1
|
Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
Collapse
Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| |
Collapse
|
2
|
Tola AJ, Missihoun TD. Ammonium sulfate-based prefractionation improved proteome coverage and detection of carbonylated proteins in Arabidopsis thaliana leaf extract. PLANTA 2023; 257:62. [PMID: 36808312 DOI: 10.1007/s00425-023-04083-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Ammonium sulfate is well known to salt out proteins at high concentrations. The study revealed that it can serve to increase by 60% the total number of identified carbonylated proteins by LC-MS/MS. Protein carbonylation is a significant post-translational modification associated with reactive oxygen species signaling in animal and plant cells. However, the detection of carbonylated proteins involved in signaling is still challenging, as they only represent a small subset of the proteome in the absence of stress. In this study, we investigated the hypothesis that a prefractionation step with ammonium sulphate will improve the detection of the carbonylated proteins in a plant extract. For this, we extracted total protein from the Arabidopsis thaliana leaves and subjected the extract to stepwise precipitation with ammonium sulfate to 40%, 60%, and 80% saturation. The protein fractions were then analyzed by liquid chromatography-tandem mass spectrometry for protein identification. We found that all the proteins identified in the non-fractionated samples were also found in the prefractionated samples, indicating no loss was incurred during the prefractionation. About 45% more proteins were identified in the fractionated samples compared to the non-fractionated total crude extract. When the prefractionation steps were combined with the enrichment of carbonylated proteins labeled with a fluorescent hydrazide probe, several carbonylated proteins, which were unseen in the non-fractionated samples, became visible in the prefractionated samples. Consistently, the prefractionation method allowed to identify 63% more carbonylated proteins by mass spectrometry compared to the number of carbonylated proteins identified from the total crude extract without prefractionation. These results indicated that the ammonium sulfate-based proteome prefractionation can be used to improve proteome coverage and identification of carbonylated proteins from a complex proteome sample.
Collapse
Affiliation(s)
- Adesola Julius Tola
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada
| | - Tagnon D Missihoun
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada.
| |
Collapse
|
3
|
Wang W, Ding S, Wang Z, Lv Q, Zhang Q. Electrochemical paper-based microfluidic device for on-line isolation of proteins and direct detection of lead in urine. Biosens Bioelectron 2021; 187:113310. [PMID: 34020224 DOI: 10.1016/j.bios.2021.113310] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023]
Abstract
In this work, we developed a microfluidic paper-based analytical device (μPAD) for the on-line isolation of proteins and the electrochemical detection of lead ions (Pb(II)) in urine samples. The patterned filter paper was prepared through the direct printing of microchannel patterns on filter paper using an office laser printer. The paper was modified with protein precipitant and was then coupled with a detachable three-electrode system. Experimental parameters, namely, modification reagents, microchannel length and width, deposition potential, and deposition time, were optimized. Then, the maximum protein concentration under which the device can function was obtained as 300 mg L-1. The linear range was 10-500 μg L-1 with a detection limit of 9 μg L-1. The effectiveness of this device was demonstrated through the quantification of Pb(II) in urine samples and the results agreed with those of atomic absorption spectrometry (AAS).
Collapse
Affiliation(s)
- Wan Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Shounian Ding
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Zhijuan Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Qing Lv
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Qing Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China.
