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Wahab MF, O'Haver TC. Wavelet transforms in separation science for denoising and peak overlap detection. J Sep Sci 2020; 43:1998-2010. [DOI: 10.1002/jssc.202000013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Muhammad Farooq Wahab
- Department of Chemistry and BiochemistryUniversity of Texas at Arlington Arlington TX USA
| | - Thomas C. O'Haver
- Department of Chemistry and BiochemistryUniversity of Maryland at College Park College Park MD USA
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2
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Harrington PDB. Multiple Versus Single Set Validation of Multivariate Models to Avoid Mistakes. Crit Rev Anal Chem 2017; 48:33-46. [DOI: 10.1080/10408347.2017.1361314] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Peter de Boves Harrington
- Center for Intelligent Chemical Instrumentation, Ohio University, Clippinger Laboratories, Athens, OH, USA
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3
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Zhang M, Sun J, Chen P. Development of a Comprehensive Flavonoid Analysis Computational Tool for Ultrahigh-Performance Liquid Chromatography-Diode Array Detection-High-Resolution Accurate Mass-Mass Spectrometry Data. Anal Chem 2017. [DOI: 10.1021/acs.analchem.7b00771] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mengliang Zhang
- Food Composition and Methods
Development Lab, Beltsville Human Nutrition Research Center, Agricultural
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705-2350, United States
| | - Jianghao Sun
- Food Composition and Methods
Development Lab, Beltsville Human Nutrition Research Center, Agricultural
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705-2350, United States
| | - Pei Chen
- Food Composition and Methods
Development Lab, Beltsville Human Nutrition Research Center, Agricultural
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705-2350, United States
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4
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Szymańska E, Brodrick E, Williams M, Davies AN, van Manen HJ, Buydens LMC. Data Size Reduction Strategy for the Classification of Breath and Air Samples Using Multicapillary Column-Ion Mobility Spectrometry. Anal Chem 2015; 87:869-75. [DOI: 10.1021/ac503857y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ewa Szymańska
- TI-COAST, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Radboud University Nijmegen, Institute for Molecules
and Materials (IMM), P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
| | - Emma Brodrick
- School
of Applied Sciences, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, CF37 1DL, United Kingdom
| | - Mark Williams
- School
of Applied Sciences, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, CF37 1DL, United Kingdom
| | - Antony N. Davies
- School
of Applied Sciences, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, CF37 1DL, United Kingdom
- AkzoNobel N.V., Supply Chain, Research and Development, Strategic Research Group - Measurement & Analytical Science, P.O. Box 10, 7400 AA, Deventer, The Netherlands
| | - Henk-Jan van Manen
- AkzoNobel N.V., Supply Chain, Research and Development, Strategic Research Group - Measurement & Analytical Science, P.O. Box 10, 7400 AA, Deventer, The Netherlands
| | - Lutgarde M. C. Buydens
- Radboud University Nijmegen, Institute for Molecules
and Materials (IMM), P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
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5
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Zhang M, Harrington PDB. Automated pipeline for classifying Aroclors in soil by gas chromatography/mass spectrometry using modulo compressed two-way data objects. Talanta 2013; 117:483-91. [DOI: 10.1016/j.talanta.2013.09.050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
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6
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Classification of cultivation locations of Panax quinquefolius L samples using high performance liquid chromatography-electrospray ionization mass spectrometry and chemometric analysis. Anal Chem 2012; 84:3628-34. [PMID: 22414002 DOI: 10.1021/ac2032832] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Panax quinquefolius L ( P. quinquefolius L) samples grown in the United States and China were analyzed with high performance liquid chromatography-mass spectrometry (HPLC-MS). Prior to classification, the two-way data sets were subjected to pretreatment including baseline correction and retention time (RT) alignment. Principal component analysis (PCA) and projected difference resolution (PDR) metrics were used to evaluate the data quality and the pretreatment effects. A fuzzy rule-building expert system (FuRES) classifier was used to classify the P. quinquefolius L samples grown in the United States and China with the optimized partial least-squares (o-PLS) classifier as the positively biased control method. A classification rate as high as 98 ± 3% with FuRES was obtained after baseline correction and RT alignment, which is equivalent to the result obtained by using the positively biased o-PLS control method (98 ± 3%). RT alignment improved the classification rates for both FuRES and o-PLS classifiers (18% improvement for the FuRES classification rate and 10% improvement for the o-PLS classification rate with baseline correction). From the rule obtained to classify the P. quinquefolius L samples grown in the United States and China, peaks were identified that can be prospective biomarkers for differentiating samples from different growth regions. HPLC-MS with chemometric analysis has the potential to be used as an authentication method for P. quinquefolius L grown in China and the United States.
