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Johnston HE, Yadav K, Kirkpatrick JM, Biggs GS, Oxley D, Kramer HB, Samant RS. Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics Sample Preparation without Magnetic Beads. Anal Chem 2022; 94:10320-10328. [PMID: 35848328 PMCID: PMC9330274 DOI: 10.1021/acs.analchem.1c04200] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Complete, reproducible extraction of protein material
is essential
for comprehensive and unbiased proteome analyses. A current gold standard
is single-pot, solid-phase-enhanced sample preparation (SP3), in which
organic solvent and magnetic beads are used to denature and capture
protein aggregates, with subsequent washes removing contaminants.
However, SP3 is dependent on effective protein immobilization onto
beads, risks losses during wash steps, and exhibits losses and greater
costs at higher protein inputs. Here, we propose solvent precipitation
SP3 (SP4) as an alternative to SP3 protein cleanup, capturing acetonitrile-induced
protein aggregates by brief centrifugation rather than magnetism—with
optional low-cost inert glass beads to simplify handling. SP4 recovered
equivalent or greater protein yields for 1–5000 μg preparations
and improved reproducibility (median protein R2 0.99 (SP4) vs 0.97 (SP3)). Deep proteome
profiling revealed that SP4 yielded a greater recovery of low-solubility
and transmembrane proteins than SP3, benefits to aggregating protein
using 80 vs 50% organic solvent, and equivalent recovery by SP4 and S-Trap.
SP4 was verified in three other labs across eight sample types and
five lysis buffers—all confirming equivalent or improved proteome
characterization vs SP3. With near-identical recovery,
this work further illustrates protein precipitation as the primary
mechanism of SP3 protein cleanup and identifies that magnetic capture
risks losses, especially at higher protein concentrations and among
more hydrophobic proteins. SP4 offers a minimalistic approach to protein
cleanup that provides cost-effective input scalability, the option
to omit beads entirely, and suggests important considerations for
SP3 applications—all while retaining the speed and compatibility
of SP3.
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Affiliation(s)
- Harvey E Johnston
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kranthikumar Yadav
- Mass Spectrometry Facility, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | | | - George S Biggs
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, United Kingdom.,GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Holger B Kramer
- Medical Research Council London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
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Do T, Guran R, Adam V, Zitka O. Use of MALDI-TOF mass spectrometry for virus identification: a review. Analyst 2022; 147:3131-3154. [DOI: 10.1039/d2an00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibilities of virus identification, including SARS-CoV-2, by MALDI-TOF mass spectrometry are discussed in this review.
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Affiliation(s)
- Tomas Do
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Roman Guran
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, CZ-612 00 Brno, Czech Republic
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3
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Benabdelkamel H, Masood A, Alanazi IO, Alfadda AA. Comparison of protein precipitation methods from adipose tissue using difference gel electrophoresis. Electrophoresis 2018; 39:1745-1753. [PMID: 29736990 DOI: 10.1002/elps.201800124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/19/2018] [Indexed: 01/19/2023]
Abstract
Proteomic methods have great potential to aid our understanding of the functional and pathological roles of adipose tissue. A critical initial step in the proteomic studies is the efficient isolation of proteins before conducting detailed analysis. In this study, three different methods were used for precipitating proteins; we analyzed samples from visceral adipose tissue, subcutaneous adipose tissue, and stromal visceral fraction extracts after chloroform/methanol, acetone, and trichloroacetic acid precipitation. The proteins recovered after the precipitation steps were examined by 2D-DIGE. Statistical analyses were carried out using simple linear regression analyses and R2 values were calculated for the intra- and inter-method comparisons. We found that all three precipitation methods provided highly reproducible protein spots that were recovered when run in duplicate using the same method of precipitation, irrespective of whether it was solvent (R2 = 0.85-0.98) or acid-based (R2 = 0.80-0.96). A higher variation and poor correlation was noted for the recovered protein spots when comparisons were made between the methods (R2 = 0.40-0.88) and also when the same method was compared between different sample types. In this study, TCA-precipitated samples were enriched in lower molecular mass proteins compared to the samples extracted by solvent-based precipitation methods.