| |
Collapse
|
4
|
Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery. Bioanalysis 2019; 11:1799-1812. [PMID: 31617391 DOI: 10.4155/bio-2019-0145] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
Collapse
|
5
|
Abundant plasma protein depletion using ammonium sulfate precipitation and Protein A affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1089:43-59. [PMID: 29758408 DOI: 10.1016/j.jchromb.2018.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/10/2018] [Accepted: 04/26/2018] [Indexed: 11/23/2022]
Abstract
Plasma is a highly valuable resource for biomarker research since it is easy obtainable and contains a high amount of information on patient health status. Although advancements in the field of proteomics enabled analysis of the plasma proteome, identification of low abundant proteins remains challenging due to high complexity and large dynamic range. In order to reduce the dynamic range of protein concentrations, a tandem depletion technique consisting of ammonium sulfate precipitation and Protein A affinity chromatography was developed. Using this method, 50% of albumin, together with other high abundant proteins such as alpha-1-antitrypsin, was depleted from the plasma sample at 20% to 40% ammonium sulfate saturation levels. In combination with immunoglobulin removal using a Protein A column, this technique delivered up to 40 new low- to medium abundance protein identifications when performing a shotgun mass spectrometry analysis. Compared to non-depleted plasma, 270 additional protein spots were observed during 2D-PAGE analysis. These results illustrate that this tandem depletion method is equivalent to commercial kits which are based on immune-affinity chromatography. Moreover, this method using Protein A immunoglobulin depletion was shown to be highly reproducible and a minimal amount of non-target proteins was depleted. The combination of ammonium sulfate precipitation and Protein A affinity chromatography offers a low cost, efficient, straightforward and reproducible alternative to commercial kits, with proteins remaining in native conformation, allowing protein activity and protein interaction studies.
Collapse
|
6
|
Kuljanin M, Brown CFC, Raleigh MJ, Lajoie GA, Flynn LE. Collagenase treatment enhances proteomic coverage of low-abundance proteins in decellularized matrix bioscaffolds. Biomaterials 2017; 144:130-143. [PMID: 28829951 DOI: 10.1016/j.biomaterials.2017.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/03/2017] [Accepted: 08/12/2017] [Indexed: 12/12/2022]
Abstract
There is great interest in the application of advanced proteomic techniques to characterize decellularized tissues in order to develop a deeper understanding of the effects of the complex extracellular matrix (ECM) composition on the cellular response to these pro-regenerative bioscaffolds. However, the identification of proteins in ECM-derived bioscaffolds is hindered by the high abundance of collagen in the samples, which can interfere with the detection of lower-abundance constituents that may be important regulators of cell function. To address this limitation, we developed a novel multi-enzyme digestion approach using treatment with a highly-purified collagenase derived from Clostridium Histolyticum to selectively deplete collagen from ECM-derived protein extracts, reducing its relative abundance from up to 90% to below 10%. Moreover, we applied this new method to characterize the proteome of human decellularized adipose tissue (DAT), human decellularized cancellous bone (DCB), and commercially-available bovine tendon collagen (BTC). We successfully demonstrated with all three sources that collagenase treatment increased the depth of detection and enabled the identification of a variety of signaling proteins that were masked by collagen in standard digestion protocols with trypsin/LysC, increasing the number of proteins identified in the DAT by ∼2.2 fold, the DCB by ∼1.3 fold, and the BTC by ∼1.6 fold. In addition, quantitative proteomics using label-free quantification demonstrated that the DAT and DCB extracts were compositionally distinct, and identified a number of adipogenic and osteogenic proteins that were consistently more highly expressed in the DAT and DCB respectively. Overall, we have developed a new processing method that may be applied in advanced mass spectrometry studies to improve the high-throughput proteomic characterization of bioscaffolds derived from mammalian tissues. Further, our study provides new insight into the complex ECM composition of two human decellularized tissues of interest as cell-instructive platforms for regenerative medicine.
Collapse
Affiliation(s)
- Miljan Kuljanin
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Cody F C Brown
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Matthew J Raleigh
- Undergraduate Medical Education, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.
| | - Lauren E Flynn
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada; Department of Chemical and Biochemical Engineering, Thompson Engineering Building, The University of Western Ontario, London, Ontario, N6A 5B9, Canada.
