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Ruan H, Xu C, Fan Z, Wang W, Li H. Radial Electric Field Driven Collision-Induced Dissociation in a Miniature Continuous Atmospheric Pressure Interfaced Ion Trap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2822-2830. [PMID: 37883684 DOI: 10.1021/jasms.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Miniature ion trap mass spectrometry with the unique ability of tandem-in-time analysis is extensively used in public security and environmental pollution detection. In this study, a novel radial electric field driven collision-induced dissociation (REFD-CID) is presented with high fragmentation efficiency for different species by adjusting the float DC, the initial kinetic energy of ions, and the pressure in a miniature continuous atmospheric pressure interfaced ion trap mass spectrometer (CAPI-ITMS). It is noteworthy that multiple fragment ions ([M+H-nC2H4]+, where n = 1, 2, 3) of triethyl phosphate were observed with a single injection of ions. The underlying mechanism of the REFD-CID revealed that the enhanced radial electric field by modulation of the float DC drove ions toward regions of intense RF field where broadband heating and dissociation of ions took place through theoretical simulations. Finally, the REFD-CID was utilized to improve the instrument performances. The existence of reagent ions led to a severe space charge effect as the ion injection duration of the CAPI-ITMS was extended to enhance the sensitivity of aniline. Through selective fragmentation of reagent ions, peak broadening and mass shift were eliminated, and meanwhile, a 28-fold improvement of aniline in a signal-to-noise ratio was achieved with the ion injection duration varying from 50 to 2500 ms. Moreover, isomeric illicit drugs (JWH-018 and acetylcodeine) were distinguished by generating multiple characteristic fragment ions, demonstrating potential applications in the identification of synthetic illicit drugs.
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Affiliation(s)
- Huiwen Ruan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), 457 Zhongshan Road, Dalian 116023, People's Republic of China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, People's Republic of China
- Dalian Key Laboratory for Online Analytical Instrumentation, 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Engineering Research Center of Breath Diagnostic Technology, Dalian 116023, People's Republic of China
| | - Chuting Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), 457 Zhongshan Road, Dalian 116023, People's Republic of China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, People's Republic of China
- Dalian Key Laboratory for Online Analytical Instrumentation, 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Engineering Research Center of Breath Diagnostic Technology, Dalian 116023, People's Republic of China
| | - Zhigang Fan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), 457 Zhongshan Road, Dalian 116023, People's Republic of China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, People's Republic of China
- Dalian Key Laboratory for Online Analytical Instrumentation, 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Engineering Research Center of Breath Diagnostic Technology, Dalian 116023, People's Republic of China
| | - Weiguo Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Key Laboratory for Online Analytical Instrumentation, 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Engineering Research Center of Breath Diagnostic Technology, Dalian 116023, People's Republic of China
| | - Haiyang Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Key Laboratory for Online Analytical Instrumentation, 457 Zhongshan Road, Dalian 116023, People's Republic of China
- Dalian Engineering Research Center of Breath Diagnostic Technology, Dalian 116023, People's Republic of China
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Yun BH, Guo J, Bellamri M, Turesky RJ. DNA adducts: Formation, biological effects, and new biospecimens for mass spectrometric measurements in humans. MASS SPECTROMETRY REVIEWS 2020; 39:55-82. [PMID: 29889312 PMCID: PMC6289887 DOI: 10.1002/mas.21570] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Hazardous chemicals in the environment and diet or their electrophilic metabolites can form adducts with genomic DNA, which can lead to mutations and the initiation of cancer. In addition, reactive intermediates can be generated in the body through oxidative stress and damage the genome. The identification and measurement of DNA adducts are required for understanding exposure and the causal role of a genotoxic chemical in cancer risk. Over the past three decades, 32 P-postlabeling, immunoassays, gas chromatography/mass spectrometry, and liquid chromatography/mass spectrometry (LC/MS) methods have been established to assess exposures to chemicals through measurements of DNA adducts. It is now possible to measure some DNA adducts in human biopsy samples, by LC/MS, with as little as several milligrams of tissue. In this review article, we highlight the formation and biological effects of DNA adducts, and highlight our advances in human biomonitoring by mass spectrometric analysis of formalin-fixed paraffin-embedded tissues, untapped biospecimens for carcinogen DNA adduct biomarker research.
