1
|
Routray D, Ghatak A, Chaturvedi P, Petijová L, Weckwerth W, Ručová D, Bačkor M, Lang I, Goga M. Comparative analysis of geotypic variations in the proteome of Nostoc commune. PLANT SIGNALING & BEHAVIOR 2024; 19:2370719. [PMID: 38913942 PMCID: PMC11197914 DOI: 10.1080/15592324.2024.2370719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 06/26/2024]
Abstract
Cyanobacterium Nostoc commune is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of N. commune with the aim to elucidate the differences of physiological trails between distant geotypes, namely Antarctic (AN) and central European (CE). The result obtained clearly showed that the AN geotype demonstrates elevated levels of total phenols, flavonoids, carotenoids, and phycobiliproteins, indicative of its adaptation to environmental stress as referred by comparison to CE sample. Additionally, we employed LC-MS analysis to investigate the proteomes of N. commune from AN and CE geotypes. In total, 1147 proteins were identified, among which 646 proteins expressed significant (up-regulation) changes in both accessions. In the AN geotype, 83 exclusive proteins were identified compared to 25 in the CE geotype. Functional classification of the significant proteins showed a large fraction involved in photosynthesis, amino acid metabolism, carbohydrate metabolism and protein biosynthesis. Further analysis revealed some defense-related proteins such as, superoxide dismutase (SOD) and glutathione reductase, which are rather explicitly expressed in the AN N. commune. The last two proteins suggest a more stressful condition in AN N. commune. In summary, our findings highlight biochemical processes that safeguard the AN geotype of N. commune from extreme environmental challenges, not recorded in CE accession, probably due to less stressful environment in Europe. This study brings the first ever proteomic analysis of N. commune, emphasizing the need for additional investigations into the climate adaptation of this species with rather plastic genome.
Collapse
Affiliation(s)
- Deepti Routray
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Arindam Ghatak
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Linda Petijová
- Department of Genetics, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Dajana Ručová
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Martin Bačkor
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ingeborg Lang
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Goga
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| |
Collapse
|
2
|
Rúbies A, Beguiristain I, Tibon J, Cortés-Francisco N, Granados M. Analysing polypeptide antibiotics residues in animal muscle tissues: The crucial role of HRMS. Food Chem 2024; 443:138481. [PMID: 38310677 DOI: 10.1016/j.foodchem.2024.138481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 10/16/2023] [Accepted: 01/15/2024] [Indexed: 02/06/2024]
Abstract
A confirmatory method for the determination of polypeptide antibiotics (bacitracin, colistin, and polymyxin B) in muscle samples has been developed. Extraction is performed with acidified methanol, and a clean-up step by solid-phase extraction with polymeric cartridges is applied. Separation by ultra-high performance liquid chromatography (UHPLC) is carried out using a solid core C18 column and gradient elution with water/acetonitrile containing 0.2% formic acid. High-resolution mass spectrometry (HRMS) (Q-Orbitrap) detection using different working modes has proved to be highly advantageous in eliminating interfering signals from endogenous matrix components. The analytical method has been successfully validated according to Commission Regulation 2021/808/EU and is currently used in a public health laboratory involved in veterinary medicines residue surveillance activities.
Collapse
Affiliation(s)
- Antoni Rúbies
- Laboratori de l'Agència de Salut Pública de Barcelona, Avinguda Drassanes 13, 08001 Barcelona, Spain
| | - Iñaki Beguiristain
- Departament d'Enginyeria Química i Química Analítica, Universitat de Barcelona, Martí Franquès 1-11, 08018 Barcelona, Spain
| | - Jojo Tibon
- Departament d'Enginyeria Química i Química Analítica, Universitat de Barcelona, Martí Franquès 1-11, 08018 Barcelona, Spain
| | - Nuria Cortés-Francisco
- Laboratori de l'Agència de Salut Pública de Barcelona, Avinguda Drassanes 13, 08001 Barcelona, Spain; Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Mercè Granados
- Departament d'Enginyeria Química i Química Analítica, Universitat de Barcelona, Martí Franquès 1-11, 08018 Barcelona, Spain.
| |
Collapse
|
3
|
Greguš M, Koller A, Ray S, Ivanov AR. Improved Data Acquisition Settings on Q Exactive HF-X and Fusion Lumos Tribrid Orbitrap-Based Mass Spectrometers for Proteomic Analysis of Limited Samples. J Proteome Res 2024; 23:2230-2240. [PMID: 38690845 PMCID: PMC11165581 DOI: 10.1021/acs.jproteome.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Deep proteomic profiling of complex biological and medical samples available at low nanogram and subnanogram levels is still challenging. Thorough optimization of settings, parameters, and conditions in nanoflow liquid chromatography-tandem mass spectrometry (MS)-based proteomic profiling is crucial for generating informative data using amount-limited samples. This study demonstrates that by adjusting selected instrument parameters, e.g., ion injection time, automated gain control, and minimally altering the conditions for resuspending or storing the sample in solvents of different compositions, up to 15-fold more thorough proteomic profiling can be achieved compared to conventionally used settings. More specifically, the analysis of 1 ng of the HeLa protein digest standard by Q Exactive HF-X Hybrid Quadrupole-Orbitrap and Orbitrap Fusion Lumos Tribrid mass spectrometers yielded an increase from 1758 to 5477 (3-fold) and 281 to 4276 (15-fold) peptides, respectively, demonstrating that higher protein identification results can be obtained using the optimized methods. While the instruments applied in this study do not belong to the latest generation of mass spectrometers, they are broadly used worldwide, which makes the guidelines for improving performance desirable to a wide range of proteomics practitioners.
Collapse
Affiliation(s)
- Michal Greguš
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Antonius Koller
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| | - Alexander R. Ivanov
- Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
| |
Collapse
|
4
|
Wang S, Collins A, Prakash A, Fexova S, Papatheodorou I, Jones AR, Vizcaíno JA. Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues. J Proteome Res 2024; 23:1948-1959. [PMID: 38717300 PMCID: PMC11165573 DOI: 10.1021/acs.jproteome.3c00741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/16/2024] [Accepted: 04/18/2024] [Indexed: 06/13/2024]
Abstract
The availability of an increasingly large amount of public proteomics data sets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions. Sus scrofa, a domestic pig, is a model organism relevant for food production and for human biomedical research. Here, we reanalyzed 14 public proteomics data sets from the PRIDE database coming from pig tissues to assess baseline (without any biological perturbation) protein abundance in 14 organs, encompassing a total of 20 healthy tissues from 128 samples. The analysis involved the quantification of protein abundance in 599 mass spectrometry runs. We compared protein expression patterns among different pig organs and examined the distribution of proteins across these organs. Then, we studied how protein abundances were compared across different data sets and studied the tissue specificity of the detected proteins. Of particular interest, we conducted a comparative analysis of protein expression between pig and human tissues, revealing a high degree of correlation in protein expression among orthologs, particularly in brain, kidney, heart, and liver samples. We have integrated the protein expression results into the Expression Atlas resource for easy access and visualization of the protein expression data individually or alongside gene expression data.
Collapse
Affiliation(s)
- Shengbo Wang
- European
Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew Collins
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Ananth Prakash
- European
Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Open
Targets, Wellcome Genome
Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Silvie Fexova
- European
Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Irene Papatheodorou
- European
Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Open
Targets, Wellcome Genome
Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Andrew R. Jones
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Juan Antonio Vizcaíno
- European
Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Open
Targets, Wellcome Genome
Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| |
Collapse
|
5
|
Humphries EM, Xavier D, Ashman K, Hains PG, Robinson PJ. High-Throughput Proteomics and Phosphoproteomics of Rat Tissues Using Microflow Zeno SWATH. J Proteome Res 2024. [PMID: 38819404 DOI: 10.1021/acs.jproteome.4c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
High-throughput tissue proteomics has great potential in the advancement of precision medicine. Here, we investigated the combined sensitivity of trap-elute microflow liquid chromatography with a ZenoTOF for DIA proteomics and phosphoproteomics. Method optimization was conducted on HEK293T cell lines to determine the optimal variable window size, MS2 accumulation time and gradient length. The ZenoTOF 7600 was then compared to the previous generation TripleTOF 6600 using eight rat organs, finding up to 23% more proteins using a fifth of the sample load and a third of the instrument time. Spectral reference libraries generated from Zeno SWATH data in FragPipe (MSFragger-DIA/DIA-NN) contained 4 times more fragment ions than the DIA-NN only library and quantified more proteins. Replicate single-shot phosphopeptide enrichments of 50-100 μg of rat tryptic peptide were analyzed by microflow HPLC using Zeno SWATH without fractionation. Using Spectronaut we quantified a shallow phosphoproteome containing 1000-3000 phosphoprecursors per organ. Promisingly, clear hierarchical clustering of organs was observed with high Pearson correlation coefficients >0.95 between replicate enrichments and median CV of 20%. The combined sensitivity of microflow HPLC with Zeno SWATH allows for the high-throughput quantitation of an extensive proteome and shallow phosphoproteome from small tissue samples.
Collapse
Affiliation(s)
- Erin M Humphries
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Dylan Xavier
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Keith Ashman
- Sciex, 96 Ricketts Road,Mount Waverley, Victoria 3149, Australia
| | - Peter G Hains
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Phillip J Robinson
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| |
Collapse
|
6
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
7
|
Geue N. Modern Electrospray Ionization Mass Spectrometry Techniques for the Characterization of Supramolecules and Coordination Compounds. Anal Chem 2024; 96:7332-7341. [PMID: 38686955 PMCID: PMC11099892 DOI: 10.1021/acs.analchem.4c01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
Mass spectrometry is routinely used for myriad applications in clinical, industrial, and research laboratories worldwide. Developments in the areas of ionization sources, high-resolution mass analyzers, tandem mass spectrometry, and ion mobility have significantly extended the repertoire of mass spectrometrists; however, for coordination compounds and supramolecules, mass spectrometry remains underexplored and arguably underappreciated. Here, the reader is guided through different tools of modern electrospray ionization mass spectrometry that are suitable for larger inorganic complexes. All steps, from sample preparation and technical details to data analysis and interpretation are discussed. The main target audience of this tutorial is synthetic chemists as well as technicians/mass spectrometrists with little experience in characterizing labile inorganic compounds.