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7
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Welker M. Proteomics for routine identification of microorganisms. Proteomics 2011; 11:3143-53. [DOI: 10.1002/pmic.201100049] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 03/31/2011] [Accepted: 04/20/2011] [Indexed: 11/10/2022]
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8
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Feng HT, Sim LC, Wan C, Wong NSC, Yang Y. Rapid characterization of protein productivity and production stability of CHO cells by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:1407-1412. [PMID: 21504006 DOI: 10.1002/rcm.5011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The biopharmaceutical industry has been in pursuit of strategies which can isolate stable and high-producing cell lines. The whole cell mass spectrometry method by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) is a rapid and simple method for cell characterization based on the differences in the fingerprints of the mass spectra. This work describes how the method was evaluated for the application of screening for stable and high-producing clones from a panel of recombinant Chinese hamster ovary (CHO) cell lines. Detectable m/z values and their relative intensities were collected and processed by partial least squares (PLS). To reduce the errors introduced by the preparation method and spectra noise, high intensity preliminary data was selected and the number of variables introduced was validated by leave-one-out cross-validation. The differences in recombinant protein productivity and titer were revealed by PLS regression with promising results. Partial least-squares discriminant analysis (PLS-DA) was applied to differentiate stable and unstable cell lines as traditional stability testing would require several months involving numerous continuous passages. Results confirmed that the whole cell MALDI-TOF method can be a powerful method for routine monitoring of bioprocesses and study can be further developed by extending the number of the cell lines tested to establish a recombinant cell line database.
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Affiliation(s)
- Hua-tao Feng
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way, Centros, Singapore 138668.
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Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 2011; 77:4136-46. [PMID: 21515723 DOI: 10.1128/aem.02418-10] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Currently, 2,610 different Salmonella serovars have been described according to the White-Kauffmann-Le Minor scheme. They are routinely differentiated by serotyping, which is based on the antigenic variability at lipopolysaccharide moieties (O antigens), flagellar proteins (H1 and H2 antigens), and capsular polysaccharides (Vi antigens). The aim of this study was to evaluate the potential of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for rapid screening and identification of epidemiologically important Salmonella enterica subsp. enterica serovars based on specific sets of serovar-identifying biomarker ions. By analyzing 913 Salmonella enterica subsp. enterica strains representing 89 different serovars using MALDI-TOF mass spectrometry, several potentially serovar-identifying biomarker ions were selected. Based on a combination of genus-, species-, subspecies-, and serovar-identifying biomarker ions, a decision tree classification algorithm was derived for the rapid identification of the five most frequently isolated Salmonella enterica serovars, Enteritidis, Typhimurium/4,[5],12:i:-, Virchow, Infantis, and Hadar. Additionally, sets of potentially serovar-identifying biomarker ions were detected for other epidemiologically interesting serovars, such as Choleraesuis, Heidelberg, and Gallinarum. Furthermore, by using a bioinformatic approach, sequence variations corresponding to single or multiple amino acid exchanges in several biomarker proteins were tentatively assigned. The inclusivity and exclusivity of the specific sets of serovar-identifying biomarker ions for the top 5 serovars were almost 100%. This study shows that whole-cell MALDI-TOF mass spectrometry can be a rapid method for prescreening S. enterica subsp. enterica isolates to identify epidemiologically important serovars and to reduce sample numbers that have to be subsequently analyzed using conventional serotyping by slide agglutination techniques.
