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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Jiang J, Zhan L, Dai L, Yao X, Qin Y, Zhu Z, Zhang M, Tong W, Wang G. Evaluation of the reliability of MS1-based approach to profile naturally occurring peptides with clinical relevance in urine samples. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022:e9369. [PMID: 35906701 DOI: 10.1002/rcm.9369] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/02/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE The profiling of natural urinary peptides is a valuable indicator of kidney condition. While front-end separation limits the speed of peptidomic profiling, MS1-based results suffer from limited peptide coverage and specificity. Clinical studies on chronic kidney disease require an effective strategy to balance the trade-off between identification depth and throughput. METHODS CKD273, a urinary proteome classifier associated with chronic kidney disease, in samples from diabetic nephropathy patients was profiled in parallel using capillary electrophoresis-mass spectrometry (CE-MS), liquid chromatography with mass spectrometry (LC-MS), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Through cross-comparison of results from MS1 of unfractionated peptides and elution-time-resolved MS1 as well as MS/MS in LC- and CE-MS approaches, we evaluated the contribution of false-positive identification to MS1-based identification and quantitation, and analyzed the benefit of front-end separation in terms of accuracy and efficiency. RESULTS In LC- and CE-MS, although MS1 data resulted in higher number of identifications than MS/MS, elution-time-dependent analysis revealed extensive interference by non-CKD273 peptides, which would contribute up to 50% to quantitation if they are not separated from genuine CKD273 peptides. In the absence of separation, MS1 data resulted in lower numbers of identifications and abundance pattern that significantly deviated from those by liquid chromatography with tandem mass spectrometry (LC-MS/MS) or capillary electrophoresis with tandem mass spectrometry (CE-MS/MS). CE showed higher identification efficiency even when less sample was used or achieved faster separation. CONCLUSIONS To ensure the reliability of MS1-based urinary peptide profiling, front-end separation should not be omitted, and elution time should be used in addition to intact mass for identification. Including MS/MS in data acquisition does not compromise the speed or identification number, while benefiting data reliability by providing real-time sequence verification.
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Affiliation(s)
- Jialu Jiang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Lingpeng Zhan
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Liuyan Dai
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Xiaopeng Yao
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Yao Qin
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Zhongqin Zhu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
| | - Mei Zhang
- Department of Endocrinology, The First Affiliated Hospital with Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Wenjun Tong
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, China
| | - Guanbo Wang
- Shenzhen Bay Laboratory, Institute for Cell Analysis, Shenzhen, China
- Biomedical Pioneering Innovation Centre, Peking University, Beijing, China
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Jin J, Gong J, Zhao L, Li Y, Wang Y, He Q. iTRAQ-based comparative proteomics analysis reveals specific urinary biomarkers for various kidney diseases. Biomark Med 2020; 14:839-854. [PMID: 32856461 DOI: 10.2217/bmm-2019-0556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/20/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Proteome studies for multiple renal diseases is bare. Methodology & results: Using isobaric tags for relative and absolute quantitation labeling, many differentially expressed proteins (DEPs) were identified in acute kidney injury (AKI), AKI + chronic kidney disease (CKD), diabetic CKD and nondiabetic CKD with or without IgA nephropathy (IgAN). Comparative analysis indicated that 34, 35, 17, 91 and 14 unique DEPs were found in AKI, AKI + CKD, CKD, diabetic CKD and nondiabetic CKD. Compared with nondiabetic CKD with IgAN, 47 unique DEPs were found in that without IgAN. Serum amyloid A1 (SAA1) and hepatocyte growth factor activator were unregulated in AKI and nondiabetic CKD without IgAN, respectively. Regenerating islet-derived protein 3-α (Reg3A) upregulation is associated with AKI and AKI + CKD patients. Conclusion: This research contributes to urinary biomarker discovery from multiple renal diseases.