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Affiliation(s)
- Hicham Benabdelkamel
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Afshan Masood
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Ibrahim O Alanazi
- National Centre for Biotechnolgy King Abdulaziz City for Science and Technology (KACST), Riyadh, Kingdom of Saudi Arabia
| | - Assim A Alfadda
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Department of Medicine, College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
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4
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Sheen H. Quantitation of yeast total proteins in sodium dodecyl sulfate–polyacrylamide gel electrophoresis sample buffer for uniform loading. Anal Biochem 2016; 498:95-7. [DOI: 10.1016/j.ab.2016.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 12/29/2015] [Accepted: 01/03/2016] [Indexed: 01/03/2023]
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5
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Comparison of sodium dodecyl sulfate depletion techniques for proteome analysis by mass spectrometry. J Chromatogr A 2015; 1418:158-166. [DOI: 10.1016/j.chroma.2015.09.042] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 12/12/2022]
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6
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Feist P, Hummon AB. Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples. Int J Mol Sci 2015; 16:3537-63. [PMID: 25664860 PMCID: PMC4346912 DOI: 10.3390/ijms16023537] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed.
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Affiliation(s)
- Peter Feist
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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Thanos S, Böhm MR, Meyer zu Hörste M, Prokosch-Willing V, Hennig M, Bauer D, Heiligenhaus A. Role of crystallins in ocular neuroprotection and axonal regeneration. Prog Retin Eye Res 2014; 42:145-61. [DOI: 10.1016/j.preteyeres.2014.06.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/06/2014] [Accepted: 06/22/2014] [Indexed: 11/30/2022]
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8
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Crowell AMJ, Wall MJ, Doucette AA. Maximizing recovery of water-soluble proteins through acetone precipitation. Anal Chim Acta 2013; 796:48-54. [PMID: 24016582 DOI: 10.1016/j.aca.2013.08.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 12/17/2022]
Abstract
Solvent precipitation is commonly used to purify protein samples, as seen with the removal of sodium dodecyl sulfate through acetone precipitation. However, in its current practice, protein loss is believed to be an inevitable consequence of acetone precipitation. We herein provide an in depth characterization of protein recovery through acetone precipitation. In 80% acetone, the precipitation efficiency for six of 10 protein standards was poor (ca. ≤15%). Poor recovery was also observed for proteome extracts, including bacterial and mammalian cells. As shown in this work, increasing the ionic strength of the solution dramatically improves the precipitation efficiency of individual proteins, and proteome mixtures (ca. 80-100% yield). This is obtained by including 1-30 mM NaCl, together with acetone (50-80%) which maximizes protein precipitation efficiency. The amount of salt required to restore the recovery correlates with the amount of protein in the sample, as well as the intrinsic protein charge, and the dielectric strength of the solution. This synergistic approach to protein precipitation in acetone with salt is consistent with a model of ion pairing in organic solvent, and establishes an improved method to recover proteins and proteome mixtures in high yield.