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Affiliation(s)
- Byeong Hwa Yun
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Jingshu Guo
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
| | - Robert J. Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, 2231 6 St. SE, Minneapolis, Minnesota, 55455, United States
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Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides. Nat Protoc 2019; 14:283-312. [PMID: 30559375 DOI: 10.1038/s41596-018-0094-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA contains not only canonical nucleotides but also a variety of modifications of the bases. In particular, cytosine and adenine are frequently modified. Determination of the exact quantity of these noncanonical bases can contribute to the characterization of the state of a biological system, e.g., determination of disease or developmental processes, and is therefore extremely important. Here, we present a workflow that includes detailed description of critical sample preparation steps and important aspects of mass spectrometry analysis and validation. In this protocol, extraction and digestion of DNA by an optimized spin-column and enzyme-based method are described. Isotopically labeled standards are added in the course of DNA digestion, which allows exact quantification by isotope dilution mass spectrometry. To overcome the major bottleneck of such analyses, we developed a short (~14-min-per-sample) ultra-HPLC (UHPLC) and triple quadrupole mass spectrometric (QQQ-MS) method. Easy calculation of the modification abundance in the genome is possible with the provided evaluation sheets. Compared to alternative methods, the quantification procedure presented here allows rapid, ultrasensitive (low femtomole range) and highly reproducible quantification of different nucleosides in parallel. Including sample preparation and evaluation, quantification of DNA modifications can be achieved in less than a week.
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Spodzieja M, Rodziewicz-Motowidło S, Szymanska A. Hyphenated Mass Spectrometry Techniques in the Diagnosis of Amyloidosis. Curr Med Chem 2019; 26:104-120. [DOI: 10.2174/0929867324666171003113019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/25/2016] [Accepted: 09/01/2016] [Indexed: 12/18/2022]
Abstract
Amyloidoses are a group of diseases caused by the extracellular deposition of proteins forming amyloid fibrils. The amyloidosis is classified according to the main protein or peptide that constitutes the amyloid fibrils. The most effective methods for the diagnosis of amyloidosis are based on mass spectrometry. Mass spectrometry enables confirmation of the identity of the protein precursor of amyloid fibrils in biological samples with very high sensitivity and specificity, which is crucial for proper amyloid typing. Due to the fact that biological samples are very complex, mass spectrometry is usually connected with techniques such as liquid chromatography or capillary electrophoresis, which enable the separation of proteins before MS analysis. Therefore mass spectrometry constitutes an important part of the so called “hyphenated techniques” combining, preferentially in-line, different analytical methods to provide comprehensive information about the studied problem. Hyphenated methods are very useful in the discovery of biomarkers in different types of amyloidosis. In systemic forms of amyloidosis, the analysis of aggregated proteins is usually performed based on the tissues obtained during a biopsy of an affected organ or a subcutaneous adipose tissue. In some cases, when the diagnostic biopsy is not possible due to the fact that amyloid fibrils are formed in organs like the brain (Alzheimer’s disease), the study of biomarkers presented in body fluids can be carried out. Currently, large-scale studies are performed to find and validate more effective biomarkers, which can be used in diagnostic procedures. We would like to present the methods connected with mass spectrometry which are used in the diagnosis of amyloidosis based on the analysis of proteins occurring in tissues, blood and cerebrospinal fluid.
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Affiliation(s)
- Marta Spodzieja
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylwia Rodziewicz-Motowidło
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Aneta Szymanska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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Honour JW, Conway E, Hodkinson R, Lam F. The evolution of methods for urinary steroid metabolomics in clinical investigations particularly in childhood. J Steroid Biochem Mol Biol 2018; 181:28-51. [PMID: 29481855 DOI: 10.1016/j.jsbmb.2018.02.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022]
Abstract
The metabolites of cortisol, and the intermediates in the pathways from cholesterol to cortisol and the adrenal sex steroids can be analysed in a single separation of steroids by gas chromatography (GC) coupled to MS to give a urinary steroid profile (USP). Steroids individually and in profile are now commonly measured in plasma by liquid chromatography (LC) coupled with MS/MS. The steroid conjugates in urine can be determined after hydrolysis and derivative formation and for the first time without hydrolysis using GC-MS, GC-MS/MS and liquid chromatography with mass spectrometry (LC-MS/MS). The evolution of the technology, practicalities and clinical applications are examined in this review. The patterns and quantities of steroids changes through childhood. Information can be obtained on production rates, from which children with steroid excess and deficiency states can be recognised when presenting with obesity, adrenarche, adrenal suppression, hypertension, adrenal tumours, intersex condition and early puberty, as examples. Genetic defects in steroid production and action can be detected by abnormalities from the GC-MS of steroids in urine. New mechanisms of steroid synthesis and metabolism have been recognised through steroid profiling. GC with tandem mass spectrometry (GC-MS/MS) has been used for the tentative identification of unknown steroids in urine from newborn infants with congenital adrenal hyperplasia. Suggestions are made as to areas for future research and for future applications of steroid profiling. As routine hospital laboratories become more familiar with the problems of chromatographic and MS analysis they can consider steroid profiling in their test repertoire although with LC-MS/MS of urinary steroids this is unlikely to become a routine test because of the availability, cost and purity of the internal standards and the complexity of data interpretation. Steroid profiling with quantitative analysis by mass spectrometry (MS) after chromatography now provides the most versatile of tests of adrenal function in childhood.