| |
Collapse
|
7
|
Brgles M, Prebeg P, Kurtović T, Ranić J, Marchetti-Deschmann M, Allmaier G, Halassy B. Optimization of tetanus toxoid ammonium sulfate precipitation process using response surface methodology. Prep Biochem Biotechnol 2017; 46:695-703. [PMID: 26760928 DOI: 10.1080/10826068.2015.1135452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Tetanus toxoid (TTd) is a highly immunogenic, detoxified form of tetanus toxin, a causative agent of tetanus disease, produced by Clostridium tetani. Since tetanus disease cannot be eradicated but is easily prevented by vaccination, the need for the tetanus vaccine is permanent. The aim of this work was to investigate the possibility of optimizing TTd purification, i.e., ammonium sulfate precipitation process. The influence of the percentage of ammonium sulfate, starting amount of TTd, buffer type, pH, temperature, and starting purity of TTd on the purification process were investigated using optimal design for response surface models. Responses measured for evaluation of the ammonium sulfate precipitation process were TTd amount (Lf/mL) and total protein content. These two parameters were used to calculate purity (Lf/mgPN) and the yield of the process. Results indicate that citrate buffer, lower temperature, and lower starting amount of TTd result in higher purities of precipitates. Gel electrophoresis combined with matrix-assisted laser desorption ionization-mass spectrometric analysis of precipitates revealed that there are no inter-protein cross-links and that all contaminating proteins have pIs similar to TTd, so this is most probably the reason for the limited success of purification by precipitation.
Collapse
Affiliation(s)
- Marija Brgles
- a Centre for Research and Knowledge Transfer , University of Zagreb , Zagreb , Croatia
| | - Pero Prebeg
- b Faculty of Mechanical Engineering and Naval Architecture , University of Zagreb , Zagreb , Croatia
| | - Tihana Kurtović
- a Centre for Research and Knowledge Transfer , University of Zagreb , Zagreb , Croatia
| | - Jelena Ranić
- c Bacterial Vaccine Department, Institute of Immunology , Zagreb , Croatia
| | | | - Günter Allmaier
- d Institute of Chemical Technologies and Analytics , Technische Universität Wien , Vienna , Austria
| | - Beata Halassy
- a Centre for Research and Knowledge Transfer , University of Zagreb , Zagreb , Croatia
| |
Collapse
|
8
|
Chutipongtanate S, Chatchen S, Svasti J. Plasma prefractionation methods for proteomic analysis and perspectives in clinical applications. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/24/2017] [Accepted: 02/10/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital; Mahidol University; Salaya Thailand
| | - Supawat Chatchen
- Department of Tropical Pediatrics, Faculty of Tropical Medicine; Mahidol University; Salaya Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry; Chulabhorn Research Institute, Krung Thep Maha Nakhon; Thailand
- Applied Biological Sciences Program; Chulabhorn Graduate Institute; Thailand
| |
Collapse
|
9
|
Liu Z, Fan S, Liu H, Yu J, Qiao R, Zhou M, Yang Y, Zhou J, Xie P. Enhanced Detection of Low-Abundance Human Plasma Proteins by Integrating Polyethylene Glycol Fractionation and Immunoaffinity Depletion. PLoS One 2016; 11:e0166306. [PMID: 27832179 PMCID: PMC5104378 DOI: 10.1371/journal.pone.0166306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/26/2016] [Indexed: 01/27/2023] Open
Abstract
The enormous depth complexity of the human plasma proteome poses a significant challenge for current mass spectrometry-based proteomic technologies in terms of detecting low-level proteins in plasma, which is essential for successful biomarker discovery efforts. Typically, a single-step analytical approach cannot reduce this intrinsic complexity. Current simplex immunodepletion techniques offer limited capacity for detecting low-abundance proteins, and integrated strategies are thus desirable. In this respect, we developed an improved strategy for analyzing the human plasma proteome by integrating polyethylene glycol (PEG) fractionation with immunoaffinity depletion. PEG fractionation of plasma proteins is simple, rapid, efficient, and compatible with a downstream immunodepletion step. Compared with immunodepletion alone, our integrated strategy substantially improved the proteome coverage afforded by PEG fractionation. Coupling this new protocol with liquid chromatography-tandem mass spectrometry, 135 proteins with reported normal concentrations below 100 ng/mL were confidently identified as common low-abundance proteins. A side-by-side comparison indicated that our integrated strategy was increased by average 43.0% in the identification rate of low-abundance proteins, relying on an average 65.8% increase of the corresponding unique peptides. Further investigation demonstrated that this combined strategy could effectively alleviate the signal-suppressive effects of the major high-abundance proteins by affinity depletion, especially with moderate-abundance proteins after incorporating PEG fractionation, thereby greatly enhancing the detection of low-abundance proteins. In sum, the newly developed strategy of incorporating PEG fractionation to immunodepletion methods can potentially aid in the discovery of plasma biomarkers of therapeutic and clinical interest.