Collapse
Affiliation(s)
- Niklas Geue
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, Department
of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
8
|
Liu Z, Zhao J, Cui K, Guo H, Li Z, Zhou Z. Detection accuracy and clinical applications of DP-TOF mass spectrometry. J Int Med Res 2024; 52:3000605241255568. [PMID: 38819085 PMCID: PMC11143829 DOI: 10.1177/03000605241255568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
OBJECTIVE Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently used in clinical microbiology laboratories. This study aimed to determine whether dual-polarity time-of-flight mass spectrometry (DP-TOF MS) could be applied to clinical nucleotide detection. METHODS This prospective study included 40 healthy individuals and 110 patients diagnosed with cardiovascular diseases. We used DP-TOF MS and Sanger sequencing to evaluate 17 loci across 11 genes associated with cardiovascular drug responses. In addition, we used DP-TOF MS to test 998 retrospectively collected clinical DNA samples with known results. RESULTS A, T, and G nucleotide detection by DP-TOF MS and Sanger sequencing revealed 100% concordance, whereas the C nucleotide concordance was 99.86%. Genotyping based on the results of the two methods showed 99.96% concordance. Regarding clinical applications, DP-TOF MS yielded a 99.91% concordance rate for known loci. The minimum detection limit for DNA was 0.4 ng; the inter-assay and intra-assay precision rates were both 100%. Anti-interference analysis showed that aerosol contamination greater than 1013 copies/µL in the laboratory environment could influence the results of DP-TOF MS. CONCLUSIONS The DP-TOF MS platform displayed good detection performance, as demonstrated by its 99.96% concordance rate with Sanger sequencing. Thus, it may be applied to clinical nucleotide detection.
Collapse
Affiliation(s)
- Zhaohui Liu
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Center of Laboratory Medicine, Fuwai Yunnan Cardiovascular Hospital, Kunming, Yunnan, China
| | - Juan Zhao
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Cui
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhikai Li
- Zhejiang Digena Diagnosis Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
9
|
Goodwin MP, Grinfeld D, Yip P, Bowen KP, Kafader JO, Kelleher NL, Senko MW. Improved Signal Processing for Mass Shifting Ions in Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:658-662. [PMID: 38286823 PMCID: PMC10990768 DOI: 10.1021/jasms.3c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The quality of data in charge detection mass spectrometry depends on accurate determination of ion charge. While the method of selective temporal overview of resonant ions (STORI) has proven to be highly enabling for determining the charge of ions that survive for variable amounts of time, it assumes that the ion frequency exactly matches the frequency being used in the calculation. Any mismatches result in low charge estimates. To address this, the misSTORI method was developed to correct these discrepancies. This can significantly reduce the charge measurement errors for samples with unstable masses. As an example, the misSTORI approach can eliminate a 5.7% charge determination error for a VP3-only AAV capsid that shifts 25 ppm in mass.
Collapse
Affiliation(s)
| | | | - Ping Yip
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Kyle P Bowen
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Jared O Kafader
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208 United States
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208 United States
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208 United States
| | - Michael W Senko
- Thermo Fisher Scientific, San Jose, California 95134, United States
| |
Collapse
|
10
|
Lu W, McBride MJ, Lee WD, Xing X, Xu X, Li X, Oschmann AM, Shen Y, Bartman C, Rabinowitz JD. Selected Ion Monitoring for Orbitrap-Based Metabolomics. Metabolites 2024; 14:184. [PMID: 38668312 PMCID: PMC11051813 DOI: 10.3390/metabo14040184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.
Collapse
Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Matthew J. McBride
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Won Dong Lee
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
| | - Xi Xing
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Xincheng Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Xi Li
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Anna M. Oschmann
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Yihui Shen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline Bartman
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
- Rutgers Cancer Institute of New Jersey (CINJ), Rutgers University, New Brunswick, NJ 08901, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
11
|
Jarrold MF. Single-Ion Mass Spectrometry for Heterogeneous and High Molecular Weight Samples. J Am Chem Soc 2024; 146:5749-5758. [PMID: 38394699 DOI: 10.1021/jacs.3c08139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In charge detection mass spectrometry (CD-MS) the mass of each individual ion is determined from the measurement of its mass to charge ratio (m/z) and charge. Performing this measurement for thousands of ions allows mass distributions to be measured for heterogeneous and high mass samples that cannot be analyzed by conventional mass spectrometry (MS). CD-MS opens the door to accurate mass measurements for samples into the giga-Dalton regime, vastly expanding the reach of MS and allowing mass distributions to be determined for viruses, gene therapies, and vaccines. Following the success of CD-MS, single-ion mass measurements have recently been performed on an Orbitrap. CD-MS and Orbitrap individual ion mass spectrometry (I2MS) are described. Illustrative examples are provided, and the prospects for higher resolution measurements discussed. In the case of CD-MS, computer simulations indicate that much higher resolving powers are within reach. The ability to perform high-resolution CD-MS analysis of heterogeneous samples will be enabling and disruptive in top-down MS as high-resolution m/z and accurate charge measurements will allow very complex m/z spectra to be unraveled.
Collapse
Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| |
Collapse
|
12
|
Dunham SD, Brodbelt JS. Enhancing Top-Down Analysis of Proteins by Combining Ultraviolet Photodissociation (UVPD), Proton-Transfer Charge Reduction (PTCR), and Gas-Phase Fractionation to Alleviate the Impact of Nondissociated Precursor Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:255-265. [PMID: 38150423 DOI: 10.1021/jasms.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Recent advances in top-down mass spectrometry strategies continue to improve the analysis of intact proteins. 193 nm ultraviolet photodissociation (UVPD) is one method well-suited for top-down analysis. UVPD is often performed using relatively low photon flux in order to limit multiple-generation dissociation of fragment ions and maximize sequence coverage. Consequently, a large portion of the precursor ion survives the UVPD process, dominates the spectrum, and may impede identification of fragment ions. Here, we explore the isolation of subpopulations of fragment ions lower and higher than the precursor ion after UVPD as a means to eliminate the impact of the surviving precursor ion on the detection of low abundance fragment ions. This gas-phase fractionation method improved sequence coverage harvested from fragment ions found in the m/z regions lower and higher than the precursor by an average factor of 1.3 and 2.3, respectively. Combining this gas-phase fractionation method with proton transfer charge reduction (PTCR) further increased the sequence coverage obtained from these m/z regions by another factor of 1.3 and 1.4, respectively. Implementing a post-UVPD fractionation + PTCR strategy with six fractionation events resulted in a sequence coverage of 75% for enolase, the highest reported for 193 nm UVPD.
Collapse
Affiliation(s)
- Sean D Dunham
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 787812, United States
| |
Collapse
|
13
|
Vosough M, Salemi A, Rockel S, Schmidt TC. Enhanced efficiency of MS/MS all-ion fragmentation for non-targeted analysis of trace contaminants in surface water using multivariate curve resolution and data fusion. Anal Bioanal Chem 2024; 416:1165-1177. [PMID: 38206346 PMCID: PMC10850027 DOI: 10.1007/s00216-023-05102-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024]
Abstract
Data-independent acquisition-all-ion fragmentation (DIA-AIF) mode of mass spectrometry can facilitate wide-scope non-target analysis of contaminants in surface water due to comprehensive spectral identification. However, because of the complexity of the resulting MS2 AIF spectra, identifying unknown pollutants remains a significant challenge, with a significant bottleneck in translating non-targeted chemical signatures into environmental impacts. The present study proposes to process fused MS1 and MS2 data sets obtained from LC-HRMS/MS measurements in non-targeted AIF workflows on surface water samples using multivariate curve resolution-alternating least squares (MCR-ALS). This enables straightforward assignment between precursor ions obtained from resolved MS1 spectra and their corresponding MS2 spectra. The method was evaluated for two sets of tap water and surface water contaminated with 14 target chemicals as a proof of concept. The data set of surface water samples consisting of 3506 MS1 and 2170 MS2 AIF mass spectral features was reduced to 81 components via a fused MS1-MS2 MCR model that describes at least 98.8% of the data. Each component summarizes the distinct chromatographic elution of components together with their corresponding MS1 and MS2 spectra. MS2 spectral similarity of more than 82% was obtained for most target chemicals. This highlights the potential of this method for unraveling the composition of MS/MS complex data in a water environment. Ultimately, the developed approach was applied to the retrospective non-target analysis of an independent set of surface water samples.
Collapse
Affiliation(s)
- Maryam Vosough
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany.
- Department of Clean Technologies, Chemistry and Chemical Engineering Research Center of Iran, P.O. Box 14335-186, Tehran, Iran.
| | - Amir Salemi
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
| | - Sarah Rockel
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
- IWW Water Centre, Moritzstr. 26, Mülheim an der Ruhr, 45476, Germany
| |
Collapse
|
14
|
Guzman UH, Martinez-Val A, Ye Z, Damoc E, Arrey TN, Pashkova A, Renuse S, Denisov E, Petzoldt J, Peterson AC, Harking F, Østergaard O, Rydbirk R, Aznar S, Stewart H, Xuan Y, Hermanson D, Horning S, Hock C, Makarov A, Zabrouskov V, Olsen JV. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nat Biotechnol 2024:10.1038/s41587-023-02099-7. [PMID: 38302753 DOI: 10.1038/s41587-023-02099-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th isolation windows, dissolving the differences between data-dependent and -independent methods. This is achieved by pairing a quadrupole Orbitrap mass spectrometer with the asymmetric track lossless (Astral) analyzer which provides >200-Hz MS/MS scanning speed, high resolving power and sensitivity, and low-ppm mass accuracy. The nDIA strategy enables profiling of >100 full yeast proteomes per day, or 48 human proteomes per day at the depth of ~10,000 human protein groups in half-an-hour or ~7,000 proteins in 5 min, representing 3× higher coverage compared with current state-of-the-art MS. Multi-shot acquisition of offline fractionated samples provides comprehensive coverage of human proteomes in ~3 h. High quantitative precision and accuracy are demonstrated in a three-species proteome mixture, quantifying 14,000+ protein groups in a single half-an-hour run.
