scholarly journals Understanding the chemical basis for the preferential ionization of specific biomolecules in mass spectrometry analysis of microbial cells

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Mass Spectrometry Analysis ◽  
Chemical Pretreatment ◽  
Maldi Tof Ms ◽  
Spectrometry Analysis ◽  
Chemical Basis ◽  
Maldi Tof ◽  
Different Types ◽  
Tof Ms

Mass spectrometry-enabled microbial identification has successfully demonstrated the feasibility of using profiled biomolecules for identifying microorganisms based on a chemometric or proteome database search approach. However, mechanisms driving the preferential ionization and detection of particular biomolecules in various types of mass spectrometry remain poorly understood. Specifically, mass spectra obtained from different microbial species remain poorly annotated with respect to the specific types of biomolecules accounting for the peaks. For example, while ribosomal proteins are known to be a significant class of biomolecules that could partially account for the profiled mass peaks in mass spectra of microorganisms, other classes of proteins and biomolecules remain poorly annotated. This raises the important question of how different mass spectrometry approaches ionize different types of biomolecules from a cellular matrix. Specifically, mass spectra of microorganisms reveal that only a couple of mass peaks could capture the phylogeny of a species. However, the proteome of a cell is much larger and more complicated, and yet is not fully profiled by different types of mass spectrometry methods. For example, electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could only provide a small snapshot of the entire bacterial proteome. It could be argued that different mass spectrometry methods provide complementary views of a particular proteome. However, the question remains, how do proteins and biomolecules interact with the different sample preparation and mass spectrometry analysis methods for generating an ion cloud for separation in a mass spectrometer? Thus, efforts could be directed towards understanding how different types of proteins could be preferentially ionized by MALDI-TOF MS. Specifically, different reagents could be used to perform chemical pretreatment on the proteome, which would subsequently be analyzed by mass spectrometry. Thus, a correlative map between types of chemical pretreatment used and the corresponding mass spectra could be obtained. Collectively, knowledge gleaned from the research would illuminate the chemical basis by which specific biomolecules are preferentially ionized under particular conditions, which would inform the development of strategies for increasing the subset of biomolecules ionized from a cellular proteome. Such chemical rules would also aid in the interpretation of mass spectra obtained, particularly in understanding the biological context of the experiment. Overall, the key goal of this research is to help answer the question: what is the biological basis and context of the mass spectrum obtained from cells?

scholarly journals Understanding the chemical basis for the preferential ionization of specific biomolecules in mass spectrometry analysis of microbial cells

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Mass Spectrometry Analysis ◽  
Chemical Pretreatment ◽  
Maldi Tof Ms ◽  
Spectrometry Analysis ◽  
Chemical Basis ◽  
Maldi Tof ◽  
Different Types ◽  
Tof Ms

Mass spectrometry-enabled microbial identification has successfully demonstrated the feasibility of using profiled biomolecules for identifying microorganisms based on a chemometric or proteome database search approach. However, mechanisms driving the preferential ionization and detection of particular biomolecules in various types of mass spectrometry remain poorly understood. Specifically, mass spectra obtained from different microbial species remain poorly annotated with respect to the specific types of biomolecules accounting for the peaks. For example, while ribosomal proteins are known to be a significant class of biomolecules that could partially account for the profiled mass peaks in mass spectra of microorganisms, other classes of proteins and biomolecules remain poorly annotated. This raises the important question of how different mass spectrometry approaches ionize different types of biomolecules from a cellular matrix. Specifically, mass spectra of microorganisms reveal that only a couple of mass peaks could capture the phylogeny of a species. However, the proteome of a cell is much larger and more complicated, and yet is not fully profiled by different types of mass spectrometry methods. For example, electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could only provide a small snapshot of the entire bacterial proteome. It could be argued that different mass spectrometry methods provide complementary views of a particular proteome. However, the question remains, how do proteins and biomolecules interact with the different sample preparation and mass spectrometry analysis methods for generating an ion cloud for separation in a mass spectrometer? Thus, efforts could be directed towards understanding how different types of proteins could be preferentially ionized by MALDI-TOF MS. Specifically, different reagents could be used to perform chemical pretreatment on the proteome, which would subsequently be analyzed by mass spectrometry. Thus, a correlative map between types of chemical pretreatment used and the corresponding mass spectra could be obtained. Collectively, knowledge gleaned from the research would illuminate the chemical basis by which specific biomolecules are preferentially ionized under particular conditions, which would inform the development of strategies for increasing the subset of biomolecules ionized from a cellular proteome. Such chemical rules would also aid in the interpretation of mass spectra obtained, particularly in understanding the biological context of the experiment. Overall, the key goal of this research is to help answer the question: what is the biological basis and context of the mass spectrum obtained from cells?