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Affiliation(s)
- Andrew M J Crowell
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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9
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Wen WS, Hsieh MC, Wang SSS. High-level expression and purification of human γD-crystallin in Escherichia coli. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Devraj K, Geguchadze R, Klinger ME, Freeman WM, Mokashi A, Hawkins RA, Simpson IA. Improved membrane protein solubilization and clean-up for optimum two-dimensional electrophoresis utilizing GLUT-1 as a classic integral membrane protein. J Neurosci Methods 2009; 184:119-23. [PMID: 19631691 DOI: 10.1016/j.jneumeth.2009.07.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 07/09/2009] [Accepted: 07/15/2009] [Indexed: 11/18/2022]
Abstract
Two-dimensional (2-D) electrophoresis remains a primary resolving tool for proteomic analyses. The final number of proteins resolved by 2-D electrophoresis depends on their respective solubility, size, charge, and isoelectric point. While water-soluble cytosolic proteins have often been well represented in 2-D maps, the same is not true with membrane proteins. Highly hydrophobic in nature, membrane proteins are poorly resolved in 2-D gels due to problems associated primarily with sample preparation. This is of especial concern in neuroscience studies where many proteins of interest are membrane bound. In the current work, we present a substantially improved sample preparation protocol for membrane proteins utilizing the GLUT-1 glucose transporter from brain microvessels as an example of a typical membrane protein. GLUT-1 (SLC2A1; solute carrier family 2 (facilitated glucose transporter), member 1) is a 55kD glycoprotein that contains 12 membrane-spanning alpha helices that impart the protein its characteristic hydrophobicity. GLUT-1 based on its amino acid sequence has a theoretical isoelectric point (pI) of 8.94. Using a combination of the non-ionic detergents, n-dodecyl-beta-maltoside (DDM) and amido sulphobetaine-14 (ASB-14) for sample solubilization, and a modification of the Bio-Rad 2-D clean-up protocol involving trichloroacetic acid (TCA)/acetone, we obtained near complete solubilization of GLUT-1 and greater than 90% recovery of this membrane protein in 1-D and 2-D Western blots. The total number of proteins resolved also increased dramatically in Deep Purple total protein stains using our improved protocol.
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Affiliation(s)
- K Devraj
- Department of Neural & Behavioral Sciences, College of Medicine, Pennsylvania State University, United States
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11
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Fischer D, Hauk TG, Müller A, Thanos S. Crystallins of the beta/gamma-superfamily mimic the effects of lens injury and promote axon regeneration. Mol Cell Neurosci 2007; 37:471-9. [PMID: 18178099 DOI: 10.1016/j.mcn.2007.11.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 10/31/2007] [Accepted: 11/07/2007] [Indexed: 10/22/2022] Open
Abstract
Adult retinal ganglion cells (RGCs) can survive axotomy and regrow lengthy axons when exposed to lens injury (LI). The neuroprotective and axon-growth-promoting effects of LI have been attributed to an infiltration of activated macrophages into the inner eye and recently also to astrocyte-derived CNTF. The present work reveals that certain purified lens proteins (crystallins) cause the effects of LI. Intravitreal injections of beta- or gamma-crystallins, but not of alpha-crystallin, strongly enhanced axon regeneration from retinal explants in culture, within peripheral nerve grafts or the crushed optic nerve. Deposition of the effective crystallins within the vitreous body was also associated with an influx of circulating macrophages and an activation of retinal astrocytes, Müller cells, and resident microglia. Furthermore beta-crystallin induced CNTF expression in retinal astrocytes and activation of CNTF's major downstream signaling pathway (JAK/STAT3) when intravitreally injected or added to the culture medium ex vivo. Consistently, in culture the addition of beta- and gamma-crystallins to the medium also increased axon regeneration from retinal explants. These results demonstrate that crystallins of the beta/gamma-superfamily are the lens-derived activators of cascades, which lead to axonal regeneration and suggest that their effects might be mediated by astrocyte-derived CNTF.
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Affiliation(s)
- Dietmar Fischer
- Department of Experimental Neurology, Medical School, University of Ulm, Albert-Einstein-Allee 11, D89081 Ulm, Germany.