Collapse
Affiliation(s)
- Zhao Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Songhua Fan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Haipeng Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Jia Yu
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Rui Qiao
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Mi Zhou
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Yongtao Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
| | - Jian Zhou
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
- * E-mail: (JZ); (PX)
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Neurobiology, Chongqing, China
- Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing, China
- * E-mail: (JZ); (PX)
| |
Collapse
|
10
|
Bollineni RC, Guldvik IJ, Grönberg H, Wiklund F, Mills IG, Thiede B. A differential protein solubility approach for the depletion of highly abundant proteins in plasma using ammonium sulfate. Analyst 2016; 140:8109-17. [PMID: 26541119 DOI: 10.1039/c5an01560j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depletion of highly abundant proteins is an approved step in blood plasma analysis by mass spectrometry (MS). In this study, we explored a precipitation and differential protein solubility approach as a fractionation strategy for abundant protein removal from plasma. Total proteins from plasma were precipitated with 90% saturated ammonium sulfate, followed by differential solubilization in 55% and 35% saturated ammonium sulfate solutions. Using a four hour liquid chromatography (LC) gradient and an LTQ-Orbitrap XL mass spectrometer, a total of 167 and 224 proteins were identified from the 55% and 35% ammonium sulfate fractions, whereas 235 proteins were found in the remaining protein fractions with at least two unique peptides. SDS-PAGE and exclusive total spectrum counts from LC-MS/MS analyses clearly showed that majority of the abundant plasma proteins were solubilized in 55% and 35% ammonium sulfate solutions, indicating that the remaining protein fraction is of potential interest for identification of less abundant plasma proteins. Serum albumin, serotransferrin, alpha-1-antitrypsin and transthyretin were the abundant proteins that were highly enriched in 55% ammonium sulfate fractions. Immunoglobulins, complement system proteins, and apolipoproteins were among other abundant plasma proteins that were enriched in 35% ammonium sulfate fractions. In the remaining protein fractions a total of 40 unique proteins were identified of which, 32 proteins were identified with at least 10 exclusive spectrum counts. According to PeptideAtlas, 9 of these 32 proteins were estimated to be present at low μg ml(-1) (0.12-1.9 μg ml(-1)) concentrations in the plasma, and 17 at low ng ml(-1) (0.1-55 ng ml(-1)) range.
Collapse
Affiliation(s)
- Ravi Chand Bollineni
- Department of Biosciences, University of Oslo, Oslo, Norway. and Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
| | - Ingrid J Guldvik
- Centre for Molecular Medicine Norway (NCMM), University of Oslo and Oslo University Hospitals, Norway
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Ian G Mills
- Centre for Molecular Medicine Norway (NCMM), University of Oslo and Oslo University Hospitals, Norway and Department of Cancer Prevention, Oslo University Hospitals, Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway. and Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
| |
Collapse
|
11
|
Gianazza E, Miller I, Palazzolo L, Parravicini C, Eberini I. With or without you — Proteomics with or without major plasma/serum proteins. J Proteomics 2016; 140:62-80. [DOI: 10.1016/j.jprot.2016.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/26/2022]
|
12
|
Zheng J, Wang L, Twarowska B, Laino S, Sparks C, Smith T, Russell R, Wang M. Caprylic acid-induced impurity precipitation from protein A capture column elution pool to enable a two-chromatography-step process for monoclonal antibody purification. Biotechnol Prog 2015; 31:1515-25. [PMID: 26280674 DOI: 10.1002/btpr.2154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 07/09/2015] [Indexed: 11/10/2022]