Collapse
Affiliation(s)
- Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Eugen Damoc
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | - Anna Pashkova
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | - Florian Harking
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Rydbirk
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susana Aznar
- Centre for Neuroscience and Stereology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Yue Xuan
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
15
|
Xu Q, Li CH, Tang CH, Huang XL, Wu LF, Zhou X, Lei SF, Deng FY. PKM2 is a Novel Osteoporosis-Associated Protein in Chinese. Endocr Res 2024; 49:92-105. [PMID: 38288985 DOI: 10.1080/07435800.2024.2310818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/16/2023] [Indexed: 04/24/2024]
Abstract
Purpose:Osteoporosis is characterized by low bone mineral density (BMD) and high risk of osteoporotic fracture (OF). Peripheral blood monocytes (PBM) can differentiate into osteoclasts to resorb bone. This study was to identify PBM-expressed proteins significant for osteoporosis in Chinese Han elderly population (>65 years), and focused on two phenotypes of osteoporosis: low BMD and OF. METHODS Label-free quantitative proteomics was employed to profile PBM proteome and to identify differentially expressed proteins (DEPs) between OF (N=27) vs. non-fractured (NF, N=24) subjects and between low BMD (N=12) vs. high BMD (N=12) subjects in women. Western blotting (WB) was conducted to validate differential expression, and ELISA to evaluate translational value for secretory protein of interest. RESULTS We discovered 59 DEPs with fold change (FC)>1.3 (P<1×10-5), and validated the significant up-regulation of pyruvate kinase isozyme 2 (PKM2) with osteoporosis (P<0.001). PKM2 protein upregulation with OF was replicated with PBM in men (P=0.04). Plasma PKM2 protein level was significantly elevated with OF in an independent sample (N=100, FC=1.68, P=0.01). Pursuant functional assays showed that extracellular PKM2 protein supplement not only promoted monocyte trans-endothelial migration, growth, and osteoclast differentiation (marker gene expression), but also inhibited osteoblast growth, differentiation (ALP gene expression), and activity. CONCLUSION The above findings suggest that PKM2 protein is a novel osteoporosis-associated functional protein in Chinese Han elderly population. It may serve as a risk biomarker and drug target for osteoporosis.
Collapse
Affiliation(s)
- Qing Xu
- School of Public Health, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University; Center for Genetic Epidemiology and Genomics, Suzhou, Jiangsu, P. R. China
| | - Chun-Hui Li
- School of Public Health, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University; Center for Genetic Epidemiology and Genomics, Suzhou, Jiangsu, P. R. China
| | - Chang-Hua Tang
- Department of Orthopedics, Sihong Hospital, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University, Suqian, Jiangsu, P. R. China
| | - Xiao-Li Huang
- Department of Orthopedics, Sihong Hospital, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University, Suqian, Jiangsu, P. R. China
| | - Long-Fei Wu
- School of Public Health, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University; Center for Genetic Epidemiology and Genomics, Suzhou, Jiangsu, P. R. China
| | - Xu Zhou
- School of Public Health, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University; Center for Genetic Epidemiology and Genomics, Suzhou, Jiangsu, P. R. China
| | - Shu-Feng Lei
- School of Public Health, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University; Center for Genetic Epidemiology and Genomics, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
- Department of Orthopedics, Changzhou Geriatric Hospital Affiliated to Soochow University, Changzhou, Jiangsu, P. R. China
| | - Fei-Yan Deng
- School of Public Health, Collaborative Innovation Center for Bone and Immunology between Sihong Hospital and Soochow University; Center for Genetic Epidemiology and Genomics, Suzhou, Jiangsu, P. R. China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, P. R. China
| |
Collapse
|
16
|
Stewart H, Grinfeld D, Wagner A, Kholomeev A, Biel M, Giannakopulos A, Makarov A, Hock C. A Conjoined Rectilinear Collision Cell and Pulsed Extraction Ion Trap with Auxiliary DC Electrodes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:74-81. [PMID: 37925680 PMCID: PMC10767742 DOI: 10.1021/jasms.3c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Ion traps are routinely directly coupled to mass analyzers, where they serve to suitably cool and shape an ion population prior to pulsed extraction into the analyzer proper. Such devices benefit from high duty cycle and transmission but suffer slow ion processing times caused by a compromise in the buffer gas pressure range that suitably dampens the ion kinetic energy without causing excessive scatter during extraction or within the analyzer. A rectilinear RF quadrupole ion trap has been characterized, conjoining a pressurized collision region with a pumped extraction region, and an unbroken RF interface for seamless ion transfer between them. Auxiliary electrodes mounted between the RF electrodes provide DC voltage gradients that serve to both guide ions through the device and position them at the extraction slot. The influence of the auxiliary DC upon the trapping RF field was measured, and suitable parameters were defined. A mode of operation was developed that allowed parallel processing of ions in both regions, enabling a repetition rate of 200 Hz when the device was coupled to a high-resolution accurate-mass analyzer.
Collapse
Affiliation(s)
- Hamish Stewart
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Dmitry Grinfeld
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Alexander Wagner
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Matthias Biel
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Alexander Makarov
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Christian Hock
- Thermo Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| |
Collapse
|
17
|
Yao L, Liu Y, Cui Y, Sun J, Xia X, Wang J, Wei Y, Chen W. Characterization and quality evaluation of QiXueShuFu Decoction based on fingerprint and ultra-performance liquid chromatography-quadrupole-orbitrap mass spectrometry. J Sep Sci 2024; 47:e2300606. [PMID: 38095460 DOI: 10.1002/jssc.202300606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 01/19/2024]
Abstract
QiXueShuFu Decoction (QXSFD) modified from the Bazhen Decoction which was originally from the classic Ming Dynasty is a traditional folk formula that boosts the body's immune system. However, its ambiguous chemical components limited its quality control evaluation. In this study, ultra-performance liquid chromatography (UPLC) fingerprint combined with multivariate analysis was used to evaluate the quality of 15 batches of QXSFD, and UPLC quadrupole-orbitrap mass spectrometry was used to further examine the chemical components in QXSFD, after which representative compounds from each disassembled prescription were selected for comparison. Fifteen batches of samples had 33 common peaks in which 11 differential components could be used as a reference for subsequent quality control. One hundred forty-three components were identified from QXSFD. Saponins were mainly derived from the monarch, terpenes from the minister, and polysaccharides and glycosides from the assistant. In addition, quantitative assay revealed that the content of ferulic acid, chlorogenic acid, 2,3,5,4'-tetrahydroxystilbene-2-O-β-D-glucoside and 3,6'-disinapoyl sucrose in the whole prescription were higher than the contents of each disassembled prescription. This is the first comprehensive quality report on the chemical components of QXSFD, which is important for pharmacodynamic material basis and quality control.
Collapse
Affiliation(s)
- Liang Yao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Yuzhen Liu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Yu Cui
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Julin Sun
- Anhui Province Maanshan Hospital of Traditional Chinese Medicine, Ma'anshan, China
| | - Xiaojian Xia
- Anhui Province Maanshan Hospital of Traditional Chinese Medicine, Ma'anshan, China
| | - Junping Wang
- Center of Pharmacy, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Yougang Wei
- Anhui Province Maanshan Hospital of Traditional Chinese Medicine, Ma'anshan, China
| | - WeiDong Chen
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
- Anhui University of Chinese Medicine, Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, China
| |
Collapse
|
18
|
Prudent R, Lemoine H, Walsh J, Roche D. Affinity selection mass spectrometry speeding drug discovery. Drug Discov Today 2023; 28:103760. [PMID: 37660985 DOI: 10.1016/j.drudis.2023.103760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/21/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Affinity selection mass spectrometry (AS-MS) has gained momentum in drug discovery. This review summarizes how this technology has slowly risen as a new paradigm in hit identification and its potential synergy with DNA encoded library technology. It presents an overview of the recent results on challenging targets and perspectives on new areas of research, such as RNA targeting with small molecules. The versatility of the approach is illustrated and strategic drivers discussed in terms of the experience of a small-medium CRO and a big pharma organization.
Collapse
Affiliation(s)
| | | | - Jarrod Walsh
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Didier Roche
- Edelris, Bioparc, Bioserra 1 Building, Lyon, France.
| |
Collapse
|
19
|
Ferreira R, Amado F, Vitorino R. Empowering peptidomics: utilizing computational tools and approaches. Bioanalysis 2023; 15:1315-1325. [PMID: 37737150 DOI: 10.4155/bio-2023-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Bioinformatics plays a critical role in the advancement of peptidomics by providing powerful tools for data analysis, interpretation and integration. Peptidomics is concerned with the study of peptides, short chains of amino acids with diverse biological functions. This area includes peptide identification and characterization, database construction, de novo sequencing, functional annotation, omics data integration and systems biology. Artificial intelligence techniques, such as machine learning and natural language processing, aid in the interpretation of peptide sequence data and the generation of biological insights. By using bioinformatics approaches, peptidomics researchers can accelerate peptide discovery, understand their functions and gain insights into complex molecular interactions.
Collapse
Affiliation(s)
- Rita Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Francisco Amado
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Universidade do Porto, Porto, Portugal
- iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| |
Collapse
|
20
|
Stewart HI, Grinfeld D, Giannakopulos A, Petzoldt J, Shanley T, Garland M, Denisov E, Peterson AC, Damoc E, Zeller M, Arrey TN, Pashkova A, Renuse S, Hakimi A, Kühn A, Biel M, Kreutzmann A, Hagedorn B, Colonius I, Schütz A, Stefes A, Dwivedi A, Mourad D, Hoek M, Reitemeier B, Cochems P, Kholomeev A, Ostermann R, Quiring G, Ochmann M, Möhring S, Wagner A, Petker A, Kanngiesser S, Wiedemeyer M, Balschun W, Hermanson D, Zabrouskov V, Makarov AA, Hock C. Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis. Anal Chem 2023; 95:15656-15664. [PMID: 37815927 PMCID: PMC10603608 DOI: 10.1021/acs.analchem.3c02856] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
The growing trend toward high-throughput proteomics demands rapid liquid chromatography-mass spectrometry (LC-MS) cycles that limit the available time to gather the large numbers of MS/MS fragmentation spectra required for identification. Orbitrap analyzers scale performance with acquisition time and necessarily sacrifice sensitivity and resolving power to deliver higher acquisition rates. We developed a new mass spectrometer that combines a mass-resolving quadrupole, the Orbitrap, and the novel Asymmetric Track Lossless (Astral) analyzer. The new hybrid instrument enables faster acquisition of high-resolution accurate mass (HRAM) MS/MS spectra compared with state-of-the-art mass spectrometers. Accordingly, new proteomics methods were developed that leverage the strengths of each HRAM analyzer, whereby the Orbitrap analyzer performs full scans with a high dynamic range and resolution, synchronized with the Astral analyzer's acquisition of fast and sensitive HRAM MS/MS scans. Substantial improvements are demonstrated over previous methods using current state-of-the-art mass spectrometers.