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12
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Fujimoto T, Miya M, Machida M, Takechi S, Kakinoki S, Kanda K, Nomura A. Improved Recovery of Human Urinary Protein for Electrophoresis. ACTA ACUST UNITED AC 2006. [DOI: 10.1248/jhs.52.718] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tetsuya Fujimoto
- Department of Pathophysiology, Hokkaido Pharmaceutical University, School of Pharmacy
| | - Makiko Miya
- Department of Pathophysiology, Hokkaido Pharmaceutical University, School of Pharmacy
| | - Maiko Machida
- Department of Pathophysiology, Hokkaido Pharmaceutical University, School of Pharmacy
| | - Shigeru Takechi
- Department of Cardiovascular Medicine, Date Red Cross Hospital
| | - Shigeo Kakinoki
- Department of Cardiovascular Medicine, Otaru Kyokai Hospital
| | - Koichi Kanda
- Department of Cardiovascular Medicine, Sapporo Kosei Hospital
| | - Akikazu Nomura
- Department of Pathophysiology, Hokkaido Pharmaceutical University, School of Pharmacy
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13
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Tantipaiboonwong P, Sinchaikul S, Sriyam S, Phutrakul S, Chen ST. Different techniques for urinary protein analysis of normal and lung cancer patients. Proteomics 2005; 5:1140-9. [PMID: 15693063 DOI: 10.1002/pmic.200401143] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Many components in urine are useful in clinical diagnosis and urinary proteins are known as important components to define many diseases such as proteinuria, kidney, bladder and urinary tract diseases. In this study, we focused on the comparison of different sample preparation methods for isolating urinary proteins prior to protein analysis of pooled healthy and lung cancer patient samples. Selective method was used for preliminary investigation of some putative urinary protein markers. Urine samples were passed first through a gel filtration column (PD-10 desalting column) to remove high salts and subsequently concentrated. Remaining interferences were removed by ultrafiltration or four precipitation methods. The analysis of urinary proteins by high-performance liquid chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed many similarities in profiles among preparation methods and a few profiles were different between normal and lung cancer patients. In contrast, the results of two-dimensional gel electrophoresis (2-DE) showed more distinctly different protein patterns. Our finding showed that the sequential preparation of urinary proteins by gel filtration and ultrafiltration could retain most urinary proteins which demonstrated the highest protein spots on 2-D gels and able to identify preliminary urinary protein markers related to cancer. Although sequential preparation of urine samples by gel filtration and protein precipitation resulted in low amounts of proteins on 2-D gels, high Mr proteins were easily detected. Therefore, there are alternative choices for urine sample preparation for studying the urinary proteome and identifying urinary protein markers important for further preclinical diagnostic and therapeutic applications.
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Thongboonkerd V, McLeish KR, Arthur JM, Klein JB. Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int 2002; 62:1461-9. [PMID: 12234320 DOI: 10.1111/j.1523-1755.2002.kid565.x] [Citation(s) in RCA: 255] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND Proteomic techniques have recently become available for large-scale protein analysis. The utility of these techniques in identification of urinary proteins is poorly defined. We constructed a proteome map of normal human urine as a reference protein database by using two differential fractionated techniques to isolate the proteins. METHODS Proteins were isolated from urine obtained from normal human volunteers by acetone precipitation or ultracentrifugation, separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and identified by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry followed by peptide mass fingerprinting. RESULTS A total of 67 protein forms of 47 unique proteins were identified, including transporters, adhesion molecules, complement, chaperones, receptors, enzymes, serpins, cell signaling proteins and matrix proteins. Acetone precipitated more acidic and hydrophilic proteins, whereas ultracentrifugation fractionated more basic, hydrophobic, and membrane proteins. Bioinformatic analysis predicted glycosylation to be the most common explanation for multiple forms of the same protein. CONCLUSIONS Combining two differential isolation techniques magnified protein identification from human urine. Proteomic analysis of urinary proteins is a promising tool to study renal physiology and pathophysiology and to determine biomarkers of renal disease.
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Affiliation(s)
- Visith Thongboonkerd
- Core Proteomics Laboratory and Molecular Signaling Group, Kidney Disease Program, Department of Medicine, University of Louisville, 570 South Preston Street, Louisville, KY 40202, USA
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