Abstract
This article presents the use of caprylic acid (CA) to precipitate impurities from the protein A capture column elution pool for the purification of monoclonal antibodies (mAbs) with the objective of developing a two chromatography step antibody purification process. A CA-induced impurity precipitation in the protein A column elution pool was evaluated as an alternative method to polishing chromatography techniques for use in the purification of mAbs. Parameters including pH, CA concentrations, mixing time, mAb concentrations, buffer systems, and incubation temperatures were evaluated on their impacts on the impurity removal, high-molecular weight (HMW) formation and precipitation step yield. Both pH and CA concentration, but not mAb concentrations and buffer systems, are key parameters that can affect host-cell proteins (HCPs) clearance, HMW species, and yield. CA precipitation removes HCPs and some HMW species to the acceptable levels under the optimal conditions. The CA precipitation process is robust at 15-25°C. For all five mAbs tested in this study, the optimal CA concentration range is 0.5-1.0%, while the pH range is from 5.0 to 6.0. A purification process using two chromatography steps (protein A capture column and ion exchange polishing column) in combination with CA-based impurity precipitation step can be used as a robust downstream process for mAb molecules with a broad range of isoelectric points. Residual CA can be effectively removed by the subsequent polishing cation exchange chromatography.
Collapse
Affiliation(s)
- Ji Zheng
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Lu Wang
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Barbara Twarowska
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Sarah Laino
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Colleen Sparks
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Timothy Smith
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Reb Russell
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| | - Michelle Wang
- Biologics Development Dept., Bristol-Myers Squibb, Bloomsbury, NJ, 08804
| |
Collapse
|
13
|
High abundant protein removal from rodent blood for biomarker discovery. Biochem Biophys Res Commun 2015; 455:84-9. [PMID: 25445603 DOI: 10.1016/j.bbrc.2014.09.137] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 12/17/2022]
Abstract
In order to realize the goal of stratified and/or personalized medicine in the clinic, significant advances in the field of biomarker discovery are necessary. Adding to the abundance of nucleic acid biomarkers being characterized, additional protein biomarkers will be needed to satisfy diverse clinical needs. An appropriate source for finding these biomarkers is within blood, as it contains tissue leakage factors as well as additional proteins that reside in blood that can be linked to the presence of disease. Unfortunately, high abundant proteins and complexity of the blood proteome present significant challenges for the discovery of protein biomarkers from blood. Animal models often enable the discovery of biomarkers that can later be translated to humans. Therefore, determining appropriate sample preparation of proteomic samples in rodent models is an important research goal. Here, we examined both mouse and rat blood samples (including both serum and plasma), for appropriate high abundant protein removal techniques for subsequent gel-based proteomic experiments. We assessed four methods of albumin removal: antibody-based affinity chromatography (MARS), Cibacron® Blue-based affinity depletion (SwellGel® Blue Albumin Removal Kit), protein-based affinity depletion (ProteaPrep Albumin Depletion Kit) and TCA/acetone precipitation. Albumin removal was quantified for each method and SDS-PAGE and 2-DE gels were used to quantify the number of protein spots obtained following albumin removal. Our results suggest that while all four approaches can effectively remove high abundant proteins, antibody-based affinity chromatography is superior to the other three methods.