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Affiliation(s)
- Juan Jin
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Jianguang Gong
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Li Zhao
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Yiwen Li
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Yunguang Wang
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
| | - Qiang He
- Department of Nephrology, Zhejiang Provincial People's Hospital, Zhejiang 310014, PR China
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang 310014, PR China
- Key Laboratory of Kidney Disease of Traditional Chinese Medicine in Zhejiang Province, Zhejiang 310014, PR China
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Winiarczyk D, Michalak K, Adaszek L, Winiarczyk M, Winiarczyk S. Urinary proteome of dogs with kidney injury during babesiosis. BMC Vet Res 2019; 15:439. [PMID: 31801572 PMCID: PMC6894246 DOI: 10.1186/s12917-019-2194-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/26/2019] [Indexed: 02/07/2023] Open
Abstract
Background Acute kidney injury is the most frequent complication of babesiosis in dogs and may provide a natural model for identifying early and specific markers of kidney injury in this species. There are limited data on urine proteomics in dogs, and none of the effect of babesiosis on the urine proteome. This study aimed to identify urinary proteins of dogs with kidney injury during the natural course of babesiosis caused by Babesia canis, and to compare them with proteins in a control group to reveal any potential biomarkers predicting renal injury before the presence of azotemia. Urine samples were collected from 10 dogs of various breeds and sex with naturally occurring babesiosis, and 10 healthy dogs. Pooled urine samples from both groups were separated by 2D (two-dimensional) electrophoresis, followed by protein identification using MALDI-TOF (matrix-assisted laser desorption ionization time of flight) mass spectrometry. Results In total, 176 proteins were identified in the urine samples from healthy dogs, and 403 proteins were identified in the urine samples from dogs with babesiosis. Of the 176 proteins, 146 were assigned exclusively to healthy dogs, and 373 of the 403 proteins were assigned exclusively to dogs with babesiosis; 30 proteins were common for both groups. Characteristic analysis of 373 proteins found in dogs with babesiosis led to the isolation of 8 proteins associated with 10 metabolic pathways involved in immune and inflammatory responses. Conclusions It was hypothesized that epithelial-mesenchymal transition might play an important role in the mechanisms underlying pathological changes in renal tissue during babesiosis, as indicated by a causal relationship network built by combining 5 of the 10 selected metabolic pathways, and 4 of the 8 proteins associated with these pathways; this network included cadherins, gonadotropin releasing hormone receptors, inflammatory responses mediated by chemokine and cytokine signalling pathways, integrins, interleukins, and TGF-β (transforming growth factor β) pathways. Those pathways were linked by interleukin-13, bone morphogenetic protein 7, α2(1) collagen, and tyrosine protein kinase Fer, which are potential biomarkers of damage during babesiosis in dogs, that might indicate early renal injury.
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Affiliation(s)
- D Winiarczyk
- Department and Clinic of Animal Internal Diseases, University of Life Sciences, Głęboka 30, 20-612, Lublin, Poland
| | - K Michalak
- Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences, Głęboka 30, 20- 612, Lublin, Poland
| | - L Adaszek
- Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences, Głęboka 30, 20- 612, Lublin, Poland
| | - M Winiarczyk
- Department of Vitreoretinal Surgery, Medical University of Lublin, Chmielna 1, 20-079, Lublin, Poland
| | - S Winiarczyk
- Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences, Głęboka 30, 20- 612, Lublin, Poland.
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Manikandan M, Deenadayalan A, Vimala A, Gopal J, Chun S. Clinical MALDI mass spectrometry for tuberculosis diagnostics: Speculating the methodological blueprint and contemplating the obligation to improvise. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Torres-Sangiao E, Holban AM, Gestal MC. Advanced Nanobiomaterials: Vaccines, Diagnosis and Treatment of Infectious Diseases. Molecules 2016; 21:molecules21070867. [PMID: 27376260 PMCID: PMC6273484 DOI: 10.3390/molecules21070867] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/21/2016] [Accepted: 06/25/2016] [Indexed: 11/16/2022] Open
Abstract
The use of nanoparticles has contributed to many advances due to their important properties such as, size, shape or biocompatibility. The use of nanotechnology in medicine has great potential, especially in medical microbiology. Promising data show the possibility of shaping immune responses and fighting severe infections using synthetic materials. Different studies have suggested that the addition of synthetic nanoparticles in vaccines and immunotherapy will have a great impact on public health. On the other hand, antibiotic resistance is one of the major concerns worldwide; a recent report of the World Health Organization (WHO) states that antibiotic resistance could cause 300 million deaths by 2050. Nanomedicine offers an innovative tool for combating the high rates of resistance that we are fighting nowadays, by the development of both alternative therapeutic and prophylaxis approaches and also novel diagnosis methods. Early detection of infectious diseases is the key to a successful treatment and the new developed applications based on nanotechnology offer an increased sensibility and efficiency of the diagnosis. The aim of this review is to reveal and discuss the main advances made on the science of nanomaterials for the prevention, diagnosis and treatment of infectious diseases. Highlighting innovative approaches utilized to: (i) increasing the efficiency of vaccines; (ii) obtaining shuttle systems that require lower antibiotic concentrations; (iii) developing coating devices that inhibit microbial colonization and biofilm formation.
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Affiliation(s)
- Eva Torres-Sangiao
- Department of Microbiology and Parasitology, University Santiago de Compostela, Galicia 15782, Spain.
| | - Alina Maria Holban
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Bucharest 060042, Romania.
| | - Monica Cartelle Gestal
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens (UGA), GA 30602, USA.
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Chen Z, Kim J. Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. BMC Urol 2016; 16:11. [PMID: 27000794 PMCID: PMC4802825 DOI: 10.1186/s12894-016-0129-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
Background Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism. Discussion We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition. Conclusion Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.
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Affiliation(s)
- Zhaohui Chen
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Medicine, University of California, Los Angeles, CA, USA.
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