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Mass spectrometry biotyper system identifies enteric bacterial pathogens directly from colonies grown on selective stool culture media. J Clin Microbiol 2010; 48:3888-92. [PMID: 20844226 DOI: 10.1128/jcm.01290-10] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We evaluated the performance and cost-effectiveness of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry-based Biotyper system for the routine identification of common enteric bacterial pathogens seen in middle Tennessee from suspicious colonies grown on selective stool culture media. A total of 304 suspicious colonies were selected and further identified from 605 stool specimens. The suspicious colonies were analyzed by the Biotyper system, and the results were compared to those from routine phenotypic methods, which identified 22 Salmonella species, 39 Shigella species, 3 enterohemorrhagic Escherichia coli (EHEC) isolates, 2 Yersinia enterocolitica isolates, 2 Campylobacter species, and 236 gastrointestinal normal flora isolates. The Biotyper system correctly identified the Salmonella species, Yersinia enterocolitica, and Campylobacter species but failed to distinguish the Shigella species and EHEC isolates from E. coli. Among the 236 normal flora isolates, 233 (98.7%) and 228 (96.6%) agreed at the genus and species levels, respectively, between the phenotypic and Biotyper methods. Organism identification scores were insignificantly different between colonies directly from selective media and subsequently from pure subculture. The entire Biotyper identification procedure, from smear preparation to final result reporting, can be completed within 30 min. The Biotyper system provides a rapid and simple screening tool for identifying many, but not all, suspicious colonies grown on selective media within 24 h after inoculation, which shortens test turnaround time by 2 to 3 days.
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Feng HT, Wong NSC, Sim LC, Wati L, Ho Y, Lee MM. Rapid characterization of high/low producer CHO cells using matrix-assisted laser desorption/ionization time-of-flight. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1226-1230. [PMID: 20391592 DOI: 10.1002/rcm.4506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
An intact-cell mass spectrometry (ICM) method using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) was evaluated for the screening of stable recombinant Chinese hamster ovary (CHO) cell lines, an important mammalian cell line in bioprocessing. With rapid and simple cell pretreatments, viabilities of cells could be rapidly distinguished on the different fingerprints of mass spectra. Detectable m/z values on cell surfaces and their relative intensities were processed by two biostatistical methods, principle components analysis (PCA) and partial least squares (PLS), with promising results. Discrimination among cell lines with different expressed recombinant proteins or different productivities could be achieved. The ICM method has the advantage of providing multiple parameters simultaneously and possesses the potential to become a powerful method for routine monitoring of bioprocesses.
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Affiliation(s)
- Hua-Tao Feng
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way, Centros, Singapore 138668.
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12
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Tang LJ, Jiang JH, Wu HL, Shen GL, Yu RQ. Using Sub-Band Reconstruction in Wavelet Space and Fourier Transform to Extract Local Features from Analytical Signals Exactly and Straightforwardly. ANAL LETT 2010. [DOI: 10.1080/00032710903491088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Mass spectrometry has become an important analytical tool in biology in the past two decades. In principle, mass spectrometry offers high-throughput, sensitive and specific analysis for many applications in microbiology, including clinical diagnostics and environmental research. Recently, several mass spectrometry methods for the classification and identification of bacteria and other microorganisms, as well as new software analysis tools, have been developed. In this Review we discuss the application range of these mass spectrometry procedures and their potential for successful transfer into microbiology laboratories.
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Zaima N, Matsuyama Y, Setou M. Principal component analysis of direct matrix-assisted laser desorption/ionization mass spectrometric data related to metabolites of fatty liver. J Oleo Sci 2009; 58:267-73. [PMID: 19367083 DOI: 10.5650/jos.58.267] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a common liver disease. NASH is characterized by fatty liver, along with inflammation. Most people with NASH are not aware of their condition, even though NASH can lead to hepatic cirrhosis. Several approaches have been tested to clarify the pathology of NASH. However, the mechanism of onset of NASH was not well-defined. In this study, a supervised multivariate analysis (principal component analysis) approach using direct matrix-assisted laser desorption/ionization mass spectrometry (dMALDI-MS) was applied to the analysis of metabolites in starvation-induced fatty liver tissue sections. This approach does not require complex pretreatments. We investigated the characteristic dynamics of metabolites in fatty liver. This approach can be applied to the analysis of human biopsy specimens of fatty liver in future studies.
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Affiliation(s)
- Nobuhiro Zaima
- Department of Molecular Anatomy, Molecular Imaging Frontier Research Center, Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu, Japan.
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