Collapse
|
14
|
Saraygord-Afshari N, Naderi-Manesh H, Naderi M. Increasing proteome coverage for gel-based human tear proteome maps: towards a more comprehensive profiling. Biomed Chromatogr 2014; 29:1056-67. [DOI: 10.1002/bmc.3392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 09/29/2014] [Accepted: 10/20/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Neda Saraygord-Afshari
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Mostafa Naderi
- Department of Ophthalmology; Bina eye hospital; Tehran Iran
| |
Collapse
|
15
|
Javanmard M, Emaminejad S, Gupta C, Provine J, Davis R, Howe R. Depletion of cells and abundant proteins from biological samples by enhanced dielectrophoresis. SENSORS AND ACTUATORS. B, CHEMICAL 2014; 193:918-924. [PMID: 26924893 PMCID: PMC4765371 DOI: 10.1016/j.snb.2013.11.100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Platforms that are sensitive and specific enough to assay low-abundance protein biomarkers, in a high throughput multiplex format, within a complex biological fluid specimen, are necessary to enable protein biomarker based diagnostics for diseases such as cancer. The signal from an assay for a low-abundance protein biomarker in a biological fluid sample like blood is typically buried in a background that arises from the presence of blood cells and from high-abundance proteins that make up 90% of the assayed protein mass. We present an automated on-chip platform for the depletion of cells and highly abundant serum proteins in blood. Our platform consists of two components, the first of which is a microfluidic mixer that mixes beads containing antibodies against the highly abundant proteins in the whole blood. This complex mixture (consisting of beads, cells, and serum proteins) is then injected into the second component of our microfluidic platform, which comprises a filter trench to capture all the cells and the beads. The size-based trapping of the cells and beads into the filter trench is significantly enhanced by leveraging additional negative dielectrophoretic forces to push the micron sized particles (cells and beads which have captured the highly abundant proteins) down into the trench, allowing the serum proteins of lower abundance to flow through. In general, dielectrophoresis using bare electrodes is incapable of producing forces beyond the low piconewton range that tend to be insufficient for separation applications. However, by using electrodes passivated with atomic layer deposition, we demonstrate the application of enhanced negative DEP electrodes together with size-based flltration induced by the filter trench, to deplete 100% of the micron sized particles in the mixture.
Collapse
Affiliation(s)
- M. Javanmard
- Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - S. Emaminejad
- Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
- Electrical Engineering Department, Stanford University, Stanford, CA, USA
| | - C. Gupta
- Electrical Engineering Department, Stanford University, Stanford, CA, USA
| | - J. Provine
- Electrical Engineering Department, Stanford University, Stanford, CA, USA
| | - R.W. Davis
- Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - R.T. Howe
- Electrical Engineering Department, Stanford University, Stanford, CA, USA
| |
Collapse
|
16
|
Changes in SeMSC, glucosinolates and sulforaphane levels, and in proteome profile in broccoli (Brassica oleracea var. Italica) fertilized with sodium selenate. Molecules 2013; 18:5221-34. [PMID: 23652991 PMCID: PMC6270319 DOI: 10.3390/molecules18055221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 04/16/2013] [Accepted: 04/27/2013] [Indexed: 11/29/2022] Open
Abstract
The aim of this work was to analyze the effect of sodium selenate fortification on the content of selenomethyl selenocysteine (SeMSC), total glucosinolates and sulforaphane, as well as the changes in protein profile of the inflorescences of broccoli (Brassica oleracea var. Italica). Two experimental groups were considered: plants treated with 100 μmol/L sodium selenate (final concentration in the pot) and control plants treated with water. Fortification began 2 weeks after transplantation and was repeated once a week during 10 weeks. Broccoli florets were harvested when they reached appropriate size. SeMSC content in broccoli florets increased significantly with sodium selenate fortification; but total glucosinolates and sulforaphane content as well as myrosinase activity were not affected. The protein profile of broccoli florets changed due to fortification with sodium selenate. Some proteins involved in general stress-responses were up-regulated, whereas down-regulated proteins were identified as proteins involved in protection against pathogens. This is the first attempt to evaluate the physiological effect of fortification with sodium selenate on broccoli at protein level. The results of this work will contribute to better understanding the metabolic processes related with selenium uptake and accumulation in broccoli.