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Affiliation(s)
- John W Honour
- Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
| | - E Conway
- Clinical Biochemistry, HSL Analytics LLP, Floor 2, 1 Mabledon Place, London, WC1H 9AX, UK
| | - R Hodkinson
- Clinical Biochemistry, HSL Analytics LLP, Floor 2, 1 Mabledon Place, London, WC1H 9AX, UK
| | - F Lam
- Clinical Biochemistry, HSL Analytics LLP, Floor 2, 1 Mabledon Place, London, WC1H 9AX, UK
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6
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Gomes NG, Pereira DM, Valentão P, Andrade PB. Hybrid MS/NMR methods on the prioritization of natural products: Applications in drug discovery. J Pharm Biomed Anal 2018; 147:234-249. [DOI: 10.1016/j.jpba.2017.07.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/17/2022]
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7
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Guo J, Villalta PW, Turesky RJ. Data-Independent Mass Spectrometry Approach for Screening and Identification of DNA Adducts. Anal Chem 2017; 89:11728-11736. [PMID: 28977750 PMCID: PMC5727898 DOI: 10.1021/acs.analchem.7b03208] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long-term exposures to environmental toxicants and endogenous electrophiles are causative factors for human diseases including cancer. DNA adducts reflect the internal exposure to genotoxicants and can serve as biomarkers for risk assessment. Liquid chromatography-multistage mass spectrometry (LC-MSn) is the most common method for biomonitoring DNA adducts, generally targeting single exposures and measuring up to several adducts. However, the data often provide limited evidence for a role of a chemical in the etiology of cancer. An "untargeted" method is required that captures global exposures to chemicals, by simultaneously detecting their DNA adducts in the genome; some of which may induce cancer-causing mutations. We established a wide selected ion monitoring tandem mass spectrometry (wide-SIM/MS2) screening method utilizing ultraperformance-LC nanoelectrospray ionization Orbitrap MSn with online trapping to enrich bulky, nonpolar adducts. Wide-SIM scan events are followed by MS2 scans to screen for modified nucleosides by coeluting peaks containing precursor and fragment ions differing by -116.0473 Da, attributed to the neutral loss of deoxyribose. Wide-SIM/MS2 was shown to be superior in sensitivity, specificity, and breadth of adduct coverage to other tested adductomic methods with detection possible at adduct levels as low as 4 per 109 nucleotides. Wide-SIM/MS2 data can be analyzed in a "targeted" fashion by generation of extracted ion chromatograms or in an "untargeted" fashion where a chromatographic peak-picking algorithm can be used to detect putative DNA adducts. Wide-SIM/MS2 successfully detected DNA adducts, derived from chemicals in the diet and traditional medicines and from lipid peroxidation products, in human prostate and renal specimens.
