienda Ospedaliera San Gerardo
- Monza
| | - Fulvio Magni
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
| | - Marina Pitto
- Department of Health Sciences
- Univ. of Milano-Bicocca
- Monza
- Italy
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16
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Sun B. Proteomics and glycoproteomics of pluripotent stem-cell surface proteins. Proteomics 2014; 15:1152-63. [DOI: 10.1002/pmic.201400300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/07/2014] [Accepted: 09/08/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Bingyun Sun
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University; Burnaby British Columbia Canada
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17
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Mermelekas G, Zoidakis J. Mass spectrometry-based membrane proteomics in cancer biomarker discovery. Expert Rev Mol Diagn 2014; 14:549-63. [DOI: 10.1586/14737159.2014.917965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Sun B, Hood L. Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res 2014; 13:2705-14. [PMID: 24754784 PMCID: PMC4053080 DOI: 10.1021/pr500187g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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The advent of proteomics technology
has transformed our understanding
of biological membranes. The challenges for studying membrane proteins
have inspired the development of many analytical and bioanalytical
tools, and the techniques of glycoproteomics have emerged as an effective
means to enrich and characterize membrane and plasma-membrane proteomes.
This Review summarizes the development of various glycoproteomics
techniques to overcome the hurdles formed by the unique structures
and behaviors of membrane proteins with a focus on N-glycoproteomics.
Example contributions of N-glycoproteomics to the understanding of
membrane biology are provided, and the areas that require future technical
breakthroughs are discussed.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6, Canada
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19
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Waas M, Bhattacharya S, Chuppa S, Wu X, Jensen DR, Omasits U, Wollscheid B, Volkman BF, Noon KR, Gundry RL. Combine and conquer: surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins. Anal Chem 2014; 86:1551-9. [PMID: 24392666 PMCID: PMC4007983 DOI: 10.1021/ac403185a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Mass spectrometry
(MS) based proteomic technologies enable the identification and quantification
of membrane proteins as well as their post-translational modifications.
A prerequisite for their quantitative and reliable MS-based bottom-up
analysis is the efficient digestion into peptides by proteases, though
digestion of membrane proteins is typically challenging due to their
inherent properties such as hydrophobicity. Here, we investigated
the effect of eight commercially available MS-compatible surfactants,
two organic solvents, and two chaotropes on the enzymatic digestion
efficiency of membrane protein-enriched complex mixtures in a multiphase
study using a gelfree approach. Multiple parameters, including the
number of peptides and proteins identified, total protein sequence
coverage, and digestion specificity were used to evaluate transmembrane
protein digestion performance. A new open-source software tool was
developed to allow for the specific assessment of transmembrane domain
sequence coverage. Results demonstrate that while Progenta anionic
surfactants outperform other surfactants when tested alone, combinations
of guanidine and acetonitrile improve performance of all surfactants
to near similar levels as well as enhance trypsin specificity to >90%,
which has critical implications for future quantitative and qualitative
proteomic studies.
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Affiliation(s)
- Matthew Waas
- Milwaukee School of Engineering , Milwaukee, Wisconsin 53202, United States
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20
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Hao J, Li W, Dan J, Ye X, Wang F, Zeng X, Wang L, Wang H, Cheng Y, Liu L, Shui W. Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics. J Proteomics 2013; 86:70-84. [DOI: 10.1016/j.jprot.2013.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/10/2013] [Accepted: 04/07/2013] [Indexed: 12/15/2022]
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21
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Lai X. Reproducible method to enrich membrane proteins with high purity and high yield for an LC-MS/MS approach in quantitative membrane proteomics. Electrophoresis 2013; 34:809-17. [PMID: 23334993 DOI: 10.1002/elps.201200503] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 11/15/2012] [Accepted: 11/24/2012] [Indexed: 12/12/2022]
Abstract
The proportionately low abundance of membrane proteins hampers their proteomic analysis, especially for a quantitative LC-MS/MS approach. To overcome this limitation, a method was developed that consists of one cell disruption step in a hypotonic reagent using liquid nitrogen, one isolation step using a low speed centrifugation, and three wash steps using high speed centrifugation. Pellets contained plasma, nuclear, and mitochondrial membranes, including their integral, peripheral, and anchored membrane proteins. The reproducibility of this method was verified by protein assay of four separate experiments with a CV of 7.7%, and by comparative LC-MS/MS label-free quantification of individual proteins between two experiments with 99% of the quantified proteins having a CV ≤30%. Western blot and LC-MS/MS results of markers for cytoplasm, nucleus, mitochondria, and their membranes indicated that the enriched membrane fraction was highly pure by the absence of, or presence of trace amounts of, nonmembrane marker proteins. The average yield of membrane proteins was 237 μg/10 million HT29-MTX cells. LC-MS/MS analysis of the membrane-enriched sample resulted in the identification of 2597 protein groups. In summary, the developed method is reproducible, produces a highly pure membrane fraction, and generates a high yield of membrane proteins.