Collapse
|
17
|
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 986] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
18
|
Mahn A, Lienqueo ME, Quilodrán C, Olivera-Nappa A. Purification of transthyretin as nutritional biomarker of selenium status. J Sep Sci 2012; 35:3184-9. [DOI: 10.1002/jssc.201200646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/21/2012] [Accepted: 08/22/2012] [Indexed: 12/16/2022]
Affiliation(s)
- Andrea Mahn
- Department of Chemical Engineering; Universidad de Santiago de Chile; Chile
| | - María Elena Lienqueo
- Department of Chemical and Biotechnology Engineering; University of Chile; Santiago Chile
| | - Claudia Quilodrán
- Department of Chemical and Biotechnology Engineering; University of Chile; Santiago Chile
| | - Alvaro Olivera-Nappa
- Department of Chemical and Biotechnology Engineering; University of Chile; Santiago Chile
| |
Collapse
|
19
|
Sahab ZJ, Kirilyuk A, Zhang L, Khamis ZI, Pompach P, Sung Y, Byers SW. Analysis of tubulin alpha-1A/1B C-terminal tail post-translational poly-glutamylation reveals novel modification sites. J Proteome Res 2012; 11:1913-23. [PMID: 22296162 PMCID: PMC3292626 DOI: 10.1021/pr2011044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tubulin-α(1A/1B) C-terminal tail (CTT) has seven glutamic acid residues among the last 11 amino acids of its sequence that are potential sites for glutamylation. Cleavage of C-terminal tyrosine resulting in the detyrosinated form of tubulin-α(1A/1B) is another major modification. These modifications among others bring about highly heterogeneous tubulin samples in brain cells and microtubules, play a major role in directing intracellular trafficking, microtubule dynamics, and mitotic events, and can vary depending on the cell and disease state, such as cancer and neurodegenerative disorders. Identified previously using primary mass spectrometry (MS) ions and partial Edman sequencing, tubulin-α(1A/1B) glutamylation was found exclusively on the E(445) residue. We here describe the analysis of tubulin-α(1A/1B) glutamylation and detyrosination after 2-DE separation, trypsin and proteinase K in-gel digestion, and nanoUPLC-ESI-QqTOF-MS/MS of mouse brain and bovine microtubules. Tyrosinated, detyrosinated, and Δ2-tubulin-α(1A/1B) CTTs were identified on the basis of a comparison of fragmentation patterns and retention times between endogenous and synthetic peptides. Stringent acceptance criteria were adapted for the identification of novel glutamylation sites. In addition to the previously identified site at E(445), glutamylation on mouse and bovine tubulin-α(1A/1B) CTTs was identified on E(441) and E(443) with MASCOT Expect values below 0.01. O-Methylation of glutamates was also observed.
Collapse
Affiliation(s)
- Ziad J Sahab
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University , Washington, DC 20007, United States.
| | | | | | | | | | | | | |
Collapse
|
20
|
Fedchenko V, Buneeva O, Kopylov A, Kaloshin A, Axenova L, Zgoda V, Medvedev A. Mass spectrometry detection of monomeric renalase in human urine. ACTA ACUST UNITED AC 2012; 58:599-607. [DOI: 10.18097/pbmc20125805599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Renalase is a recently discovered secretory protein, which is suggested to play a role (which still remains elusive) in regulation of blood pressure. Earlier it was purified from urine of healthy volunteers by means of ammonium sulfate fractionation and subsequent affinity chromatography (Xu et al. (2005) J. Clin. Invest., 115, 1275). The resultant purified preparation of renalase contained 2 proteins with molecular masses of 35 and 67-75 kDa. The authors believed that the latter represents a dimerization (aggregation) product of the 35 kDa protein. In this study we have detected relanase in urinary samples of 2 of 6 volunteers only after immunoaffinity enrichment of urinary samples subjected to ammonium sulfate precipitation. Electrophoresis of the purified preparation also demonstrated the presence of 2 proteins with molecular masses of 35 and 66 kDa, respectively. Mass spectrometry analysis of these proteins identified 35 and 66 kDa proteins as renalase and serum albumin, respectively. Thus, our results do not support suggestion on formation of renalase dimers and they indicate that urinary renalase excretion significantly varies in humans.
Collapse
Affiliation(s)
- V.I. Fedchenko
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - O.A. Buneeva
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - A.T. Kopylov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - A.A. Kaloshin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - L.N. Axenova
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - V.G. Zgoda
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - A.E. Medvedev
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| |
Collapse
|