Collapse
Affiliation(s)
- Hamish I. Stewart
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Dmitry Grinfeld
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Johannes Petzoldt
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Toby Shanley
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Matthew Garland
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Eduard Denisov
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Eugen Damoc
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Martin Zeller
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Tabiwang N. Arrey
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Anna Pashkova
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Santosh Renuse
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | - Amirmansoor Hakimi
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | - Andreas Kühn
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Matthias Biel
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Arne Kreutzmann
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Bernd Hagedorn
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Immo Colonius
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Adrian Schütz
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Arne Stefes
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Ankit Dwivedi
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Daniel Mourad
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Max Hoek
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Philipp Cochems
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | | | - Robert Ostermann
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Gregor Quiring
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | - Sascha Möhring
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Alexander Wagner
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - André Petker
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | | | | | - Wilko Balschun
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| | - Daniel Hermanson
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo
Fisher Scientific, 355
River Oaks Pkwy, San Jose, California 95134, United States
| | | | - Christian Hock
- Thermo
Fisher Scientific, 11 Hannah-Kunath Str., 28199 Bremen, Germany
| |
Collapse
|
21
|
Wang X, Liu H, Shu L, Yao Y, Xu Y, Wei J, Li Y. Rapid identification of chemical constituents in Hugan tablets by ultra-performance liquid chromatography-quadrupole-exactive orbitrap mass spectrometry. J Sep Sci 2023; 46:e2300302. [PMID: 37568249 DOI: 10.1002/jssc.202300302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/23/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
Hugan tablet is a Chinese medicine preparation. It is composed of Bupleuri Radix, Artemisiae Scopariae Herba, Isatidis Radix, Schisandrae Chinensis Fructus, Suis Fellis Pulvis, and Vigna radiata L. It has the effects of dispersing stagnated liver qi, strengthening the spleen and eliminating food to be used for the treatment of chronic hepatitis and early cirrhosis. However, the chemical composition of Hugan tablet is complex and not fully understood, which hampers the research in pharmacology. In this study, a reliable method for the rapid analysis and identification of the chemical components in Hugan tablet by their characteristic fragments and neutral losses using ultra-performance liquid chromatography-quadrupole-exactive orbitrap mass spectrometry was developed. A total of 144 chemical components were tentatively identified, including 57 organic acids, 19 flavonoids, 23 alkaloids, 18 lignans, 7 saponins, and 20 others. These components may be the active ingredients of Hugan tablet. The established method can systematically and rapidly analyze the chemical components in Hugan tablet, which provides a basis for the pharmacodynamic substance study and is meaningful for the quality control of Hugan tablet.
Collapse
Affiliation(s)
- Xiaowen Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Huiru Liu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Lexin Shu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Yaqi Yao
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Yanyan Xu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Jinxia Wei
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| | - Yubo Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, P. R. China
| |
Collapse
|
22
|
Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023; 22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.
Collapse
Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
| | - Allis Chien
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | | | - Anthony W Herren
- UC Davis Genome Center, Proteomics Core, University of California Davis, Davis California, USA
| | - Jenny Kim Kim
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Ryan D Leib
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | - Purvi Patel
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Jian Min Ren
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Yiying Zhu
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Bhavin Patel
- Thermo Fisher Scientific, Rockford, Illinois, USA
| |
Collapse
|
23
|
Disela R, Bussy OL, Geldhof G, Pabst M, Ottens M. Characterisation of the E. coli HMS174 and BLR host cell proteome to guide purification process development. Biotechnol J 2023; 18:e2300068. [PMID: 37208824 DOI: 10.1002/biot.202300068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/21/2023]
Abstract
Mass-spectrometry-based proteomics is increasingly employed to monitor purification processes or to detect critical host cell proteins in the final drug substance. This approach is inherently unbiased and can be used to identify individual host cell proteins without prior knowledge. In process development for the purification of new biopharmaceuticals, such as protein subunit vaccines, a broader knowledge of the host cell proteome could promote a more rational process design. Proteomics can establish qualitative and quantitative information on the complete host cell proteome before purification (i.e., protein abundances and physicochemical properties). Such information allows for a more rational design of the purification strategy and accelerates purification process development. In this study, we present an extensive proteomic characterisation of two E. coli host cell strains widely employed in academia and industry to produce therapeutic proteins, BLR and HMS174. The established database contains the observed abundance of each identified protein, information relating to their hydrophobicity, the isoelectric point, molecular weight, and toxicity. These physicochemical properties were plotted on proteome property maps to showcase the selection of suitable purification strategies. Furthermore, sequence alignment allowed integration of subunit information and occurrences of post-translational modifications from the well-studied E. coli K12 strain.
Collapse
Affiliation(s)
- Roxana Disela
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | | | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Marcel Ottens
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
24
|
Stincone P, Pakkir Shah AK, Schmid R, Graves LG, Lambidis SP, Torres RR, Xia SN, Minda V, Aron AT, Wang M, Hughes CC, Petras D. Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform. Anal Chem 2023; 95:12673-12682. [PMID: 37578818 PMCID: PMC10469366 DOI: 10.1021/acs.analchem.3c01202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that automatic gain control, microscans, mass resolving power, and dynamic exclusion are the most critical parameters, whereas collision energy, TopN, and isolation width had moderate and apex trigger, monoisotopic selection, and isotopic exclusion minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.
Collapse
Affiliation(s)
- Paolo Stincone
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Abzer K. Pakkir Shah
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Robin Schmid
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Praha 6, Czech Republic
| | - Lana G. Graves
- Faculty
of Mathematics and Natural Sciences, Environmental Systems Analysis, University of Tübingen, Tübingen 72076, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin 12587, Germany
| | - Stilianos P. Lambidis
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Ralph R. Torres
- University
of California San Diego, Scripps Institution of Oceanography, La Jolla, California 92093, United States
| | - Shu-Ning Xia
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| | - Vidit Minda
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
- Department
of Pharmacology and Pharmaceutical Sciences, University of Missouri−Kansas City, Kansas City, Missouri 64108, United States
| | - Allegra T. Aron
- Department
of Chemistry and Biochemistry, University
of Denver, Denver, Colorado 80210, United States
| | - Mingxun Wang
- Department
of Computer Science, University of California
Riverside, Riverside, California 92507, United States
| | - Chambers C. Hughes
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
- Department
of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology
and Infection Medicine, University of Tübingen, Tübingen 72076, Germany
- German
Center for Infection Research, Partner Site
Tübingen, Tübingen 72076, Germany
| | - Daniel Petras
- Cluster
of Excellence-Controlling Microbes to Fight Infection, University of Tübingen, Tübingen 72076, Germany
| |
Collapse
|
25
|
Konorev D, Bellamri M, Wu CF, Wu MT, Turesky RJ. High-Field Asymmetric Waveform Ion Mobility Spectrometry Analysis of Carcinogenic Aromatic Amines in Tobacco Smoke with an Orbitrap Tribrid Mass Spectrometer. Chem Res Toxicol 2023; 36:1419-1426. [PMID: 37462928 PMCID: PMC10530005 DOI: 10.1021/acs.chemrestox.3c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Smoking is a risk factor for bladder cancer (BC), although the specific chemicals responsible for BC remain uncertain. Considerable research has focused on aromatic amines (AAs), including o-toluidine (o-tol), o-anisidine (o-anis), 2-naphthylamine (2-NA), and 4-aminobiphenyl (4-ABP), which are linked to human BC based on elevated BC incidence in occupationally exposed factory workers. These AAs arise at nanogram levels per combusted cigarette. The unambiguous identification of AAs, particularly low-molecular-weight monocyclic AAs in tobacco smoke extracts, by liquid chromatography-mass spectrometry (LC-MS) is challenging due to their poor performance on reversed-phase columns and co-elution with isobaric interferences from the complex tobacco smoke matrix. We employed a tandem liquid-liquid and solid-phase extraction method to isolate AAs from the basic fraction of tobacco smoke condensate (TSC) and utilized high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to high-resolution accurate mass (HRAM) Orbitrap LC-MS2 to assay AAs in TSC. The employment of FAIMS greatly reduced sample complexity by removing precursor co-isolation interfering species at the MS1 scan stage, resulting in dramatically improved signal-to-noise of the precursor ions and cleaner, high-quality MS2 spectra for unambiguous identification and quantification of AAs in TSC. We demonstrate the power of LC/FAIMS/MS2 by characterizing and quantifying two low-molecular-weight carcinogenic AAs, o-tol and o-anis, in TSC, using stable isotopically labeled internal standards. These results demonstrate the power of FAIMS in trace-level analyses of AA carcinogens in the complex tobacco smoke matrix.
Collapse
Affiliation(s)
- Dmitri Konorev
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455
- IDEXX Laboratories, Inc, 1 IDEXX Dr, Westbrook, ME 04092
| | - Medjda Bellamri
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Chia-Fang Wu
- International Master Program of Translational Medicine, National United University, Miaoli, Taiwan
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Ming Tsang Wu
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Robert J. Turesky
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
26
|
Lillja J, Duncan KD, Lanekoff I. Ion-to-Image, i2i, a Mass Spectrometry Imaging Data Analysis Platform for Continuous Ionization Techniques. Anal Chem 2023; 95:11589-11595. [PMID: 37505508 PMCID: PMC10413325 DOI: 10.1021/acs.analchem.3c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023]
Abstract
Mass spectrometry imaging (MSI) techniques generate data that reveal spatial distributions of molecules on a surface with high sensitivity and selectivity. However, processing large volumes of mass spectrometry data into useful ion images is not trivial. Furthermore, data from MSI techniques using continuous ionization sources where data are acquired in line scans require different data handling strategies compared to data collected from pulsed ionization sources where data are acquired in grids. In addition, for continuous ionization sources, the pixel dimensions are influenced by the mass spectrometer duty cycle, which, in turn, can be controlled by the automatic gain control (AGC) for each spectrum (pixel). Currently, there is a lack of data-handling software for MSI data generated with continuous ionization sources and AGC. Here, we present ion-to-image (i2i), which is a MATLAB-based application for MSI data acquired with continuous ionization sources, AGC, high resolution, and one or several scan filters. The source code and a compiled installer are available at https://github.com/LanekoffLab/i2i. The application includes both quantitative, targeted, and nontargeted data processing strategies and enables complex data sets to be processed in minutes. The i2i application has high flexibility for generating, processing, and exporting MSI data both from simple full scans and more complex scan functions interlacing MSn and SIM scan data sets, and we anticipate that it will become a valuable addition to the existing MSI software toolbox.