scholarly journals Rapid classification and prediction of COVID-19 severity by MALDI-TOF mass spectrometry analysis of serum peptidome

2020 ◽  
Author(s):  
Rosa M. Gomila ◽  
Gabriel Martorell ◽  
Pablo A. Fraile-Ribot ◽  
Antonio Doménech-Sánchez ◽  
Antonio Oliver ◽  
...  
Keyword(s):  
Machine Learning ◽  
Mass Spectrometry ◽  
Favourable Outcome ◽  
Mass Spectrometry Analysis ◽  
Learning Approaches ◽  
Maldi Tof Ms ◽  
Spectrometry Analysis ◽  
Maldi Tof ◽  
Critical Patients ◽  
Tof Ms

ABSTRACTClassification and early detection of severe COVID-19 patients is urgently required to establish an effective treatment. Here, we tested the utility of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to classify and predict the severity of COVID-19 in a clinical setting. We used this technology to analyse the mass spectra profiles of the sera from 80 COVID-19 patients, clinically classified as mild (33), severe (26) and critical (21), and 20 healthy controls. We found a clear variability of the serum peptidome profile depending on COVID-19 severity. Seventy-eight peaks were significantly different and 12 at least four fold more intense in the set of critical patients than in the mild ones. Analysis of the resulting matrix of peak intensities by machine learning approaches classified severe (severe and critical) and non-severe (mild) patients with a 90% of accuracy. Furthermore, machine learning predicted correctly the favourable outcome of the severe patients in 85% of the cases and the unfavourable in 38% of the cases. Finally, liquid chromatography mass spectrometry analysis of sera identified five proteins that were significantly upregulated in the critical patients. They included serum amyloid proteins A1 and A2, which probably yielded the most intense peaks with m/z 11,530 and 11,686 detected by MALDI-TOF MS.In summary, we demonstrated the potential of the MALDI-TOF MS as a bench to bedside technology to aid clinicians in their decisions to classify COVID-19 patients and predict their evolution.

scholarly journals Characterization of aliphatic hyperbranched polyesters by MALDI-TOF mass spectrometry

2007 ◽  
Vol 61 (6) ◽  
pp. 333-341
Author(s):  
Jasna Vukovic ◽  
Slobodan Jovanovic ◽  
Manfred Lechner
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Degree Of Polymerization ◽  
Side Reactions ◽  
Maldi Tof Ms ◽  
Hyperbranched Polyesters ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
Tof Ms

In this work, MALDI-TOF mass spectrometry was used for the characterization of aliphatic hyperbranched polyesters (AHBP), synthesized from 2,2-bis(hydroxymethyl)propionic acid (bis-MPA) and di-trimethylolpropane. From the obtained results it was concluded that it was not possible to take complete advantages of MALDI-TOF MS in this particular case, since the AHBP used in this work were polydisperse. The intensity of the signals from the high mass tail of these samples (pseudo generation higher than four) was underestimated and insufficient to distinguish it from the baseline and to use it for the analysis of the spectra. As a consequence of that, lower values of the Mn were obtained. At the same time, Mw were also underestimated, which led to very low values of the polydispersity index. On the other hand, it was possible to obtain molar masses of individual molecules from the MALDI-TOF mass spectra of AHBP and to qualitatively determine the extent of cyclization (side reactions) at each degree of polymerization. Using the adequate set of equations and results obtained from MALDI-TOF mass spectra of AHBP, every signal from the spectra was identified. The obtained results show that formation of poly(bis-MPA), intramolecular esterification and intramolecular etherification occurred as side reactions during the synthesis of these polyesters. The relative amount of the cycles increases with the number of pseudo generation (from the second up to the fifth pseudo generation). It was also observed that the relative proportion of the signals which represent cyclic structures increases with the increasing degree of polymerization. In this work the basic principles of MALDI-TOF MS are also presented, as well as, a review of adequate published articles.

scholarly journals A novel and rapid approach to yeast differentiation using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

2003 ◽  
Vol 17 (1) ◽  
pp. 31-38 ◽  
Author(s):  
Richard E. Sherburn ◽  
Richard O. Jenkins
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Time Of Flight ◽  
Laser Desorption ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

Matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF-MS) was investigated as a method for the rapid identification of yeast cells. Following pretreatment of yeast samples with a cell wall digesting enzyme (lyticase), distinct and reproducible mass spectra over them/zrange 2,000 to 16,000 were obtained by MALDI-TOF-MS. Using an optimised procedure, characteristic mass spectra that distinguished between Candida spp. and between strains of Saccharomyces cerevisiae were produced. The approach offers the potential for rapid differentiation of yeasts in clinical diagnosis and in the fermentation industries.

