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Xu D, Dai X, Zhang L, Cai Y, Chen K, Wu J, Dong L, Shen L, Yang J, Zhao J, Zhou Y, Mei Z, Wei W, Zhang Z, Xiong N. Mass spectrometry for biomarkers, disease mechanisms, and drug development in cerebrospinal fluid metabolomics. Trends Analyt Chem 2024; 173:117626. [DOI: 10.1016/j.trac.2024.117626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
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Masood A, Benabdelkamel H, Alfadda AA. Obesity Proteomics: An Update on the Strategies and Tools Employed in the Study of Human Obesity. High Throughput 2018; 7:ht7030027. [PMID: 30213114 PMCID: PMC6164994 DOI: 10.3390/ht7030027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
Proteomics has become one of the most important disciplines for characterizing cellular protein composition, building functional linkages between protein molecules, and providing insight into the mechanisms of biological processes in a high-throughput manner. Mass spectrometry-based proteomic advances have made it possible to study human diseases, including obesity, through the identification and biochemical characterization of alterations in proteins that are associated with it and its comorbidities. A sizeable number of proteomic studies have used the combination of large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography in combination with mass spectrometry, for high-throughput protein identification. These studies have applied proteomics to comprehensive biochemical profiling and comparison studies while using different tissues and biological fluids from patients to demonstrate the physiological or pathological adaptations within their proteomes. Further investigations into these proteome-wide alterations will enable us to not only understand the disease pathophysiology, but also to determine signature proteins that can serve as biomarkers for obesity and related diseases. This review examines the different proteomic techniques used to study human obesity and discusses its successful applications along with its technical limitations.
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Affiliation(s)
- Afshan Masood
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia.
| | - Hicham Benabdelkamel
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia.
| | - Assim A Alfadda
- Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia.
- Department of Medicine, College of Medicine, King Saud University, P.O. Box 2925 (38), Riyadh 11461, Saudi Arabia.
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Wu Y, Li L. Sample normalization methods in quantitative metabolomics. J Chromatogr A 2015; 1430:80-95. [PMID: 26763302 DOI: 10.1016/j.chroma.2015.12.007] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 12/31/2022]
Abstract
To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts.
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Affiliation(s)
- Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada.
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Ho HP, Rathod P, Louis M, Tada CK, Rahaman S, Mark KJ, Leng J, Dana D, Kumar S, Lichterfeld M, Chang EJ. Studies on quantitative phosphopeptide analysis by matrix-assisted laser desorption/ionization mass spectrometry without label, chromatography or calibration curves. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2681-9. [PMID: 25380489 PMCID: PMC4225566 DOI: 10.1002/rcm.7063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 05/12/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope labeling methods are effective for protein and peptide quantification, but limited in their multiplexing capacity, cost-effectiveness and dynamic range. This study investigates MALDI-MS-based quantification of peptide phosphorylation without labeling, and aims to overcome the shot-to-shot variability of MALDI using a mathematical transformation and extended data acquisition times. METHODS A linear relationship between the reciprocal of phosphopeptide mole fraction and the reciprocal of phosphorylated-to-unphosphorylated signal ratio is derived, and evaluated experimentally using three separate phosphopeptide systems containing phosphorylated serine, threonine and tyrosine residues: mixtures of phosphopeptide and its des-phospho-analog with known stoichiometry measured by vacuum MALDI-linear ion trap mass spectrometry and fit to the linear model. The model is validated for quantifying in vitro phosphorylation assays with inhibition studies on Cdk2/cyclinA. RESULTS Dynamic range of picomoles to femtomoles, good accuracy (deviations of 1.5-3.0% from expected values) and reproducibility (relative standard deviation (RSD) = 4.3-6.3%) are achieved. Inhibition of cyclin-dependent kinase phosphorylation by the classical inhibitors olomoucine and r-roscovitine was evaluated and IC50 values found to be in agreement with reported literature values. These results, achieved with single-point calibration, without isotope or chromatography, compare favorably to those arrived at using isotope dilution (p > 0.5 for accuracy). CONCLUSIONS The mathematical relationship derived here can be applied to a method that we term Double Reciprocal Isotope-free Phosphopeptide Quantification (DRIP-Q), as a strategy for quantification of in vitro phosphorylation assays, the first MALDI-based, isotope- and calibration curve-free method of its type. These results also pave the way for further systematic studies investigating the effect of peptide composition and experimental conditions on quantitative, label-free MALDI.
