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1.
PLoS One ; 15(8): e0234098, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32817616

RESUMO

In French Guiana, the malaria, a parasitic infection transmitted by Anopheline mosquitoes, remains a disease of public health importance. To prevent malaria transmission, the main effective way remains Anopheles control. For an effective control, accurate Anopheles species identification is indispensable to distinguish malaria vectors from non-vectors. Although, morphological and molecular methods are largely used, an innovative tool, based on protein pattern comparisons, the Matrix Assisted Laser Desorption / Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) profiling, emerged this last decade for arthropod identification. However, the limited mosquito fauna diversity of reference MS spectra remains one of the main drawback for its large usage. The aim of the present study was then to create and to share reference MS spectra for the identification of French Guiana Anopheline species. A total of eight distinct Anopheles species, among which four are malaria vectors, were collected in 6 areas. To improve Anopheles identification, two body parts, legs and thoraxes, were independently submitted to MS for the creation of respective reference MS spectra database (DB). This study underlined that double checking by MS enhanced the Anopheles identification confidence and rate of reliable classification. The sharing of this reference MS spectra DB should make easier Anopheles species monitoring in endemic malaria area to help malaria vector control or elimination programs.


Assuntos
Anopheles/classificação , Mosquitos Vetores/classificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Animais , Anopheles/química , Guiana Francesa , Malária/classificação , Malária/transmissão , Especificidade da Espécie , Tórax
2.
BMC Infect Dis ; 20(1): 578, 2020 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-32758181

RESUMO

BACKGROUND: Gram-positive anaerobic (GPA) bacteria inhabit different parts of the human body as commensals but can also cause bacteremia. In this retrospective observational study, we analyzed GPA bacteremia pathogens before (2013-2015) and after (2016-2018) the introduction of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). METHOD: We conducted a retrospective observational study by searching the microbiology database to identify all positive GPA blood cultures of patients with GPA bacteremia diagnosed using the new technique, MALDI-TOF MS, between January 1, 2016 and December 31, 2018; and using a conventional phenotypic method between January 1, 2013 and December 31, 2015 at a single tertiary center in Japan. Parvimonas micra (P. micra) (17.5%) was the second most frequently identified GPA (MALDI-TOF MS); we then retrospectively reviewed electronic medical records for 25 P. micra bacteremia cases at our hospital. We also conducted a literature review of published cases in PubMed from January 1, 1980, until December 31, 2019; 27 cases were retrieved. RESULTS: Most cases of P. micra bacteremia were identified after 2015, both, at our institute and from the literature review. They were of mostly elderly patients and had comorbid conditions (malignancies and diabetes). In our cases, laryngeal pharynx (7/25, 28%) and gastrointestinal tract (GIT; 6/25, 24%) were identified as the most likely sources of bacteremia; however, the infection source was not identified in 9 cases (36%). P. micra bacteremia were frequently associated with spondylodiscitis (29.6%), oropharyngeal infection (25.9%), intra-abdominal abscess (14.8%), infective endocarditis (11.1%), septic pulmonary emboli (11.1%), and GIT infection (11.1%) in the literature review. Almost all cases were treated successfully with antibiotics and by abscess drainage. The 30-day mortalities were 4 and 3.7% for our cases and the literature cases, respectively. CONCLUSIONS: Infection sites of P. micra are predominantly associated with GIT, oropharyngeal, vertebral spine, intra-abdominal region, pulmonary, and heart valves. Patients with P. micra bacteremia could have good prognosis following appropriate treatment.


Assuntos
Bacteriemia/diagnóstico , Firmicutes/química , Bactérias Gram-Positivas/química , Infecções por Bactérias Gram-Positivas/sangue , Infecções por Bactérias Gram-Positivas/diagnóstico , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/uso terapêutico , Bacteriemia/tratamento farmacológico , Bacteriemia/microbiologia , Hemocultura , Discite/microbiologia , Feminino , Firmicutes/isolamento & purificação , Trato Gastrointestinal/microbiologia , Bactérias Gram-Positivas/isolamento & purificação , Infecções por Bactérias Gram-Positivas/tratamento farmacológico , Infecções por Bactérias Gram-Positivas/microbiologia , Humanos , Japão , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Orofaringe/microbiologia , Estudos Retrospectivos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Resultado do Tratamento , Adulto Jovem
3.
Nat Biotechnol ; 38(10): 1168-1173, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32733106