scholarly journals Discrimination of Bacillus cereus Group Members by MALDI-TOF Mass Spectrometry

2021 ◽  
Vol 9 (6) ◽  
pp. 1202
Author(s):  
Viviana Manzulli ◽  
Valeria Rondinone ◽  
Alessandro Buchicchio ◽  
Luigina Serrecchia ◽  
Dora Cipolletta ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Bacillus Cereus ◽  
Mass Spectra ◽  
Critical Time ◽  
Principal Component ◽  
Etiologic Agent ◽  
Bacillus Cereus Group ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Matrix-Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry (MALDI-TOF MS) technology is currently increasingly used in diagnostic laboratories as a cost effective, rapid and reliable routine technique for the identification and typing of microorganisms. In this study, we used MALDI-TOF MS to analyze a collection of 160 strains belonging to the Bacillus cereus group (57 B. anthracis, 49 B. cereus, 1 B. mycoides, 18 B. wiedmannii, 27 B. thuringiensis, 7 B. toyonensis and 1 B. weihenstephanensis) and to detect specific biomarkers which would allow an unequivocal identification. The Main Spectra Profiles (MSPs) were added to an in-house reference library, expanding the current commercial library which does not include B. toyonensis and B. wiedmannii mass spectra. The obtained mass spectra were statistically compared by Principal Component Analysis (PCA) that revealed seven different clusters. Moreover, for the identification purpose, were generated dedicate algorithms for a rapid and automatic detection of characteristic ion peaks after the mass spectra acquisition. The presence of specific biomarkers can be used to differentiate strains within the B. cereus group and to make a reliable identification of Bacillus anthracis, etiologic agent of anthrax, which is the most pathogenic and feared bacterium of the group. This could offer a critical time advantage for the diagnosis and for the clinical management of human anthrax even in case of bioterror attacks.

Evaluation of serum profiles changes after neoadjuvant chemotherapy for breast cancer using MALDI-TOF/MS procedure

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e22072-e22072
Author(s):  
D. Hawke ◽  
C. Mazouni ◽  
F. André ◽  
K. Baggerly ◽  
K. Baggerly ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mass Spectrometry ◽  
Neoadjuvant Chemotherapy ◽  
Residual Disease ◽  
Differentially Expressed ◽  
Mass Spectrometry Analysis ◽  
Her2 Positive ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

e22072 Evaluation of serum profiles changes after neoadjuvant chemotherapy for breast cancer using MALDI-TOF / MS procedure. Background: Response to primary chemotherapy (CT) for breast cancer is heterogeneous among patients and a more tailored treatment would be beneficial in term of reducing exposure to an unnecessary toxicity and optimization of response rates. Mass spectrometry analysis of serum might be helpful in detecting specific changes in response to primary CT. Methods: An applied Biosystems 4700 Proteomics Analyzer matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer was used. A breast cancer cohort of 78 sera samples from 39 HER2 positive patients consisting of matched pretreatment and (6 months) posttreatment samples was used. Blood samples were collected serially before each treatment cycle every 3 weeks of neoadjuvant CT. Samples were divided into those who achieved pathological complete response (pCR, n= 20) and those who had residual disease (RD, n=19). Low-mass differentially expressed peptides were identified using MALDI-TOF/TOF. Results: This procedure yielded a total of 2329 and 3152 peaks respectively, for the responders and non-responders. Biological variation analysis revealed a total of 32 peaks for responders and 643 peaks for non-responders to be differentially regulated with a false discovery rate less than 20%. A total of 8 differentially expressed proteins were identified from their peptides after digestion and LC-MALDI-TOF/TOF. Four in tumors with pCR (AFM, C3, hemopexin, SAP) and four proteins in the RD group were identified (AP1, hemopexin, Complement B, amyloid P component) Conclusions: Our study suggests that MALDI mass spectrometry may be used to predict the tumor response to neoadjuvant chemotherapy. Proteomic analysis may be useful in developing tailored chemotherapy for breast cancer. No significant financial relationships to disclose.

scholarly journals Formation of carbohydrate-functionalised polystyrene and glass slides and their analysis by MALDI-TOF MS

2012 ◽  
Vol 8 ◽  
pp. 753-762 ◽  
Author(s):  
Martin J Weissenborn ◽  
Johannes W Wehner ◽  
Christopher J Gray ◽  
Robert Šardzík ◽  
Claire E Eyers ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometric ◽  
Mass Spectrometry Analysis ◽  
Spectrometric Analysis ◽  
Spectrometry Analysis ◽  
Maldi Tof ◽  
Glass Slides ◽  
Array Format ◽  
Tof Ms