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Affiliation(s)
- Jingshu Guo
- Masonic Cancer Center, College of Pharmacy, 2231 Sixth Street SE, Minneapolis, Minnesota 55455
- Department of Medicinal Chemistry, College of Pharmacy, 2231 Sixth Street SE, Minneapolis, Minnesota 55455
| | - Peter W. Villalta
- Masonic Cancer Center, College of Pharmacy, 2231 Sixth Street SE, Minneapolis, Minnesota 55455
| | - Robert J. Turesky
- Masonic Cancer Center, College of Pharmacy, 2231 Sixth Street SE, Minneapolis, Minnesota 55455
- Department of Medicinal Chemistry, College of Pharmacy, 2231 Sixth Street SE, Minneapolis, Minnesota 55455
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8
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Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
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9
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Guo J, Turesky RJ. Human Biomonitoring of DNA Adducts by Ion Trap Multistage Mass Spectrometry. ACTA ACUST UNITED AC 2016; 66:7.24.1-7.24.25. [PMID: 27584705 DOI: 10.1002/cpnc.12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Humans are continuously exposed to hazardous chemicals in the environment. These chemicals or their electrophilic metabolites can form adducts with genomic DNA, which can lead to mutations and the initiation of cancer. The identification of DNA adducts is required for understanding exposure and the etiological role of a genotoxic chemical in cancer risk. The analytical chemist is confronted with a great challenge because the levels of DNA adducts generally occur at <1 adduct per 10(7) nucleotides, and the amount of tissue available for measurement is limited. Ion trap mass spectrometry has emerged as an important technique to screen for DNA adducts because of the high level sensitivity and selectivity, particularly when employing multi-stage scanning (MS(n) ). The product ion spectra provide rich structural information and corroborate the adduct identities even at trace levels in human tissues. Ion trap technology represents a significant advance in measuring DNA adducts in humans. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jingshu Guo
- Masonic Cancer Center and Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota
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10
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Marcos J, Pozo OJ. Current LC-MS methods and procedures applied to the identification of new steroid metabolites. J Steroid Biochem Mol Biol 2016; 162:41-56. [PMID: 26709140 DOI: 10.1016/j.jsbmb.2015.12.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/25/2015] [Accepted: 12/11/2015] [Indexed: 12/31/2022]
Abstract
The study of the metabolism of steroids has a long history; from the first characterizations of the major metabolites of steroidal hormones in the pre-chromatographic era, to the latest discoveries of new forms of excretions. The introduction of mass spectrometers coupled to gas chromatography at the end of the 1960's represented a major breakthrough for the elucidation of new metabolites. In the last two decades, this technique is being complemented by the use of liquid chromatography-mass spectrometry (LC-MS). In addition of becoming fundamental in clinical steroid determinations due to its excellent specificity, throughput and sensitivity, LC-MS has emerged as an exceptional tool for the discovery of new steroid metabolites. The aim of the present review is to provide an overview of the current LC-MS procedures used in the quest of novel metabolic products of steroidal hormones and exogenous steroids. Several aspects regarding LC separations are first outlined, followed by a description of the key processes that take place in the mass spectrometric analysis, i.e. the ionization of the steroids in the source and the fragmentation of the selected precursor ions in the collision cell. The different analyzers and approaches employed together with representative examples of each of them are described. Special emphasis is placed on triple quadrupole analyzers (LC-MS/MS), since they are the most commonly employed. Examples on the use of precursor ion scan, neutral loss scan and theoretical selected reaction monitoring strategies are also explained.
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Affiliation(s)
- Josep Marcos
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain; Toxicology Department, Labco Diagnostics, Verge de Guadalupe 18, 08950 Esplugues de Llobregat, Spain
| | - Oscar J Pozo
- Bioanalysis Research Group, IMIM, Hospital del Mar, Doctor Aiguader 88, 08003 Barcelona, Spain.
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11
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Abstract
Drug absorption, distribution, metabolism, excretion and toxicology study is one important step in drug discovery and development. MS imaging has become one of the popular methods in this field. Here, selected ionization methods such as matrix-assisted laser desorption/ionization, secondary ion MS and desorption electrospray ionization have been briefly discussed. To differentiate drug and drug metabolites from endogenous compounds present in the biological system, exact mass and/or tandem MS is necessary. As a result, mass analyzers such as time-of-flight, Fourier transform ion cyclotron resonance or Orbitrap are often the method of choice and are briefly introduced.
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12
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Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ. Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat Protoc 2015; 10:887-903. [PMID: 25996789 DOI: 10.1038/nprot.2015.055] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Here we describe the use of data-independent acquisition (DIA) on a Q-Exactive mass spectrometer for the detection and quantification of peptides in complex mixtures using the Skyline Targeted Proteomics Environment (freely available online at http://skyline.maccosslab.org). The systematic acquisition of mass spectrometry (MS) or tandem MS (MS/MS) spectra by DIA is in contrast to DDA, in which the acquired MS/MS spectra are only suitable for the identification of a stochastically sampled set of peptides. Similarly to selected reaction monitoring (SRM), peptides can be quantified from DIA data using targeted chromatogram extraction. Unlike SRM, data acquisition is not constrained to a predetermined set of target peptides. In this protocol, a spectral library is generated using data-dependent acquisition (DDA), and chromatograms are extracted from the DIA data for all peptides in the library. As in SRM, quantification using DIA data is based on the area under the curve of extracted MS/MS chromatograms. In addition, a quality control (QC) method suitable for DIA based on targeted MS/MS acquisition is detailed. Not including time spent acquiring data, and time for database searching, the procedure takes ∼1-2 h to complete. Typically, data acquisition requires roughly 1-4 h per sample, and a database search will take 0.5-2 h to complete.