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Affiliation(s)
- Hsin-Pin Ho
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Pratikkumar Rathod
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Marissa Louis
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Christine K. Tada
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Sherida Rahaman
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Kevin J. Mark
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
- Department of Natural Sciences, LaGuardia Community College, The City University of New York, Long Island City, NY, USA
| | - Jin Leng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Dibyendu Dana
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Queens, NY USA
| | - Sanjai Kumar
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Queens, NY USA
- Department of Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Emmanuel J. Chang
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
- Department of Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Address reprint requests to Emmanuel Chang; York College, 94-20 Guy R. Brewer Blvd, Jamaica, NY 11451, 718-262-3778 (phone), 718-262-2652 (fax),
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Huang YQ, Wang QY, Liu JQ, Hao YH, Yuan BF, Feng YQ. Isotope labelling – paired homologous double neutral loss scan-mass spectrometry for profiling of metabolites with a carboxyl group. Analyst 2014; 139:3446-54. [DOI: 10.1039/c4an00312h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The development of a method for non-targeted screening of metabolites with a carboxyl group by high performance liquid chromatography-mass spectrometry with paired homologous double neutral loss scan mode afterin vitroisotope labelling was reported.
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Affiliation(s)
- Yun-Qing Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072, China
| | - Qiu-Yi Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072, China
| | - Jia-Qi Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072, China
| | - Yan-Hong Hao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072, China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072, China
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Torde RG, Therrien AJ, Shortreed MR, Smith LM, Lamos SM. Multiplexed analysis of cage and cage free chicken egg fatty acids using stable isotope labeling and mass spectrometry. Molecules 2013; 18:14977-88. [PMID: 24317525 PMCID: PMC4249618 DOI: 10.3390/molecules181214977] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/29/2013] [Accepted: 12/02/2013] [Indexed: 01/04/2023] Open
Abstract
Binary stable isotope labeling couple with LC-ESI-MS has been used as a powerful non-targeted approach for the relative quantification of lipids, amino acids, and many other important metabolite classes. A multiplexed approach using three or more isotopic labeling reagents greatly reduces analytical run-time while maintaining excellent sensitivity and reproducibility. Three isotopic cholamine labeling reagents have been developed to take advantage of the pre-ionized character of cholamine, for ESI, and the ease by which stable isotopes can be incorporated into the cholamine structure. These three cholamine labeling reagents have been used to relatively quantify three fatty acid samples simultaneously. The quantification resulted in the observation of 12 fatty acids that had an average absolute error of 0.9% and an average coefficient of variation of 6.1%. Caged versus cage-free isotope labeling experiments showed that cage-free eggs have an increased level of omega-3 fatty acids as compared to caged eggs. This multiplexed fatty acid analysis provides an inexpensive and expedited tool for broad-based lipid profiling that will further aid discoveries in the mechanisms of fatty acid action in cells.
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Affiliation(s)
- Richard G. Torde
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, VT 05405, USA; E-Mail:
| | - Andrew J. Therrien
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA; E-Mail:
| | - Michael R. Shortreed
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, USA; E-Mails: (M.R.S.); (L.M.S.)
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, USA; E-Mails: (M.R.S.); (L.M.S.)
| | - Shane M. Lamos
- Department of Chemistry and Physics, Saint Michael’s College, 1 Winooski Park, Colchester, VT 05439, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-802-654-2842; Fax: +1-802-654-2236
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Kang C, Zhou Y, Du Z, Bian Z, Wang J, Qiu X, Gao L, Sun Y. Dehydrogenation and dehalogenation of amines in MALDI-TOF MS investigated by isotopic labeling. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1318-1324. [PMID: 24338887 DOI: 10.1002/jms.3296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 10/05/2013] [Accepted: 10/13/2013] [Indexed: 06/03/2023]
Abstract
Secondary and tertiary amines have been reported to form [M-H](+) that correspond to dehydrogenation in matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI-TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N-benzyl group, which resulted in the formation of [M-D](+) and [M-H](+) ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N-benzyl group showed high-intensity [M-D](+) and [M-H](+) ion peaks, whereas those of secondary amines showed low-intensity ion peaks. Ratios between the peak intensities of [M-D](+) and [M-H](+) greater than 1 suggested chemoselective dehydrogenation at the N-benzyl groups. The presence of an electron donor group on the N-benzyl groups enhanced the selectivity. The dehalogenation of amines with an N-(4-halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI-TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules.
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Affiliation(s)
- Chuanqing Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
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