Collapse
Affiliation(s)
- Johan Lillja
- Department
of Chemistry − BMC, Uppsala University, Uppsala, 752 37, Sweden
| | - Kyle D. Duncan
- Department
of Chemistry − BMC, Uppsala University, Uppsala, 752 37, Sweden
- Department
of Chemistry, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
| | - Ingela Lanekoff
- Department
of Chemistry − BMC, Uppsala University, Uppsala, 752 37, Sweden
| |
Collapse
|
27
|
Zhou Y, Jiang X, Wang X, Huang J, Li T, Jin H, He J. Promise of spatially resolved omics for tumor research. J Pharm Anal 2023; 13:851-861. [PMID: 37719191 PMCID: PMC10499658 DOI: 10.1016/j.jpha.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 09/19/2023] Open
Abstract
Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures. By interacting with the microenvironment, tumor cells undergo dynamic changes in gene expression and metabolism, resulting in spatiotemporal variations in their capacity for proliferation and metastasis. In recent years, the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis. By preserving location information while obtaining a large number of gene and molecular data, spatially resolved metabolomics (SRM) and spatially resolved transcriptomics (SRT) approaches can offer new ideas and reliable tools for the in-depth study of tumors. This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques, as well as a review of their applications in cancer-related fields.
Collapse
Affiliation(s)
- Yanhe Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xinyi Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianpeng Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Tong Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongtao Jin
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, 10050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing, 10050, China
| |
Collapse
|
28
|
Kritikos N, Bletsou A, Konstantinou C, Neofotistos AD, Kousoulos C, Dotsikas Y. Determination of Response Factors for Analytes Detected during Migration Studies, Strategy and Internal Standard Selection for Risk Minimization. Molecules 2023; 28:5772. [PMID: 37570741 PMCID: PMC10421053 DOI: 10.3390/molecules28155772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/21/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Migration studies are one of the few domains of pharmaceutical analysis employing wide-scope screening methodologies. The studies involve the detection of contaminants within pharmaceutical products that arise from the interaction between the formulation and materials. Requiring both qualitative and quantitative data, the studies are conducted using Liquid Chromatography or Gas Chromatography coupled to a mass spectrometer (LC-MS and GC-MS). While mass spectrometry allows wide-scope analyte detection and identification at the very low Analytical Evaluation Threshold (AET) levels used in these studies, MS detectors are far from "universal response" detectors. Regulation brings the application of uncertainty factors into the picture to limit the risk of potential analytes detected escaping report and further evaluation; however, whether the application of a default value can cover any or all relevant applications is still debatable. The current study evaluated the response of species usually detected in migration studies, generating a suitable representative sample, analyzing said species, and creating a strategy and evaluation mechanism for acceptable classification of the detected species. Incorporating novel methodologies, i.e., Design of Experiments (DoE) for Design Space generation, the LC-MS-based methodology is also evaluated for its robustness in changes performed.
Collapse
Affiliation(s)
- Nikolaos Kritikos
- QualiMetriX S.A., 579 Mesogeion Avenue, Agia Paraskevi, 15343 Athens, Greece; (N.K.); (A.B.); (C.K.); (A.-D.N.)
| | - Anna Bletsou
- QualiMetriX S.A., 579 Mesogeion Avenue, Agia Paraskevi, 15343 Athens, Greece; (N.K.); (A.B.); (C.K.); (A.-D.N.)
| | - Christina Konstantinou
- QualiMetriX S.A., 579 Mesogeion Avenue, Agia Paraskevi, 15343 Athens, Greece; (N.K.); (A.B.); (C.K.); (A.-D.N.)
| | | | - Constantinos Kousoulos
- QualiMetriX S.A., 579 Mesogeion Avenue, Agia Paraskevi, 15343 Athens, Greece; (N.K.); (A.B.); (C.K.); (A.-D.N.)
| | - Yannis Dotsikas
- Laboratory of Pharmaceutical Analysis, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15784 Athens, Greece
| |
Collapse
|
29
|
Cáceres-Jiménez S, Rodríguez-Solana R, Dobani S, Pourshahidi K, Gill C, Moreno-Rojas JM, Almutairi TM, Crozier A, Pereira-Caro G. UHPLC-HRMS Spectrometric Analysis: Method Validation and Plasma and Urinary Metabolite Identification after Mango Pulp Intake. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37471325 DOI: 10.1021/acs.jafc.3c03846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
After an acute intake of 300 g of mango purée by 10 subjects, 0 and 24 h urine and plasma samples were analyzed by high-performance liquid chromatography-high-resolution mass spectrometry. The method was first validated for 44 reference polyphenols in terms of linearity, specificity, limits of detection and quantification, intra-day and inter-day precision, recovery, and matrix effects in two biological matrices. After method validation, a total of 94 microbial-derived phenolic catabolites, including 15 cinnamic acids, 3 phenylhydracrylic acids, 14 phenylpropanoic acids, 12 phenylacetic acids, 28 benzoic acids, 2 mandelic acids, 15 hydroxybenzenes, and 5 hippuric acid derivatives, were identified or tentatively identified in urine and/or plasma. These results establish the value of the UHPLC-HRMS protocol and the use of authentic standards to obtain a detailed and accurate picture of mango polyphenol metabolites, together with their phase II conjugated metabolites, in human bioavailability studies.
Collapse
Affiliation(s)
- Salud Cáceres-Jiménez
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, Córdoba 14004, Spain
- Departamento de Bromatología y Tecnología de los Alimentos, Campus Rabanales, Ed. Darwin-anexo, Universidad de Córdoba, Córdoba 14071, Spain
| | - Raquel Rodríguez-Solana
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, Córdoba 14004, Spain
| | - Sara Dobani
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT1 6DN, U.K
| | - Kirsty Pourshahidi
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT1 6DN, U.K
| | - Chris Gill
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT1 6DN, U.K
| | - José Manuel Moreno-Rojas
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, Córdoba 14004, Spain
- Foods for Health Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba 14004, Spain
| | - Tahani M Almutairi
- Department of Chemistry, King Saud University, Riyadh 11451, Saudi Arabia
| | - Alan Crozier
- Department of Chemistry, King Saud University, Riyadh 11451, Saudi Arabia
- School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Gema Pereira-Caro
- Department of Agroindustry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez-Pidal, Córdoba 14004, Spain
- Foods for Health Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba 14004, Spain
| |
Collapse
|
30
|
He Y, Shishkova E, Peters-Clarke TM, Brademan DR, Westphall MS, Bergen D, Huang J, Huguet R, Senko MW, Zabrouskov V, McAlister GC, Coon JJ. Evaluation of the Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics. Anal Chem 2023; 95:10655-10663. [PMID: 37389810 PMCID: PMC10528367 DOI: 10.1021/acs.analchem.3c01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a powerful technology to globally profile protein abundances, activities, interactions, and modifications. The extreme complexity of proteomics samples, which often contain hundreds of thousands of analytes, necessitates continuous development of MS techniques and instrumentation to improve speed, sensitivity, precision, and accuracy, among other analytical characteristics. Here, we systematically evaluated the Orbitrap Ascend Tribrid mass spectrometer in the context of shotgun proteomics, and we compared its performance to that of the previous generation of Tribrid instruments─the Orbitrap Eclipse. The updated architecture of the Orbitrap Ascend includes a second ion-routing multipole (IRM) in front of the redesigned C-trap/Orbitrap and a new ion funnel that allows gentler ion introduction, among other changes. These modifications in Ascend hardware configuration enabled an increase in parallelizable ion injection time during higher-energy collisional dissociation (HCD) Orbitrap tandem MS (FTMS2) analysis of ∼5 ms. This enhancement was particularly valuable in the analyses of limited sample amounts, where improvements in sensitivity resulted in up to 140% increase in the number of identified tryptic peptides. Further, analysis of phosphorylated peptides enriched from the K562 human cell line yielded up to ∼50% increase in the number of unique phosphopeptides and localized phosphosites. Strikingly, we also observed a ∼2-fold boost in the number of detected N-glycopeptides, likely owing to the improvements in ion transmission and sensitivity. In addition, we performed the multiplexed quantitative proteomics analyses of TMT11-plex labeled HEK293T tryptic peptides and observed 9-14% increase in the number of quantified peptides. In conclusion, the Orbitrap Ascend consistently outperformed its predecessor the Orbitrap Eclipse in various bottom-up proteomic analyses, and we anticipate that it will generate reproducible and in-depth datasets for numerous proteomic applications.
Collapse
Affiliation(s)
- Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | | | | | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - David Bergen
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | | | | | | | | | | | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| |
Collapse
|
31
|
Yan Y, Schmitt L, Khramchenkova A, Lengyel J. Ion transmission in an electrospray ionization-mass spectrometry interface using an S-lens. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4955. [PMID: 37401114 DOI: 10.1002/jms.4955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/24/2023] [Accepted: 06/03/2023] [Indexed: 07/05/2023]
Abstract
We present the design and performance of an in-house built electrospray ionization-mass spectrometry (ESI-MS) interface equipped with an S-lens ion guide. The ion source was designed specifically for our ion beam experiments to investigate the chemical reactivity and deposition of the clusters and nanoparticles. It includes standard ESI-MS interface components, such as nanoelectrospray, ion transfer capillary, and the S-lens. A custom design enables systematic optimization of all relevant factors influencing ion formation and transfer through the interface. By varying the ESI voltage and flow rate, we determined the optimal operating conditions for selected silica emitters. A comparison of the pulled silica emitters with different tip inner diameters reveals that the total ion current is highest for the largest tip, whereas a tip with the smallest diameter exhibited the highest transmission efficiency through the ESI-MS interface. Ion transmission through the transfer capillary is strongly limited by its length, but the loss of ions can be reduced by increasing the capillary voltage and temperature. The S-lens was characterized over a wide range of RF frequencies and amplitudes. Maximum ion current was detected at RF amplitudes greater than 50 V peak-to-peak (p/p) and frequencies above 750 kHz, with a stable ion transmission region of about 20%. A factor of 2.6 increase in total ion current is observed for 650 kHz as RF amplitudes reach 400 V p/p. Higher RF amplitudes also focus the ions into a narrow beam, which mitigates their losses when passing through the ion guide.