RESUMO

Detection of SARS-CoV-2 using RT-PCR and other advanced methods can achieve high accuracy. However, their application is limited in countries that lack sufficient resources to handle large-scale testing during the COVID-19 pandemic. Here, we describe a method to detect SARS-CoV-2 in nasal swabs using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and machine learning analysis. This approach uses equipment and expertise commonly found in clinical laboratories in developing countries. We obtained mass spectra from a total of 362 samples (211 SARS-CoV-2-positive and 151 negative by RT-PCR) without prior sample preparation from three different laboratories. We tested two feature selection methods and six machine learning approaches to identify the top performing analysis approaches and determine the accuracy of SARS-CoV-2 detection. The support vector machine model provided the highest accuracy (93.9%), with 7% false positives and 5% false negatives. Our results suggest that MALDI-MS and machine learning analysis can be used to reliably detect SARS-CoV-2 in nasal swab samples.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Algoritmos , Biotecnologia , Técnicas de Laboratório Clínico/estatística & dados numéricos , Infecções por Coronavirus/epidemiologia , Países em Desenvolvimento , Reações Falso-Negativas , Reações Falso-Positivas , Humanos , Aprendizado de Máquina , Mucosa Nasal/virologia , Pandemias , Pneumonia Viral/epidemiologia , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/estatística & dados numéricos , Máquina de Vetores de Suporte
4.
BMC Infect Dis ; 20(1): 619, 2020 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-32831055

RESUMO

BACKGROUND: Neisseria macacae was discovered in the oral cavity of monkeys in 1983. In humans, it has been isolated from the upper respiratory tract of neutropenic patients. However, only two cases of N. macacae bacteremia have been reported in a 65-year-old man with infective endocarditis and a 5-month-old child with fever and petechiae. There are no reports of infections in cancer patients. Here, we present two cases of N. macacae bacteremia in cancer patients. CASE PRESENTATION: In the first case, a 42-year-old woman who underwent ovarian cancer surgery presented with duodenal invasion associated with multiple lymph node metastasis. N. macacae was isolated from her blood culture and identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). In the second case, a 69-year-old woman with a long-standing history of esophagogastric junction cancer presented with fever. She had stage IVB cancer with lung, bone, and multiple lymph node metastasis. The last chemotherapy was administered 5 weeks before N. macacae was detected using MALDI-TOF MS and nitrate test negative. In both cases, transthoracic echography showed no vegetation. Antibiotics were administered for 14 and 13 days in the first and second cases, respectively. In both cases, fever alleviated on day 4 of antibiotic administration. Both patients were discharged after their conditions improved. CONCLUSIONS: This, to our knowledge, is the first report of N. macacae bacteremia in cancer patients. Both patients, mucosal damage was observed in the upper gastrointestinal tract. Therefore, exclusion diagnosis suggested that bacteremia invasion was caused by mucosal rupture in both cases. Both cases responded well to treatment with ß-lactam antibiotics and improved after 2 weeks. Modifying the treatment based on the source of the infection may shorten the treatment period. Therefore, further research on N. macacae bacteremia is necessary. Immunocompromised patients such as those with cancer are susceptible to mucosal damage by unusual bacterial species such as N. macacae despite not having contact with monkeys.


Assuntos
Bacteriemia/tratamento farmacológico , Bacteriemia/microbiologia , Neisseria/patogenicidade , Adulto , Idoso , Antibacterianos/uso terapêutico , Hemocultura/métodos , Endocardite Bacteriana/microbiologia , Neoplasias Esofágicas/microbiologia , Junção Esofagogástrica/patologia , Feminino , Humanos , Masculino , Neisseria/genética , Neisseria/isolamento & purificação , Neoplasias Ovarianas/microbiologia , RNA Ribossômico 16S , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos
5.
J Chromatogr A ; 1626: 461335, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32797820

RESUMO

On-spot fixed-charge derivatization has been suggested for the modification of α-amino acids for their analysis by thin layer chromatography/matrix-assisted laser desorption ionization (TLC/MALDI) mass spectrometry. The approach was based on post-chromatographic treatment of separated analytes by tris(2,6-dimethoxyphenyl)methenium salt and triethylamine. The reaction proceeded smoothly in mild conditions and gave rise to pink-red colored derivatives, containing permanent positive charge. Their MALDI mass spectra, recorded directly from TLC plates, revealed intense peaks corresponding to decarboxylated cationic parts. All derivatives are characterized by high ionization efficiency, which indicates the high sensitivity of the developed method for analyzing amino acids. Applicability of the method to analysis of amino acids was demonstrated on artificial mixtures and dietary supplement.