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Affiliation(s)
- Xianyin Lai
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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22
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Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L. N-glycoproteome of E14.Tg2a mouse embryonic stem cells. PLoS One 2013; 8:e55722. [PMID: 23405203 PMCID: PMC3565968 DOI: 10.1371/journal.pone.0055722] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/29/2012] [Indexed: 11/19/2022] Open
Abstract
E14.Tg2a mouse embryonic stem (mES) cells are a widely used host in gene trap and gene targeting techniques. Molecular characterization of host cells will provide background information for a better understanding of functions of the knockout genes. Using a highly selective glycopeptide-capture approach but ordinary liquid chromatography coupled mass spectrometry (LC-MS), we characterized the N-glycoproteins of E14.Tg2a cells and analyzed the close relationship between the obtained N-glycoproteome and cell-surface proteomes. Our results provide a global view of cell surface protein molecular properties, in which receptors seem to be much more diverse but lower in abundance than transporters on average. In addition, our results provide a systematic view of the E14.Tg2a N-glycosylation, from which we discovered some striking patterns, including an evolutionarily preserved and maybe functionally selected complementarity between N-glycosylation and the transmembrane structure in protein sequences. We also observed an environmentally influenced N-glycosylation pattern among glycoenzymes and extracellular matrix proteins. We hope that the acquired information enhances our molecular understanding of mES E14.Tg2a as well as the biological roles played by N-glycosylation in cell biology in general.
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Affiliation(s)
- Bingyun Sun
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (LH); (BS)
| | - Li Ma
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Xiaowei Yan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Denis Lee
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Vinita Alexander
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Laura J. Hohmann
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Cynthia Lorang
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Lalangi Chandrasena
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Qiang Tian
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (LH); (BS)
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23
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Shukla HD, Vaitiekunas P, Cotter RJ. Advances in membrane proteomics and cancer biomarker discovery: current status and future perspective. Proteomics 2012; 12:3085-104. [PMID: 22890602 DOI: 10.1002/pmic.201100519] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 07/05/2012] [Accepted: 07/27/2012] [Indexed: 02/06/2023]
Abstract
Membrane proteomic analysis has been proven to be a promising tool for identifying new and specific biomarkers that can be used for prognosis and monitoring of various cancers. Membrane proteins are of great interest particularly those with functional domains exposed to the extracellular environment. Integral membrane proteins represent about one-third of the proteins encoded by the human genome and assume a variety of key biological functions, such as cell-to-cell communication, receptor-mediated signal transduction, selective transport, and pharmacological actions. More than two-thirds of membrane proteins are drug targets, highlighting their immensely important pharmaceutical significance. Most plasma membrane proteins and proteins from other cellular membranes have several PTMs; for example, glycosylation, phosphorylation, and nitrosylation, and moreover, PTMs of proteins are known to play a key role in tumor biology. These modifications often cause change in stoichiometry and microheterogeneity in a protein molecule, which is apparent during electrophoretic separation. Furthermore, the analysis of glyco- and phosphoproteome of cell membrane presents a number of challenges mainly due to their low abundance, their large dynamic range, and the inherent hydrophobicity of membrane proteins. Under pathological conditions, PTMs, such as phosphorylation and glycosylation are frequently altered and have been recognized as a potential source for disease biomarkers. Thus, their accurate differential expression analysis, along with differential PTM analysis is of paramount importance. Here we summarize the current status of membrane-based biomarkers in various cancers, and future perspective of membrane biomarker research.