Collapse
Affiliation(s)
- Yihui Yan
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Lucas Schmitt
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Anastasiya Khramchenkova
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Jozef Lengyel
- Chair of Physical Chemistry, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| |
Collapse
|
32
|
Liu J, Zhao H, Chang X, Li X, Zhang Y, Zhu B, Wang X. Investigation of aroma characteristics of seven Chinese commercial sunflower seed oils using a combination of descriptive Analysis, GC-quadrupole-MS, and GC-Orbitrap-MS. Food Chem X 2023; 18:100690. [PMID: 37179977 PMCID: PMC10172861 DOI: 10.1016/j.fochx.2023.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The aroma characteristics of seven commercial Chinese sunflower seed oils were investigated in this study using descriptive analysis, headspace solid-phase microextraction coupled with GC-quadrupole-MS (LRMS, low-resolution mass spectrometry), and GC-Orbitrap-MS (HRMS, high-resolution mass spectrometry). GC-Orbitrap-MS quantified 96 compounds, including 18 alcohols, 12 esters, 7 ketones, 20 terpenoids, 11 pyrazines, 6 aldehydes, 6 furans, 6 benzene ring-containing compounds, 3 sulfides, 2 alkanes, and 5 nitrogen-containing compounds. Moreover, 22 compounds including 5 acids, 1 amide, and 16 aldehydes were quantified using GC-Quadrupole-MS. To our knowledge, 23 volatile compounds were reported for the first time in sunflower seed oil. All the seven samples were found to have a 'roasted sunflower seeds' note, 'sunflower seeds aroma' note and 'burnt aroma' note and only five of them had 'fried instant noodles' note, three had 'sweet' note and two had 'puffed food' note. Partial least squares regression was used to screen the candidate key volatiles that caused the aroma differences among these seven samples. It was observed that 'roasted sunflower seeds' note was positively correlated with 1-octen-3-ol, n-heptadehyde and dimethyl sulfone, whereas the 'fried instant noodles' and 'puffed food' demonstrated a positive correlation with pentanal, 3-methylbutanal, hexanal, (E)-2-hexenal and 2-pentylfuran. Our findings provide information to the producers and developers for quality control and improvement of sunflower seed oil.
Collapse
Affiliation(s)
- Jiani Liu
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Department of Food Science, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Huimin Zhao
- COFCO Nutrition and Health Research Institute, Beijing 102209, China
| | - Xiaomin Chang
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Department of Food Science, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaolong Li
- COFCO Nutrition and Health Research Institute, Beijing 102209, China
| | - Yu Zhang
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Department of Food Science, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Baoqing Zhu
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Department of Food Science, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Corresponding author at: Beijing Key Laboratory of Food Processing and Safety in Forestry, Department of Food Science, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (B. Zhu).
| | - Xiangyu Wang
- COFCO Nutrition and Health Research Institute, Beijing 102209, China
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Beijing 102209, China
- Beijing Engineering Laboratory of Geriatric Nutrition Food Research, Beijing 102209, China
- Corresponding author at: Beijing Key Laboratory of Food Processing and Safety in Forestry, Department of Food Science, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (B. Zhu).
| |
Collapse
|
33
|
Mathew A, Giskes F, Lekkas A, Greisch JF, Eijkel GB, Anthony IGM, Fort K, Heck AJR, Papanastasiou D, Makarov AA, Ellis SR, Heeren RMA. An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319176 DOI: 10.1021/jasms.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry (MS)-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for the comprehensive study of the higher-order molecular structure of macromolecular assemblies (MMAs). A bespoke TOF analyzer has been coupled to the higher-energy collisional dissociation cell of an ultrahigh mass range hybrid quadrupole-Orbitrap MS. A 193 nm excimer laser was employed to photofragment MMA ions. A combination of microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphor screen-TPX3CAM assemblies have been used as axial and orthogonal imaging detectors, respectively. The instrument can operate in four different modes, where the UVPD-generated fragment ions from the native MMA ions can be measured with high-mass resolution or imaged in a mass-resolved manner to reveal the relative positions of the UVPD fragments postdissociation. This information is intended to be utilized for retrieving higher-order molecular structural details that include the conformation, subunit stoichiometry, and molecular interactions as well as to understand the dissociation dynamics of the MMAs in the gas phase.
Collapse
Affiliation(s)
- Anjusha Mathew
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Frans Giskes
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Alexandros Lekkas
- Fasmatech Science and Technology, Demokritos NCSR, 15310 Agia Paraskevi, Athens, Greece
| | - Jean-François Greisch
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gert B Eijkel
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Ian G M Anthony
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Kyle Fort
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Alexander A Makarov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry (IMS), Maastricht University, 6229 ER Maastricht, The Netherlands
| |
Collapse
|
34
|
Zhang DX, Wang MY, Lin WB, Qu S, Ji L, Xu C, Kan H, Dong K. Recent advances in emerging application of functional materials in sample pretreatment methods for liquid chromatography-mass spectrometry analysis of plant growth regulators: A mini-review. J Chromatogr A 2023; 1704:464130. [PMID: 37302252 DOI: 10.1016/j.chroma.2023.464130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/04/2023] [Accepted: 06/03/2023] [Indexed: 06/13/2023]
Abstract
Plant growth regulators (PGRs) are a class of small molecular compounds, which can remarkably affect the physiological process of plants. The complex plant matrix along with a wide polarity range and unstable chemical properties of PGRs hinder their trace analysis. In order to obtain a reliable and accurate result, a sample pretreatment process must be carried out, including eliminating the interference of the matrix effect and pre-concentrating the analytes. In recent years, the research of functional materials in sample pretreatment has experienced rapid growth. This review comprehensively overviews recent development in functional materials covering one-dimensional materials, two-dimensional materials, and three-dimensional materials applied in the pretreatment of PGRs before liquid chromatography-mass spectrometry (LC-MS) analysis. Besides, the advantages and limitations of the above functionalized enrichment materials are discussed, and their future trends have been prospected. The work could be helpful to bring new insights for researchers engaged in functional materials in sample pretreatment of PGRs based on LC-MS.
Collapse
Affiliation(s)
- Dong-Xue Zhang
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Ming-Yue Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Wen-Bo Lin
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Shuai Qu
- Biology Institute of Jilin province, 1244 Qianjin Street, Changchun 130012, Jilin, China
| | - Li Ji
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Chen Xu
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China
| | - Hong Kan
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China.
| | - Kai Dong
- College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, Jilin, China.
| |
Collapse
|
35
|
Ren W, Sun M, Shi X, Wang T, Wang Y, Wang C, Li M. Progress of Mass Spectrometry-Based Lipidomics in the Dairy Field. Foods 2023; 12:foods12112098. [PMID: 37297344 DOI: 10.3390/foods12112098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
Lipids play important biological roles, such as providing essential fatty acids and signaling. The wide variety and structural diversity of lipids, and the limited technical means to study them, have seriously hampered the resolution of the mechanisms of action of lipids. With advances in mass spectrometry (MS) and bioinformatic technologies, large amounts of lipids have been detected and analyzed quickly using MS-based lipidomic techniques. Milk lipids, as complex structural metabolites, play a crucial role in human health. In this review, the lipidomic techniques and their applications to dairy products, including compositional analysis, quality identification, authenticity identification, and origin identification, are discussed, with the aim of providing technical support for the development of dairy products.
Collapse
Affiliation(s)
- Wei Ren
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| | - Mengqi Sun
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| | - Xiaoyuan Shi
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| | - Tianqi Wang
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| | - Yonghui Wang
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| | - Changfa Wang
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| | - Mengmeng Li
- School of Agricultural Science and Engineering, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252000, China
| |
Collapse
|
36
|
Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2023. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
Collapse
Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| |
Collapse
|
37
|
Liu YJ, Bian Y, Zhang Y, Zhang YX, Ren A, Lin SH, Feng XS, Zhang XY. Diuretics in Different Samples: Update on the Pretreatment and Analysis Techniques. Crit Rev Anal Chem 2023:1-33. [PMID: 37130012 DOI: 10.1080/10408347.2023.2202260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Diuretics are drugs that promote the excretion of water and electrolytes in the body and produce diuretic effects. Clinically, they are often used in the treatment of edema caused by various reasons and hypertension. In sports, diuretics are banned by the World Anti-Doping Agency (WADA). Therefore, in order to monitor blood drug concentration, identify drug quality and maintain the fairness of sports competition, accurate, rapid, highly selective and sensitive detection methods are essential. This review provides a comprehensive summary of the pretreatment and detection of diuretics in various samples since 2015. Commonly used techniques to extract diuretics include liquid-liquid extraction, liquid-phase microextraction, solid-phase extraction, solid-phase microextraction, among others. Determination methods include methods based on liquid chromatography, fluorescent spectroscopy, electrochemical sensor method, capillary electrophoresis and so on. The advantages and disadvantages of various pretreatment and analytical techniques are elaborated. In addition, future development prospects of these techniques are discussed.
Collapse
Affiliation(s)
- Ya-Jie Liu
- School of Pharmacy, China Medical University, Shenyang, China
| | - Yu Bian
- School of Pharmacy, China Medical University, Shenyang, China
| | - Yuan Zhang
- School of Pharmacy, China Medical University, Shenyang, China
| | - Yi-Xin Zhang
- School of Pharmacy, China Medical University, Shenyang, China
| | - Ai Ren
- School of Pharmacy, China Medical University, Shenyang, China
| | - Shu-Han Lin
- School of Food Science and Engineering, Dalian Ocean University, Dalian, China
| | - Xue-Song Feng
- School of Pharmacy, China Medical University, Shenyang, China
| | - Xin-Yuan Zhang
- School of Forensic Medicine, China Medical University, Shenyang, China
| |
Collapse
|
38
|
DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
Collapse
Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
39
|
Domínguez-López I, Lozano-Castellón J, Vallverdú-Queralt A, Jáuregui O, Martínez-González MÁ, Hu FB, Fitó M, Ros E, Estruch R, Lamuela-Raventós RM. Urinary metabolomics of phenolic compounds reveals biomarkers of type-2 diabetes within the PREDIMED trial. Biomed Pharmacother 2023; 162:114703. [PMID: 37062219 DOI: 10.1016/j.biopha.2023.114703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND Phenolic compounds have been associated with protective effects against type-2 diabetes (T2D). We used a metabolomics approach to determine urinary phenolic metabolites associated with T2D and fasting plasma glucose. METHODS This case-control study within the PREDIMED trial included 200 participants at high cardiovascular risk, 102 of whom were diagnosed with T2D. A panel of urinary phenolic compounds were analysed using a novel method based on liquid chromatography coupled to mass spectrometry. Multivariate statistics and adjusted logistic regressions were applied to determine the most discriminant compounds and their association with T2D. The relationship between the discriminant phenolic compounds and plasma glucose was assessed using multivariable linear regressions. RESULTS A total of 41 phenolic compounds were modeled in the orthogonal projection to latent structures discriminant analysis, and after applying adjusted logistic regressions two were selected as discriminant: dihydrocaffeic acid (OR = 0.22 (CI 95 %: 0.09; 0.52) per 1-SD, p-value = 0.021) and genistein diglucuronide (OR = 0.72 (CI 95%: 0.59; 0.88) per 1-SD, p-value = 0.021). Both metabolites were associated with a lower risk of suffering from T2D, but only dihydrocaffeic acid was inversely associated with plasma glucose (β = -17.12 (95 % CI: -29.92; -4.32) mg/dL per 1-SD, p-value = 0.009). CONCLUSIONS A novel method using a metabolomics approach was developed to analyse a panel of urinary phenolic compounds for potential associations with T2D, and two metabolites, dihydrocaffeic acid and genistein diglucuronide, were found to be associated with a lower risk of this condition.