Glycans functionalised with hydrophobic trityl groups were synthesised and adsorbed onto polystyrene and glass slides in an array format. The adsorbed glycans could be analysed directly on these minimally conducting surfaces by MALDI-TOF mass spectrometry analysis after aluminium tape was attached to the underside of the slides. Furthermore, the trityl group appeared to act as an internal matrix and no additional matrix was necessary for the MS analysis. Thus, trityl groups can be used as simple hydrophobic, noncovalently linked anchors for ligands on surfaces and at the same time facilitate the in situ mass spectrometric analysis of such ligands.

scholarly journals MALDI-ToF mass spectrometry analysis with molecular genetic identification of Vibrio spp. in the system of the monitoring of vibrio flora of surface water reservoirs

2014 ◽  
Vol 19 (6) ◽  
pp. 27-36
Author(s):  
L. V Mironova ◽  
E. A Basov ◽  
M. V Afanasev ◽  
Zh. Yu Khunkheeva ◽  
S. K Mitkeeva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Surface Water ◽  
Protein Profiling ◽  
Mass Spectrometry Analysis ◽  
Water Reservoirs ◽  
Maldi Tof Ms ◽  
Maldi Tof Mass Spectrometry ◽  
Maldi Tof ◽  
Vibrio Spp ◽  
Tof Ms

There is presented the assessment of the efficacy of the application of direct protein profiling on the basis of MALDI-ToF mass-spectrometry for identification of Vibrio spp. during monitoring of Vibrio flora in surface water reservoirs implemented in the network of cholera surveillance. The comparison of results of the MALDI-ToF MS and bacteriological detection of taxonomic belonging of583 colonies morphologically similar to Vibrio cholerae (isolated in bacteriological examination of samples from environmental objects in Irkutsk city in 2012-2013) with following random identification based on 16S rRNA and rpoB gene structure showed high diagnostic sensitivity and specificity of mass-spectrometry. The findings determine the expediency of the inclusion of MALDI-ToF MS in the layout of microbiological examination in the monitoring of Vibrio flora in surface water reservoirs.

MALDI-TOF MS and ESI-LTQ-Orbitrap tandem mass spectrometry reveal specific porphyranase activity from a Pseudoalteromonas atlantica bacterial extract

RSC Advances ◽  
2015 ◽  
Vol 5 (98) ◽  
pp. 80793-80803 ◽  
Author(s):  
C. Przybylski ◽  
G. Correc ◽  
M. Fer ◽  
F. Gonnet ◽  
W. Helbert ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Building Blocks ◽  
Mass Spectrometry Analysis ◽  
Tandem Mass ◽  
Protein Extract ◽  
Maldi Tof Ms ◽  
Spectrometry Analysis ◽  
Pseudoalteromonas Atlantica ◽  
Tof Ms

Mass spectrometry analysis highlighted an unprecedented β-methyl-porphyranase activity in protein extract fromPseudoalteromonas atlantica, which can accommodate the methylated building blocks of porphyran.

Study on the Structure of Mangrove Polyflavonoid Tannins with MALDI-TOF Mass Spectrometry and NMR

2012 ◽  
Vol 554-556 ◽  
pp. 1988-1993 ◽  
Author(s):  
Liang Liang Zhang ◽  
Yong Mei Wang ◽  
Dong Mei Wu ◽  
Man Xu ◽  
Jia Hong Chen
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectra ◽  
Degree Of Polymerization ◽  
Epicatechin Gallate ◽  
Mangrove Species ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Rhizophora Apiculata ◽  
13C Nuclear Magnetic Resonance ◽  
Tof Ms

The properties of polyflavonoid tannins from the mangrove species depend on their structure in terms of monomer units, their mean degree of polymerization and the linkage-type between flavan-3-ol units with a considerable range of structural variation. Polyflavonoid tannins were characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), which were too difficult to be resolved by other techniques. MALDI-TOF mass spectra of polyflavonoid tannins of four mangrove species in Rhizophoraceae, Kandelia candel, Ceriops tagal, Bruguiera cylindrica and Rhizophora apiculata showed as follows: (1) procyanidin oligomers formed by catechin/epicatechin, and catechin-3-O-rhamnoside monomers were present in great proportions; epigallocatechin and epicatechin gallate monomers were not detected; (2) the doubly linked structure of A-type procyanidins were also evident from the mass spectra of K. candel; (3) there were major differences in polyflavonoid tannin structure among mangrove species; and (4) the distribution of tannin oligomers, and the number-average degree of polymerization obtained by MALDI-TOF MS appeared to compare well with the results obtained by 13C nuclear magnetic resonance (NMR) analysis.

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