scholarly journals The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1683
Author(s):  
Marek Šebela ◽  
Martin Raus ◽  
Vladan Ondřej ◽  
Petr Hašler
Keyword(s):  
Mass Spectra ◽  
Enzyme Inhibitors ◽  
Intact Cell ◽  
Metabolic Inhibitors ◽  
Correct Identification ◽  
Prolonged Incubation ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
Synechococcus Sp ◽  
The Impact

The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10−5 M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).

scholarly journals Network Analysis Based on Unique Spectral Features Enables an Efficient Selection of Genomically Diverse Operational Isolation Units

2021 ◽  
Vol 9 (2) ◽  
pp. 416
Author(s):  
Charles Dumolin ◽  
Charlotte Peeters ◽  
Evelien De Canck ◽  
Nico Boon ◽  
Peter Vandamme
Keyword(s):  
Network Analysis ◽  
Hierarchical Clustering ◽  
Mass Spectra ◽  
Spectral Features ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
Diversity Studies ◽  
Technical Sample ◽  
Efficient Selection ◽  
Selection Of

Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships.

scholarly journals Incubation with Cu(II) and Zn(II) salts enhances MALDI-TOF mass spectra of amyloid-beta and α-synuclein toward in vivo analysis

2017 ◽  
Vol 53 (2) ◽  
pp. 162-171 ◽  
Author(s):  
Andrea R. Kelley ◽  
Madeline E. Colley ◽  
George Perry ◽  
Stephan B.H. Bach
Keyword(s):  
Amyloid Beta ◽  
Mass Spectra ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
In Vivo Analysis

Quantitative Interpretation of MALDI-TOF Mass Spectra of Imperfect Carbosilane Dendrimers

2007 ◽  
Vol 79 (4) ◽  
pp. 1639-1645 ◽  
Author(s):  
Alena Krupková ◽  
Jan Čermák ◽  
Zuzana Walterová ◽  
Jiří Horský
Keyword(s):  
Mass Spectra ◽  
Quantitative Interpretation ◽  
Carbosilane Dendrimers ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra

Identification of Bacterial Proteins Observed in MALDI TOF Mass Spectra from Whole Cells

1999 ◽  
Vol 71 (15) ◽  
pp. 3226-3230 ◽  
Author(s):  
Ricky D. Holland ◽  
Christopher R. Duffy ◽  
Fatemeh Rafii ◽  
John B. Sutherland ◽  
Thomas M. Heinze ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Whole Cells ◽  
Bacterial Proteins ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra

scholarly journals Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra

2007 ◽  
Vol 24 (1) ◽  
pp. 63-70 ◽  
Author(s):  
D. Mantini ◽  
F. Petrucci ◽  
P. Del Boccio ◽  
D. Pieragostino ◽  
M. Di Nicola ◽  
...  
Keyword(s):  
Independent Component Analysis ◽  
Mass Spectra ◽  
Component Analysis ◽  
Independent Component ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra

scholarly journals Comparison of MALDI-TOF mass spectra of [PdCl(dien)]Cl and [Ru(en)2Cl2]Cl acquired with different matrices

2011 ◽  
Vol 76 (12) ◽  
pp. 1687-1701 ◽  
Author(s):  
Bojana Damnjanovic ◽  
Biljana Petrovic ◽  
Jasmina Dimitric-Markovic ◽  
Marijana Petkovic
Keyword(s):  
Transition Metal Complexes ◽  
Mass Spectra ◽  
Hydroxycinnamic Acid ◽  
Dihydroxybenzoic Acid ◽  
Ionization Time ◽  
Maldi Tof ◽  
Ru Complex ◽  
Maldi Tof Mass Spectra ◽  
The Matrix ◽  
Flavonoid Quercetin