Collapse
Affiliation(s)
- Inés Domínguez-López
- Polyphenol Research Group, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelon (UB), Av. de Joan XXII, 27-31, 08028 Barcelona, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), Universitat de Barcelona (UB), Santa Coloma de Gramanet, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Julián Lozano-Castellón
- Polyphenol Research Group, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelon (UB), Av. de Joan XXII, 27-31, 08028 Barcelona, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), Universitat de Barcelona (UB), Santa Coloma de Gramanet, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Anna Vallverdú-Queralt
- Polyphenol Research Group, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelon (UB), Av. de Joan XXII, 27-31, 08028 Barcelona, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), Universitat de Barcelona (UB), Santa Coloma de Gramanet, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Olga Jáuregui
- Centres Científics i Tecnològics de la Universitat de Barcelona (CCiTUB), 08028 Barcelona, Spain
| | - Miguel Ángel Martínez-González
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; Department of Preventive Medicine and Public Health, University of Navarra, IdiSNA, 31008 Pamplona, Spain
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Montserrat Fitó
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; Unit of Cardiovascular Risk and Nutrition, Institut Hospital del Mar de Investigaciones Médicas (IMIM), 08007 Barcelona, Spain
| | - Emilio Ros
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; Department of Endocrinology, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Ramon Estruch
- Institut de Nutrició i Seguretat Alimentària (INSA), Universitat de Barcelona (UB), Santa Coloma de Gramanet, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain; Department of Internal Medicine, Hospital Clinic, Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Rosa M Lamuela-Raventós
- Polyphenol Research Group, Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelon (UB), Av. de Joan XXII, 27-31, 08028 Barcelona, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), Universitat de Barcelona (UB), Santa Coloma de Gramanet, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain.
| |
Collapse
|
40
|
Cadang L, Tam CYJ, Moore BN, Fichtl J, Yang F. A Highly Efficient Workflow for Detecting and Identifying Sequence Variants in Therapeutic Proteins with a High Resolution LC-MS/MS Method. Molecules 2023; 28:molecules28083392. [PMID: 37110623 PMCID: PMC10144261 DOI: 10.3390/molecules28083392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Large molecule protein therapeutics have steadily grown and now represent a significant portion of the overall pharmaceutical market. These complex therapies are commonly manufactured using cell culture technology. Sequence variants (SVs) are undesired minor variants that may arise from the cell culture biomanufacturing process that can potentially affect the safety and efficacy of a protein therapeutic. SVs have unintended amino acid substitutions and can come from genetic mutations or translation errors. These SVs can either be detected using genetic screening methods or by mass spectrometry (MS). Recent advances in Next-generation Sequencing (NGS) technology have made genetic testing cheaper, faster, and more convenient compared to time-consuming low-resolution tandem MS and Mascot Error Tolerant Search (ETS)-based workflows which often require ~6 to 8 weeks data turnaround time. However, NGS still cannot detect non-genetic derived SVs while MS analysis can do both. Here, we report a highly efficient Sequence Variant Analysis (SVA) workflow using high-resolution MS and tandem mass spectrometry combined with improved software to greatly reduce the time and resource cost associated with MS SVA workflows. Method development was performed to optimize the high-resolution tandem MS and software score cutoff for both SV identification and quantitation. We discovered that a feature of the Fusion Lumos caused significant relative under-quantitation of low-level peptides and turned it off. A comparison of common Orbitrap platforms showed that similar quantitation values were obtained on a spiked-in sample. With this new workflow, the amount of false positive SVs was decreased by up to 93%, and SVA turnaround time by LC-MS/MS was shortened to 2 weeks, comparable to NGS analysis speed and making LC-MS/MS the top choice for SVA workflow.
Collapse
Affiliation(s)
- Lance Cadang
- Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
| | - Chi Yan Janet Tam
- Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
| | | | - Juergen Fichtl
- Pharma Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Feng Yang
- Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
| |
Collapse
|
41
|
Guo S, Qiu S, Cai Y, Wang Z, Yang Q, Tang S, Xie Y, Zhang A. Mass spectrometry-based metabolomics for discovering active ingredients and exploring action mechanism of herbal medicine. Front Chem 2023; 11:1142287. [PMID: 37065828 PMCID: PMC10102349 DOI: 10.3389/fchem.2023.1142287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Natural products derived from herbal medicine are a fruitful source of lead compounds because of their structural diversity and potent bioactivities. However, despite the success of active compounds derived from herbal medicine in drug discovery, some approaches cannot effectively elucidate the overall effect and action mechanism due to their multi-component complexity. Fortunately, mass spectrometry-based metabolomics has been recognized as an effective strategy for revealing the effect and discovering active components, detailed molecular mechanisms, and multiple targets of natural products. Rapid identification of lead compounds and isolation of active components from natural products would facilitate new drug development. In this context, mass spectrometry-based metabolomics has established an integrated pharmacology framework for the discovery of bioactivity-correlated constituents, target identification, and the action mechanism of herbal medicine and natural products. High-throughput functional metabolomics techniques could be used to identify natural product structure, biological activity, efficacy mechanisms, and their mode of action on biological processes, assisting bioactive lead discovery, quality control, and accelerating discovery of novel drugs. These techniques are increasingly being developed in the era of big data and use scientific language to clarify the detailed action mechanism of herbal medicine. In this paper, the analytical characteristics and application fields of several commonly used mass spectrometers are introduced, and the application of mass spectrometry in the metabolomics of traditional Chinese medicines in recent years and its active components as well as mechanism of action are also discussed.
Collapse
Affiliation(s)
- Sifan Guo
- International Advanced Functional Omics Platform, Scientific Experiment Center and Hainan General Hospital, College of Chinese Medicine, Hainan Medical University, Haikou, China
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center and Hainan General Hospital, College of Chinese Medicine, Hainan Medical University, Haikou, China
- *Correspondence: Shi Qiu, ; Songqi Tang, ; Yiqiang Xie, ; Aihua Zhang,
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhibo Wang
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Qiang Yang
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center and Hainan General Hospital, College of Chinese Medicine, Hainan Medical University, Haikou, China
- *Correspondence: Shi Qiu, ; Songqi Tang, ; Yiqiang Xie, ; Aihua Zhang,
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center and Hainan General Hospital, College of Chinese Medicine, Hainan Medical University, Haikou, China
- *Correspondence: Shi Qiu, ; Songqi Tang, ; Yiqiang Xie, ; Aihua Zhang,
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center and Hainan General Hospital, College of Chinese Medicine, Hainan Medical University, Haikou, China
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
- *Correspondence: Shi Qiu, ; Songqi Tang, ; Yiqiang Xie, ; Aihua Zhang,
| |
Collapse
|
42
|
Smirnova EV, Rakitina TV, Ziganshin RH, Saratov GA, Arapidi GP, Belogurov AA, Kudriaeva AA. Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics. Cells 2023; 12:cells12060944. [PMID: 36980286 PMCID: PMC10047773 DOI: 10.3390/cells12060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe2+ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.
Collapse
Affiliation(s)
- Evgeniya V Smirnova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Rustam H Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - George A Saratov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Alexey A Belogurov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of Russian Federation, 127473 Moscow, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| |
Collapse
|
43
|
Fu Y, Brown CJ, Johnson JT, Marsh BM, Gilbert JR, Feng E, Kenttämaa HI. Modification of a Quadrupole/Orbitrap/Linear Quadrupole Ion Trap Tribrid Mass Spectrometer for Diagnostic Gas-Phase Ion-Molecule Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:426-434. [PMID: 36797211 DOI: 10.1021/jasms.2c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Tandem mass spectrometry based on diagnostic gas-phase ion-molecule reactions represents a robust method for functional group identification in unknown compounds. To date, most of these reactions have been studied using unit-resolution instruments, such as linear quadrupole ion traps and triple quadrupoles, which cannot be used to obtain elemental composition information for the species of interest. In this study, a high-resolution mass spectrometer, a quadrupole/orbitrap/linear quadrupole ion trap tribrid, was modified by installing a portable reagent inlet system to obtain high-resolution data for ion-molecule reactions. Examination of a previously published test system, the reaction between protonated 1,1'-sulfonyldiimizadole with 2-methoxypropene, demonstrated the ability to perform ion-molecule reactions on the modified tribrid mass spectrometer. High-resolution data were obtained for ion-molecule reactions of three isobaric ions (protonated glycylalanine, protonated glutamine, and protonated lysine) with diethylmethoxyborane. On the basis of these data, the isobaric ions can be differentiated based on both their measured accurate mass as well as the different product ions they generated upon the ion-molecule reactions. In a different experiment, analyte ions were subjected to collision-induced dissociation (CID), and the structures of the resulting fragment ions were examined via diagnostic ion-molecule reactions. This experiment allows for the functional group interrogation of fragment ions and can be used to improve the understanding of the structures of fragment ions generated in the gas phase.
