scholarly journals Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectrometry Data

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Charles Dumolin ◽  
Maarten Aerts ◽  
Bart Verheyde ◽  
Simon Schellaert ◽  
Tim Vandamme ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Low Cost ◽  
Laser Desorption ◽  
Taxonomic Resolution ◽  
Laser Desorption Ionization ◽  
Data Set ◽  
Ionization Time ◽  
Maldi Tof ◽  
Global Similarity

ABSTRACT The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption–ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.

scholarly journals Characterization of Potential Protein Biomarkers for Major Depressive Disorder Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4457
Author(s):  
Chieh-Hsin Lin ◽  
Hung Su ◽  
Chung-Chieh Hung ◽  
Hsien-Yuan Lane ◽  
Jentaie Shiea
Keyword(s):  
Mass Spectrometry ◽  
Time Of Flight ◽  
Laser Desorption ◽  
Healthy Controls ◽  
Laser Desorption Ionization ◽  
Major Depressive ◽  
Ionization Time ◽  
Maldi Tof ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

Matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometry is a sensitive analytical tool for characterizing various biomolecules in biofluids. In this study, MALDI-TOF was used to characterize potential plasma biomarkers for distinguishing patients with major depressive disorder (MDD) from patients with schizophrenia and healthy controls. To avoid interference from albumin—the predominant protein in plasma—the plasma samples were pretreated using acid hydrolysis. The results obtained by MALDI-TOF were also validated by electrospray ionization-quadrupole time-of-flight (ESI-QTOF) mass spectrometry. The analytical results were further treated with principal component analysis (PCA), hierarchical clustering analysis (HCA), and receiver operating characteristic (ROC) curve analysis. The statistical analyses showed that MDD patients could be distinguished from schizophrenia patients and healthy controls by the lack of apolipoprotein C1 (Apo C1), which, in fact, was detected in healthy controls and schizophrenia patients. This protein is suggested to be a potential plasma biomarker for distinguishing MDD patients from healthy controls and schizophrenia patients. Since sample preparation for MALDI-TOF is very simple, high-throughput plasma apolipoprotein analysis for clinical purposes is feasible.

scholarly journals Performance of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identifying Clinical Malassezia Isolates

2016 ◽  
Vol 55 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Julie Denis ◽  
Marie Machouart ◽  
Florent Morio ◽  
Marcela Sabou ◽  
Catherine Kauffmann-LaCroix ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Time Of Flight ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Desorption Ionization ◽  
Maldi Tof ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

ABSTRACT The genus Malassezia comprises commensal yeasts on human skin. These yeasts are involved in superficial infections but are also isolated in deeper infections, such as fungemia, particularly in certain at-risk patients, such as neonates or patients with parenteral nutrition catheters. Very little is known about Malassezia epidemiology and virulence. This is due mainly to the difficulty of distinguishing species. Currently, species identification is based on morphological and biochemical characteristics. Only molecular biology techniques identify species with certainty, but they are time-consuming and expensive. The aim of this study was to develop and evaluate a matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) database for identifying Malassezia species by mass spectrometry. Eighty-five Malassezia isolates from patients in three French university hospitals were investigated. Each strain was identified by internal transcribed spacer sequencing. Forty-five strains of the six species Malassezia furfur , M. sympodialis , M. slooffiae , M. globosa , M. restricta , and M. pachydermatis allowed the creation of a MALDI-TOF database. Forty other strains were used to test this database. All strains were identified by our Malassezia database with log scores of >2.0, according to the manufacturer's criteria. Repeatability and reproducibility tests showed a coefficient of variation of the log score values of <10%. In conclusion, our new Malassezia database allows easy, fast, and reliable identification of Malassezia species. Implementation of this database will contribute to a better, more rapid identification of Malassezia species and will be helpful in gaining a better understanding of their epidemiology.

scholarly journals Rapid and Robust Identification of the Agents of Black-Grain Mycetoma by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2017 ◽  
Vol 55 (8) ◽  
pp. 2521-2528 ◽  
Author(s):  
Mark Fraser ◽  
Andrew M. Borman ◽  
Elizabeth M. Johnson
Keyword(s):  
Mass Spectrometry ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Accurate Identification ◽  
Ionization Time ◽  
Content Type ◽  
Desorption Ionization ◽  
Maldi Tof ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