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Affiliation(s)
- Hem D Shukla
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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24
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Surface glycoproteomic analysis of hepatocellular carcinoma cells by affinity enrichment and mass spectrometric identification. Glycoconj J 2012; 29:411-24. [DOI: 10.1007/s10719-012-9420-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 06/05/2012] [Accepted: 06/12/2012] [Indexed: 12/30/2022]
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25
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Gundry RL, Riordon DR, Tarasova Y, Chuppa S, Bhattacharya S, Juhasz O, Wiedemeier O, Milanovich S, Noto FK, Tchernyshyov I, Raginski K, Bausch-Fluck D, Tae HJ, Marshall S, Duncan SA, Wollscheid B, Wersto RP, Rao S, Van Eyk JE, Boheler KR. A cell surfaceome map for immunophenotyping and sorting pluripotent stem cells. Mol Cell Proteomics 2012; 11:303-16. [PMID: 22493178 DOI: 10.1074/mcp.m112.018135] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Induction of a pluripotent state in somatic cells through nuclear reprogramming has ushered in a new era of regenerative medicine. Heterogeneity and varied differentiation potentials among induced pluripotent stem cell (iPSC) lines are, however, complicating factors that limit their usefulness for disease modeling, drug discovery, and patient therapies. Thus, there is an urgent need to develop nonmutagenic rapid throughput methods capable of distinguishing among putative iPSC lines of variable quality. To address this issue, we have applied a highly specific chemoproteomic targeting strategy for de novo discovery of cell surface N-glycoproteins to increase the knowledge-base of surface exposed proteins and accessible epitopes of pluripotent stem cells. We report the identification of 500 cell surface proteins on four embryonic stem cell and iPSCs lines and demonstrate the biological significance of this resource on mouse fibroblasts containing an oct4-GFP expression cassette that is active in reprogrammed cells. These results together with immunophenotyping, cell sorting, and functional analyses demonstrate that these newly identified surface marker panels are useful for isolating iPSCs from heterogeneous reprogrammed cultures and for isolating functionally distinct stem cell subpopulations.
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Affiliation(s)
- Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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26
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Williamson AJK, Whetton AD. The requirement for proteomics to unravel stem cell regulatory mechanisms. J Cell Physiol 2011; 226:2478-83. [PMID: 21792904 DOI: 10.1002/jcp.22610] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Stem cells are defined by their ability to self-renew and to differentiate, the processes whereby these events are achieved is the subject of much investigation. These studies include cancer stem cell populations, where eradication of this specific population is the ultimate goal of treatment. Whilst cellular signalling events and transcription factor complex-mediated changes in gene expression have been analysed in some detail within stem cells, full systematic understanding of the events promoting self-renewal or the commitment process leading to formation of a specific cell type require a systems biology approach. This in turn demands a need for proteomic analysis of post-translational regulation of protein levels, protein interactions, protein post-translational modification (e.g. ubiquitination, methylation, acetylation, phosphorylation) to identify networks for stem cell regulation. Furthermore, the phenomenon of induced pluripotency via cellular reprogramming also can be understood optimally using combined molecular biology and proteomics approaches; here we describe current research employing proteomics and mass spectrometry to dissect stem cell regulatory mechanisms.
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Affiliation(s)
- Andrew J K Williamson
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie's NHS Foundation Trust, Wolfson Molecular Imaging Centre, Withington, Manchester, UK.
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27
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Gundry RL, Burridge PW, Boheler KR. Pluripotent stem cell heterogeneity and the evolving role of proteomic technologies in stem cell biology. Proteomics 2011; 11:3947-61. [PMID: 21834136 DOI: 10.1002/pmic.201100100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/29/2011] [Accepted: 06/08/2011] [Indexed: 12/13/2022]
Abstract
Stem cells represent obvious choices for regenerative medicine and are invaluable for studies of human development and drug testing. The proteomic landscape of pluripotent stem cells (PSCs), in particular, is not yet clearly defined; consequently, this field of research would greatly benefit from concerted efforts designed to better characterize these cells. In this concise review, we provide an overview of stem cell potency, highlight the types and practical implications of heterogeneity in PSCs and provide a detailed analysis of the current view of the pluripotent proteome in a unique resource for this rapidly evolving field. Our goal in this review is to provide specific insights into the current status of the known proteome of both mouse and human PSCs. This has been accomplished by integrating published data into a unified PSC proteome to facilitate the identification of proteins, which may be informative for the stem cell state as well as to reveal areas where our current view is limited. These analyses provide insight into the challenges faced in the proteomic analysis of PSCs and reveal one area--the cell surface subproteome--that would especially benefit from enhanced research efforts.