In this work, the matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectra of two cationic complexes, i.e., [PdCl(dien)]Cl and [Ru(en)2Cl2]Cl, acquired under different conditions were analyzed. The spectra were recorded with three matrices with or without trifluoroacetic acid (TFA), i.e., two traditional matrices, i.e., 2,5-dihydroxybenzoic acid and ?-cyano-hydroxycinnamic acid, and one flavonoid, quercetin. The spectra acquired with quercetin appeared to be the simplest, whereas in the spectra obtained with other matrices, peaks arising either from the addition of matrix molecules or from the fragmentation products were detectable. Addition of TFA did not complicate the spectra of the Pd(II) and Ru(III) complexes when the traditional matrices were used. On the other hand, the spectra of Pd complex were simpler, whereas the addition of TFA in the case of the Ru complex resulted in a higher number of peaks, some of which could not be identified. Taken together, the results of this study once more emphasize the differences arising in the MALDI-TOF mass spectra of transition metal complexes in dependence on the applied matrix.

scholarly journals Automatic acquisition of MALDI-TOF mass spectra

Analusis ◽  
1998 ◽  
Vol 26 (10) ◽  
pp. 36-36 ◽  
Author(s):  
D. Suckau ◽  
L. Cornett ◽  
K. O. Kräuter
Keyword(s):  
Mass Spectra ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
Automatic Acquisition

scholarly journals Suitable reporting for the reproducible research: an added value in the analysis of proteomics data

2017 ◽  
Author(s):  
Eugenio Del Prete ◽  
Angelo Facchiano ◽  
Aldo Profumo ◽  
Claudia Angelini ◽  
Paolo Romano
Keyword(s):  
Mass Spectra ◽  
Computer Code ◽  
Added Value ◽  
Reproducible Research ◽  
Proteomics Data ◽  
Statistical Validation ◽  
Current Output ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
R Packages

Introduction Computational reproducibility refers to the possibility of reconstructing all the steps of a workflow that connects raw data, processed data and results: it is a fundamental issue in the omic studies because of the complex and high-dimensional nature of the involved data. The analysis of omics data needs to exploit multi-step workflows including pre-processing, elaboration, statistical validation, interpretation and presentation. Although some analysis platforms are able to ensure computational reproducibility for different omics studies, they do not provide explicit information about the executed code. The availability of the code increases the quality of research in terms of transparency and knowledge transfer. Moreover, it allows other researchers to reproduce the results in a local system, make a comparison among the results and re-use computer code for analyzing different dataset. Methods Geena 2 is a robust web tool for MALDI-ToF mass spectra pre-processing. Its main output is the list of common peaks identified by aligning average spectra originated from groups of replicates from different samples. Intermediate results are also made available. GeenaR is an extension of Geena 2 still under development. Its objective is the integration in the platform of some R libraries, which may provide advanced statistical analyses, thus enriching the current output. It is noteworthy that many R packages follow the reproducible research philosophy.For the aims of GeenaR, the following R packages and tools have been considered: R-Markdown, knitr and spin. The implementation of these resources on an existing web platform can be an added value for its reporting features, since it improves the creation of a report about the work carried out, especially with reference to the code. Results and Discussion One of the aims of both Geena 2 and GeenaR is facilitating the users in analyzing MALDI-ToF mass spectra by providing a web-interface that allows to upload data, select different algorithms and parameters, execute the analysis in order to obtain results according to a specific demand. Thanks to the novel reproducible research module implemented in GeenaR, the system generates a report containing all the steps performed. More in details, the report will provide: date and time of the execution, the R libraries used for the process, chunks of code for main elaborations, selected parameters (either by the users or by the system), uploaded data in MALDIquant ‘Mass Spectrum’ class type, numerical and graphical results, short explanation about the workflow, version of the system and of the packages. GeenaR generates the results in a compressed archive, with separated log and graphical results, and a report, both in R-Markdown and in HTML format. It is important to underline strongly that reproducible research is not an optional, but a fundamental component of a good computational practice, which becomes essential in computational biology.

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