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Affiliation(s)
- Jarrett D Egertson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Yue Xuan
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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13
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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14
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Kind T, Fiehn O. Advances in structure elucidation of small molecules using mass spectrometry. BIOANALYTICAL REVIEWS 2010; 2:23-60. [PMID: 21289855 PMCID: PMC3015162 DOI: 10.1007/s12566-010-0015-9] [Citation(s) in RCA: 298] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 08/03/2010] [Indexed: 12/22/2022]
Abstract
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Kind
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
| | - Oliver Fiehn
- Genome Center–Metabolomics, University of California Davis, Davis, CA 95616 USA
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15
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Protéomique et cancer du sein : à la recherche de nouveaux biomarqueurs diagnostiques et théragnostiques. Bull Cancer 2010; 97:321-39. [DOI: 10.1684/bdc.2010.1061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Liao L, McClatchy DB, Yates JR. Shotgun proteomics in neuroscience. Neuron 2009; 63:12-26. [PMID: 19607789 DOI: 10.1016/j.neuron.2009.06.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 06/10/2009] [Accepted: 06/10/2009] [Indexed: 11/27/2022]
Abstract
Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.
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Affiliation(s)
- Lujian Liao
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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17
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Sassin NA, Everhart SC, Cline JI, Ervin KM. Photodissociation and collisional cooling of rhodamine 575 cations in a quadrupole ion trap. J Chem Phys 2008; 128:234305. [DOI: 10.1063/1.2931553] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Bertucci F, Goncalves A. Clinical proteomics and breast cancer: strategies for diagnostic and therapeutic biomarker discovery. Future Oncol 2008; 4:271-87. [PMID: 18407739 DOI: 10.2217/14796694.4.2.271] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A major challenge of breast cancer research is the identification of accurate biomarkers that improve screening, early diagnosis, prediction of aggressiveness, and prediction of therapeutic response or toxicity, as well as the identification of new molecular therapeutic targets. The new proteomic techniques promise to be valuable for identifying such tissue and serum markers. The different techniques currently applied to clinical samples of breast cancer and the most important results obtained are summarized in this review.
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Affiliation(s)
- François Bertucci
- Institut Paoli-Calmettes and UMR599, Centre de Recherche en Cancérologie de Marseille, Département d'Oncologie Moléculaire, 232, Bd Sainte-Marguerite 13009 Marseille, France.
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19
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Ohta D, Shibata D, Kanaya S. Metabolic profiling using Fourier-transform ion-cyclotron-resonance mass spectrometry. Anal Bioanal Chem 2007; 389:1469-75. [PMID: 17922113 DOI: 10.1007/s00216-007-1650-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 09/20/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
Abstract
With the aid of the extreme resolving power of Fourier-transform ion-cyclotron-resonance mass spectrometry (FT-ICR/MS), we have developed a metabolomics platform for high-throughput metabolic profiling and metabolite candidate identification integrating a data-processing system, the Dr.DMASS program ( http://kanaya.naist.jp/DrDMASS/ ), and a metabolite-species database, KNApSAcK ( http://kanaya.aist-nara.ac.jp/KNApSAcK/ ). We discuss the potential of this FT-ICR/MS-based metabolic profiling scheme as a general metabolomics tool by clarification of plant metabolic disorders and specific metabolite accumulation patterns caused by herbicidal enzyme inhibitors.
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Affiliation(s)
- Daisaku Ohta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan.
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20
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Mead JA, Shadforth IP, Bessant C. Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics 2007; 7:2769-86. [PMID: 17654461 DOI: 10.1002/pmic.200700152] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
As proteomic MS has increased in throughput, so has the demand to catalogue the increasing number of peptides and proteins observed by the community using this technique. As in other 'omics' fields, this brings obvious scientific benefits such as sharing of results and prevention of unnecessary repetition, but also provides technical insights, such as the ability to compare proteome coverage between different laboratories, or between different proteomic platforms. Journals are also moving towards mandating that proteomics data be submitted to public repositories upon publication. In response to these demands, several web-based repositories have been established to store protein and peptide identifications derived from MS data, and a similar number of peptide identification software pipelines have emerged to deliver identifications to these repositories. This paper reviews the latest developments in public domain peptide and protein identification databases and describes the analysis pipelines that feed them. Recent applications of the tools to pertinent biological problems are examined, and through comparing and contrasting the capabilities of each system, the issues facing research users of web-based repositories are explored. Future developments and mechanisms to enhance system functionality and user-interfacing opportunities are also suggested.
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Affiliation(s)
- Jennifer A Mead
- Cranfield Health, Cranfield University, Silsoe, Bedfordshire, UK
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