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Affiliation(s)
- Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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28
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Huang QY, Huang HQ. Differential expression profile of membrane proteins in zebrafish (Danio rerio
) brain exposed to methyl parathion. Proteomics 2011; 11:3743-56. [DOI: 10.1002/pmic.201100084] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 12/12/2022]
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29
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Zhang W, Zhao C, Wang S, Fang C, Xu Y, Lu H, Yang P. Coating cells with cationic silica-magnetite nanocomposites for rapid purification of integral plasma membrane proteins. Proteomics 2011; 11:3482-90. [PMID: 21751343 DOI: 10.1002/pmic.201000211] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 03/22/2011] [Accepted: 06/01/2011] [Indexed: 01/17/2023]
Affiliation(s)
- Wei Zhang
- Department of Chemistry, Fudan University, Shanghai, P R China
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30
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Zhou H, Wang F, Wang Y, Ning Z, Hou W, Wright TG, Sundaram M, Zhong S, Yao Z, Figeys D. Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor. Mol Cell Proteomics 2011; 10:O111.008425. [PMID: 21749988 DOI: 10.1074/mcp.o111.008425] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
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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Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Canada
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31
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Miskevich F, Davis A, Leeprapaiwong P, Giganti V, Kostić NM, Angel LA. Metal complexes as artificial proteases in proteomics: A palladium(II) complex cleaves various proteins in solutions containing detergents. J Inorg Biochem 2011; 105:675-83. [DOI: 10.1016/j.jinorgbio.2011.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 01/14/2011] [Accepted: 01/18/2011] [Indexed: 11/15/2022]
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32
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Hughes CS, Nuhn AA, Postovit LM, Lajoie GA. Proteomics of human embryonic stem cells. Proteomics 2011; 11:675-90. [DOI: 10.1002/pmic.201000407] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 09/13/2010] [Accepted: 10/14/2010] [Indexed: 01/01/2023]
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33
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Elschenbroich S, Kim Y, Medin JA, Kislinger T. Isolation of cell surface proteins for mass spectrometry-based proteomics. Expert Rev Proteomics 2010; 7:141-54. [PMID: 20121483 DOI: 10.1586/epr.09.97] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Defining the cell surface proteome has profound importance for understanding cell differentiation and cell-cell interactions, as well as numerous pathogenic abnormalities. Owing to their hydrophobic nature, plasma membrane proteins that reside on the cell surface pose analytical challenges and, despite efforts to overcome difficulties, remain under-represented in proteomic studies. Limitations in the classically employed ultracentrifugation-based approaches have led to the invention of more elaborate techniques for the purification of cell surface proteins. Three of these methods--cell surface coating with cationic colloidal silica beads, biotinylation and chemical capture of surface glycoproteins--allow for marked enrichment of this subcellular proteome, with each approach offering unique advantages and characteristics for different experiments. In this article, we introduce the principles of each purification method and discuss applications from the recent literature.
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34
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Elschenbroich S, Ignatchenko V, Sharma P, Schmitt-Ulms G, Gramolini AO, Kislinger T. Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J Proteome Res 2010; 8:4860-9. [PMID: 19670906 DOI: 10.1021/pr900318k] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
High-resolution peptide separation is pivotal for successful shotgun proteomics. The need for capable techniques propels invention and improvement of ever more sophisticated approaches. Recently, Agilent Technologies has introduced the OFFGEL fractionator, which conducts peptide separation by isoelectric focusing in an off-gel setup. This platform has been shown to accomplish high resolution of peptides for diverse sample types, yielding valuable advantages over comparable separation techniques. In this study, we deliver the first comparison of the newly emerging OFFGEL approach to the well-established on-line MudPIT platform. Samples from a membrane-enriched fraction isolated from murine C2C12 cells were subjected to replicate analysis by OFFGEL (12 fractions, pH 3-10) followed by RP-LC-MS/MS or 12-step on-line MudPIT. OFFGEL analyses yielded 1398 proteins (identified by 10,269 peptides), while 1428 proteins (11,078 peptides) were detected with the MudPIT approach. Thus, our data shows that both platforms produce highly comparable results in terms of protein/peptide identifications and reproducibility for the sample type analyzed. We achieve more accurate peptide focusing after OFFGEL fractionation with 88% of all peptides binned to a single fraction, as compared to 61% of peptides detected in only one step in MudPIT analyses. Our study suggests that both platforms are equally capable of high quality peptide separation of a sample with medium complexity, rendering them comparably valuable for comprehensive proteomic analyses.