Collapse
Affiliation(s)
- Yue Fu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Christopher J Brown
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Joshua T Johnson
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Brett M Marsh
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Jeffrey R Gilbert
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Erlu Feng
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| |
Collapse
|
44
|
The Metabolites and Mechanism Analysis of Genistin against Hyperlipidemia via the UHPLC-Q-Exactive Orbitrap Mass Spectrometer and Metabolomics. Molecules 2023; 28:molecules28052242. [PMID: 36903488 PMCID: PMC10005657 DOI: 10.3390/molecules28052242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Genistin, an isoflavone, has been reported to have multiple activities. However, its improvement of hyperlipidemia is still unclear, and the same is true with regard to its mechanism. In this study, a high-fat diet (HFD) was used to induce a hyperlipidemic rat model. The metabolites of genistin in normal and hyperlipidemic rats were first identified to cause metabolic differences with Ultra-High-Performance Liquid Chromatography Quadrupole Exactive Orbitrap Mass Spectrometry (UHPLC-Q-Exactive Orbitrap MS). The relevant factors were determined via ELISA, and the pathological changes of liver tissue were examined via H&E staining and Oil red O staining, which evaluated the functions of genistin. The related mechanism was elucidated through metabolomics and Spearman correlation analysis. The results showed that 13 metabolites of genistin were identified in plasma from normal and hyperlipidemic rats. Of those metabolites, seven were found in normal rat, and three existed in two models, with those metabolites being involved in the reactions of decarbonylation, arabinosylation, hydroxylation, and methylation. Three metabolites, including the product of dehydroxymethylation, decarbonylation, and carbonyl hydrogenation, were identified in hyperlipidemic rats for the first time. Accordingly, the pharmacodynamic results first revealed that genistin could significantly reduce the level of lipid factors (p < 0.05), inhibited lipid accumulation in the liver, and reversed the liver function abnormalities caused by lipid peroxidation. For metabolomics results, HFD could significantly alter the levels of 15 endogenous metabolites, and genistin could reverse them. Creatine might be a beneficial biomarker for the activity of genistin against hyperlipidemia, as revealed via multivariate correlation analysis. These results, which have not been reported in the previous literature, may provide the foundation for genistin as a new lipid-lowering agent.
Collapse
|
45
|
van Drooge BL, Prats RM, Jaén C, Grimalt JO. Determination of subpicogram levels of airborne polycyclic aromatic hydrocarbons for personal exposure monitoring assessment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:368. [PMID: 36749431 PMCID: PMC9905180 DOI: 10.1007/s10661-023-10953-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
A method based on the use of GC coupled to Q-exactive Orbitrap mass spectrometry (GC-Orbitrap-MS) has been developed for the analysis of polycyclic aromatic hydrocarbons (PAHs) at sub-picogram levels. Outdoor ambient air particulate matter (PM2.5) and standard reference materials (SRM2260a) were analyzed in full scan mode showing low instrumental uncertainties (1-22%) and high linearity over a wide concentration range (0.5 pg and 500 pg/μL). Good reproducibility was obtained compared to the use of conventional single quadrupole GC-MS of PM samples. The quantification limit of the GC-Orbitrap-MS method for full scan analysis of PAHs in outdoor ambient air PM samples was 0.5 pg/μL. This low limit allowed the analysis of PAHs in samples collected with low volumes (< 0.5 m3), such as punch samples from whole filters or filter strips from personal exposure monitoring equipment. PAHs were successfully analyzed in filter strips from real-time Aethalometer AE51 equivalent black carbon (eBC) analyzers used in urban and rural sites, and in personal exposure monitors of firefighters during prescribed burns. The correlations between PAHs and eBC in these analyses were very strong (r2 ≥ 0.93). However, the equations obtained reflected the dominance of different emission sources, such as traffic in urban areas, wood burning for domestic heating, or wildfires. The method reported here affords the analyses of PAHs in high precision studies of atmospheric PM samples, e.g., high frequency sampling of low volumes, affording personal exposure monitoring assessments.
Collapse
Affiliation(s)
- Barend L. van Drooge
- Dept. Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDÆA-CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Raimon M. Prats
- Dept. Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDÆA-CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Clara Jaén
- Dept. Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDÆA-CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Joan O. Grimalt
- Dept. Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish National Research Council (IDÆA-CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain
| |
Collapse
|
46
|
Shen S, Kapphahn RJ, Zhang M, Qian S, Montezuma SR, Shang P, Ferrington DA, Qu J. Quantitative Proteomics of Human Retinal Pigment Epithelium Reveals Key Regulators for the Pathogenesis of Age-Related Macular Degeneration. Int J Mol Sci 2023; 24:3252. [PMID: 36834668 PMCID: PMC9959910 DOI: 10.3390/ijms24043252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of blindness in elderly people, with limited treatment options available for most patients. AMD involves the death of retinal pigment epithelium (RPE) and photoreceptor cells, with mitochondria dysfunction being a critical early event. In the current study, we utilized our unique resource of human donor RPE graded for AMD presence and severity to investigate proteome-wide dysregulation involved in early AMD. Organelle-enriched fractions of RPE were isolated from donors with early AMD (n = 45) and healthy age-matched controls (n = 32) and were analyzed by UHR-IonStar, an integrated proteomics platform enabling reliable and in-depth proteomic quantification in large cohorts. A total of 5941 proteins were quantified with excellent analytical reproducibility, and with further informatics analysis, many biological functions and pathways were found to be significantly dysregulated in donor RPE samples with early AMD. Several of these directly pinpointed changes in mitochondrial functions, e.g., translation, ATP metabolic process, lipid homeostasis, and oxidative stress. These novel findings highlighted the value of our proteomics investigation by allowing a better understanding of the molecular mechanisms underlying early AMD onset and facilitating both treatment development and biomarker discovery.
Collapse
Affiliation(s)
- Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Rebecca J. Kapphahn
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Shuo Qian
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Sandra R. Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Peng Shang
- Doheny Eye Institute, Pasadena, CA 91103, USA
| | - Deborah A. Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
- Doheny Eye Institute, Pasadena, CA 91103, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| |
Collapse
|
47
|
Sun DM, Zhang Y, Zhou Y, Feng XS, Zhang XY. Progress of Pretreatment and Analytical Methods of Proton Pump Inhibitors: An Update since 2010. Crit Rev Anal Chem 2023:1-26. [PMID: 36654243 DOI: 10.1080/10408347.2023.2166782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Proton pump inhibitors (PPIs) are the most commonly used medication for stomach secretion disorders. However, when it comes to safe, discreet pharmaceutical practice, widely recognized preparational and analytical method(s) for PPIs with sensitivity, selectivity, speed and high accuracy still remains underdeveloped. For this reason, this paper sets out to make a comprehensive review of the preparation and determination methods for PPIs based on multiple matrices since 2010. We have integrated newly-developed techniques (such as solid phase extraction, liquid phase micro-extraction, and solid phase micro-extraction) into conventional sample preparational methods. On the other hand, our analytical techniques include liquid chromatography, supercritical fluid chromatography, capillary electrophoresis, and employment of sensors. In addition, we have identified the pros and cons of each technique and have forecast their future developmental trends.
Collapse
Affiliation(s)
- De-Mei Sun
- School of Pharmacy, China Medical University, Shenyang, China
| | - Yuan Zhang
- School of Pharmacy, China Medical University, Shenyang, China
| | - Yu Zhou
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue-Song Feng
- School of Pharmacy, China Medical University, Shenyang, China
| | - Xin-Yuan Zhang
- School of Forensic Medicine, China Medical University, Shenyang, China
| |
Collapse
|
48
|
Butalewicz JP, Sanders JD, Clowers BH, Brodbelt JS. Improving Ion Mobility Mass Spectrometry of Proteins through Tristate Gating and Optimization of Multiplexing Parameters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:101-108. [PMID: 36469482 DOI: 10.1021/jasms.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Coupling drift tube ion mobility (IM) to Fourier transform mass spectrometry (FT-MS) affords the opportunity for gas-phase separation of ions based on size and conformation with high-resolution mass analysis. However, combining IM and FT-MS is challenging because ions exit the drift tube on a much faster time scale than the rate of mass analysis. Fourier transform (FT) and Hadamard transform multiplexing methods have been implemented to overcome the duty-cycle mismatch, offering new avenues for obtaining high-resolution, high-mass-accuracy analysis of mobility-selected ions. The gating methods used to integrate the drift tube with the FT mass analyzer discriminate against the transmission of large, low-mobility ions owing to the well-known gate depletion effect. Tristate gating strategies have been shown to increase ion transmission for drift tube IM-FT-MS systems through implementation of dual ion gating, controlling the quantity and timing of ions through the drift tube to reduce losses of slow-moving ions. Here we present an optimized set of multiplexing parameters for tristate gating ion mobility of several proteins on an Orbitrap mass spectrometer and further report parameters for increased ion transmission and mobility resolution as well as decreased experimental times from 15 min down to 30 s. On average, peak intensities in the arrival time distributions (ATDs) for ubiquitin increased 2.1× on average, while those of myoglobin increased by 1.5× with a resolving power increase on average of 11%.
Collapse
Affiliation(s)
- Jamie P Butalewicz
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
49
|
Determination of disperse dyes on polyester fibers by UHPLC-Orbitrap MS. Sci Justice 2023; 63:83-89. [PMID: 36631185 DOI: 10.1016/j.scijus.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/01/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
The determination of fiber dyes is important in forensic investigations. Although a variety of fiber dyes detection methods have been established, the sensitive and accurate determination of trace fiber dyes remains a challenge due to the possible interferences caused by complex environmental matrix and various fiber additives. Orbitrap mass spectrometry (Orbitrap MS) is a type of high-resolution mass spectrometry with high qualitative accuracy and detection sensitivity which highly meet the identification requirements of fiber dyes in real cases. However, the application of Orbitrap MS in fiber dye analysis is limited. In this regard, this study used polyester fiber, which is the most commonly-found fiber in forensic cases, as a model and established a UHPLC-Orbitrap MS method to analyze disperse dyes on polyester fibers. Using the optimized UHPLC-Orbitrap MS method, nine disperse dyes were accurately identified and well separated, and the limits of detection ranged between 0.1 ng/mL and 5.0 ng/mL. The developed method was applied to analyze actual fiber samples, and dyes from single fibers of 1 mm in length could be accurately detected. The established method is sensitive, accurate, and demonstrates good application prospects.
Collapse
|
50
|
Feng F, Zhang W, Chai Y, Guo D, Chen X. Label-free target protein characterization for small molecule drugs: recent advances in methods and applications. J Pharm Biomed Anal 2023; 223:115107. [DOI: 10.1016/j.jpba.2022.115107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
|