ABSTRACTEumycetoma, a chronic fungal infection endemic in India, Indonesia, and parts of Africa and South and Central America, follows traumatic implantation of saprophytic fungi and frequently requires radical surgery or amputation in the absence of appropriate treatment. Fungal species that can cause black-grain mycetomas includeMadurellaspp.,Falciformisporaspp.,Trematosphaeria grisea,Nigrograna mackinnonii,Pseudochaetosphaeronema larense,Medicopsis romeroi, andEmarelliaspp.Rhytidhysteron rufulumandParathyridaria percutaneacause similar subcutaneous infections, but these infections lack the draining sinuses and fungal grains characteristic of eumycetoma. Accurate identification of the agents of subcutaneous fungal infection is essential to guide appropriate antifungal therapy. Since phenotypic identification of the causative fungi is often difficult, time-consuming molecular approaches are currently required. In the study described here we evaluated whether matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry might allow the accurate identification of eumycetoma agents and related fungi. A panel of 57 organisms corresponding to 10 different species from confirmed cases of eumycetoma and subcutaneous pedal masses, previously formally identified by PCR amplification and sequencing of internal transcribed spacer 1 (ITS1), was employed. Representative isolates of each species were used to create reference MALDI-TOF spectra, which were then used for the identification of the remaining isolates in a user-blinded manner. Here, we demonstrate that MALDI-TOF mass spectrometry accurately identified all of the test isolates, with 100%, 90.4%, and 67.3% of isolates achieving log scores greater than 1.8, 1.9, and 2.0, respectively.

scholarly journals Current Status of Matrix-Assisted Laser Desorption/Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in Clinical Diagnostic Microbiology

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4775
Author(s):  
Sachio Tsuchida ◽  
Hiroshi Umemura ◽  
Tomohiro Nakayama
Keyword(s):  
Mass Spectrometry ◽  
Laser Desorption ◽  
Clinical Applications ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms ◽  
Matrix Assisted Laser

Mass spectrometry (MS), a core technology for proteomics and metabolomics, is currently being developed for clinical applications. The identification of microorganisms in clinical samples using matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS) is a representative MS-based proteomics application that is relevant to daily clinical practice. This technology has the advantages of convenience, speed, and accuracy when compared with conventional biochemical methods. MALDI-TOF MS can shorten the time used for microbial identification by about 1 day in routine workflows. Sample preparation from microbial colonies has been improved, increasing the accuracy and speed of identification. MALDI-TOF MS is also used for testing blood, cerebrospinal fluid, and urine, because it can directly identify the microorganisms in these liquid samples without prior culture or subculture. Thus, MALDI-TOF MS has the potential to improve patient prognosis and decrease the length of hospitalization and is therefore currently considered an essential tool in clinical microbiology. Furthermore, MALDI-TOF MS is currently being combined with other technologies, such as flow cytometry, to expand the scope of clinical applications.

Can Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF) Enhance Antimicrobial Stewardship Efforts in the Acute Care Setting?

2013 ◽  
Vol 34 (9) ◽  
pp. 990-995 ◽  
Author(s):  
Pranita D. Tamma ◽  
Kennard Tan ◽  
Veronique R. Nussenblatt ◽  
Alison E. Turnbull ◽  
Karen C. Carroll ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Time Of Flight ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Desorption Ionization ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

We evaluated 222 hospitalized patients whose clinical isolates were tested using standard methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF). MALDI-TOF could have reduced time to appropriate therapy for 28.8% and 44.6% patients based on the treating physician's choices and stewardship team recommendations, respectively. Clinicians should be aware of scenarios in which MALDI-TOF can optimize antibiotic therapy.

scholarly journals Peaks of Promise and Peril: Screening for Antibiotic Resistance by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

2015 ◽  
Vol 54 (1) ◽  
pp. 5-6 ◽  
Author(s):  
Neil W. Anderson
Keyword(s):  
Mass Spectrometry ◽  
Time Of Flight ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Maldi Tof Mass Spectrometry ◽  
Desorption Ionization ◽  
Maldi Tof ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

An article in this issue of theJournal of Clinical Microbiology(J.-H. Youn, S. K. Drake, R. A. Weingarten, K. M. Frank, J. P. Dekker, and A. F. Lau, J Clin Microbiol 53:35–42, 2015,http://dx.doi.org/10.1128/JCM.01643-15) describes the use of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry for the detection of organisms carrying ablaKPC-containing plasmid. This powerful and promising application highlights the challenges of using MALDI-TOF mass spectrometry for purposes other than organism identification.

scholarly journals Iodine-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Sai Raghuveer Chava
Keyword(s):  
Mass Spectrometry ◽  
Time Of Flight ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Desorption Ionization ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Adsorption and desorption of iodine-containing α-cyano-4-hydroxycinnamic acid (aCCa) matrix species were studied using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The MALDI-TOF MS method showed that ca. 0.8- 1.4 monolayer (~ 100 ppm) of iodine-containing species was adsorbed at the surface and assisted in desorption and ionization of a protein digest peptides or peptides varying in isoelectric potential. At low laser power, desorption of analytes in protonated and sodiated form was observed but not iodine cluster relative to aCCa without iodine, suggesting a two-electron reduction process to form the protonated pseudo molecular ion, although adsorption on the surface would lead to oxidation of iodide to iodine. The addition of iodine to matrix has been demonstrated to greatly facilitate the MALDI-TOF MS process and is a valuable tool when complex protein mixtures need to be analyzed.

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