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35
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36
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Ghosh D, Lippert D, Krokhin O, Cortens JP, Wilkins JA. Defining the membrane proteome of NK cells. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1-25. [PMID: 19946888 DOI: 10.1002/jms.1696] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The present study was initiated to define the composition of the membrane proteome of the Natural Killer (NK) like cell line YTS. Isolated membranes were treated with reagents that have been reported to remove peripheral membrane proteins. Additional steps involving trifluoroethanol (TFE) were introduced in an effort to remove remaining nonintegral membrane proteins. This treatment resulted in the release of a subset of proteins without any apparent disruption of membrane integrity. The membranes were solubilized and digested with trypsin in 25% TFE. The resulting peptides were separated using an off-line two-dimensional reversed phase LC technique at alkaline and acidic pHs. Mass spectrometric analysis identified 1843 proteins with high confidence scores. On the basis of the presence of transmembrane regions or evidence of posttranslational modifications and prediction algorithms, approximately 40% of the identified proteins were predicted as plausible membrane proteins. The remaining species were largely involved in cellular processes and molecular functions that could be predicted to be transiently associated with membranes. The analytical approaches presented in this study offer robust generic methods for the identification and characterization of membrane proteins. These observations highlight the fact that the membrane is a dynamic entity that is composed of integral and stably associated proteins.
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Affiliation(s)
- Dhimankrishna Ghosh
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 3P4 Canada
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37
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Ye X, Johann DJ, Hakami RM, Xiao Z, Meng Z, Ulrich RG, Issaq HJ, Veenstra TD, Blonder J. Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS. J Proteomics 2009; 73:112-22. [PMID: 19709643 PMCID: PMC3159575 DOI: 10.1016/j.jprot.2009.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 08/17/2009] [Accepted: 08/18/2009] [Indexed: 12/24/2022]
Abstract
Proteomic profiling of membrane proteins is of vital importance in the search for disease biomarkers and drug development. However, the slow pace in this field has resulted mainly from the difficulty to analyze membrane proteins by mass spectrometry (MS). The objective of this investigation was to explore and optimize solubilization of membrane proteins for shotgun membrane proteomics of the CD14 human monocytes by examining different systems that rely on: i) an organic solvent (methanol) ii) an acid-labile detergent 3-[3-(1,1-bisalkyloxyethyl)pyridin-1-yl]propane-1-sulfonate (PPS), iii) a combination of both agents (methanol+PPS). Solubilization efficiency of different buffers was first compared using bacteriorhodopsin as a model membrane protein. Selected approaches were then applied on a membrane subproteome isolated from a highly enriched human monocyte population that was approximately 98% positive for CD14 expression as determined by FACS analysis. A methanol-based buffer yielded 194 proteins of which 93 (48%) were mapped as integral membrane proteins. The combination of methanol and acid-cleavable detergent gave similar results; 203 identified proteins of which 93 (46%) were mapped integral membrane proteins. However, employing PPS 216 proteins were identified of which 75 (35%) were mapped as integral membrane proteins. These results indicate that methanol alone or in combination with PPS yielded significantly higher membrane protein identification/enrichment than the PPS alone.
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Affiliation(s)
- Xiaoying Ye
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., NCI at Frederick, Frederick, Maryland 21702-1201, USA
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Brewis IA, Gadella BM. Sperm surface proteomics: from protein lists to biological function. Mol Hum Reprod 2009; 16:68-79. [PMID: 19717474 DOI: 10.1093/molehr/gap077] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proteomics technologies have matured significantly in recent years and proteomics driven research articles in reproductive biology and medicine are increasingly common. The key challenge is to move from lists of identified proteins to informed understanding of biological function. This review introduces the range of proteomics workflows most commonly used for protein identification before focusing on the mammalian sperm cell at fertilization as an exemplar for proteomic studies. We review the work of others on entire cells but then argue that proper subcellular fractionation and proper solubilization strategies offers critical advantages to achieving increased biological understanding. In relation to understanding initial gamete recognition events at fertilization (capacitation, zona binding and acrosomal exocytosis) it is imperative to study the sperm surface proteome by using purified plasma membrane fractions. Although this task is challenging there are now strategies at our disposal to achieve comprehensive coverage of the proteins at the sperm surface. Within this context it is also important to understand the milieu of the sperm cell during transit from the testis to the oviduct as proteins (or other entities) from the genital tract epithelia and fluids may also affect the composition and organization of proteins on the sperm surface. Finally the arguments presented for studying the cell plasma membrane proteome to understand the role of the cell surface equally apply to all cell types with important roles in reproductive function.
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Affiliation(s)
- Ian A Brewis
- Department of Infection, Immunity and Biochemistry, Henry Wellcome Building, School of Medicine, Heath Park, Cardiff University, Cardiff CF14 4XN, UK.
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