Assuntos
Aminoácidos/análise , Cromatografia em Camada Delgada/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Aminoácidos/química , Etilaminas/química
6.
Nat Commun ; 11(1): 3556, 2020 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-32678093

RESUMO

Early cancer detection greatly increases the chances for successful treatment, but available diagnostics for some tumours, including lung adenocarcinoma (LA), are limited. An ideal early-stage diagnosis of LA for large-scale clinical use must address quick detection, low invasiveness, and high performance. Here, we conduct machine learning of serum metabolic patterns to detect early-stage LA. We extract direct metabolic patterns by the optimized ferric particle-assisted laser desorption/ionization mass spectrometry within 1 s using only 50 nL of serum. We define a metabolic range of 100-400 Da with 143 m/z features. We diagnose early-stage LA with sensitivity~70-90% and specificity~90-93% through the sparse regression machine learning of patterns. We identify a biomarker panel of seven metabolites and relevant pathways to distinguish early-stage LA from controls (p < 0.05). Our approach advances the design of metabolic analysis for early cancer detection and holds promise as an efficient test for low-cost rollout to clinics.


Assuntos
Adenocarcinoma de Pulmão/sangue , Biomarcadores Tumorais/sangue , Neoplasias Pulmonares/sangue , Aprendizado de Máquina , Adenocarcinoma de Pulmão/metabolismo , Adenocarcinoma de Pulmão/patologia , Detecção Precoce de Câncer , Humanos , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Metabolômica , Sensibilidade e Especificidade , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos
7.
Prostate ; 80(13): 1071-1086, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32687633

RESUMO

BACKGROUND: The emergence of reactive stroma is a hallmark of prostate cancer (PCa) progression and a potential source for prognostic and diagnostic markers of PCa. Collagen is a main component of reactive stroma and changes systematically and quantitatively to reflect the course of PCa, yet has remained undefined due to a lack of tools that can define collagen protein structure. Here we use a novel collagen-targeting proteomics approach to investigate zonal regulation of collagen-type proteins in PCa prostatectomies. METHODS: Prostatectomies from nine patients were divided into zones containing 0%, 5%, 20%, 70% to 80% glandular tissue and 0%, 5%, 25%, 70% by mass of PCa tumor following the McNeal model. Tissue sections from zones were graded by a pathologist for Gleason score, percent tumor present, percent prostatic intraepithelial neoplasia and/or inflammation (INF). High-resolution accurate mass collagen targeting proteomics was done on a select subset of tissue sections from patient-matched tumor or nontumor zones. Imaging mass spectrometry was used to investigate collagen-type regulation corresponding to pathologist-defined regions. RESULTS: Complex collagen proteomes were detected from all zones. COL17A and COL27A increased in zones of INF compared with zones with tumor present. COL3A1, COL4A5, and COL8A2 consistently increased in zones with tumor content, independent of tumor size. Collagen hydroxylation of proline (HYP) was altered in tumor zones compared with zones with INF and no tumor. COL3A1 and COL5A1 showed significant changes in HYP peptide ratios within tumor compared with zones of INF (2.59 ± 0.29, P value: .015; 3.75 ± 0.96 P value .036, respectively). By imaging mass spectrometry COL3A1 showed defined localization and regulation to tumor pathology. COL1A1 and COL1A2 showed gradient regulation corresponding to PCa pathology across zones. Pathologist-defined tumor regions showed significant increases in COL1A1 HYP modifications compared with COL1A2 HYP modifications. Certain COL1A1 and COL1A2 peptides could discriminate between pathologist-defined tumor and inflammatory regions. CONCLUSIONS: Site-specific posttranslational regulation of collagen structure by proline hydroxylation may be involved in reactive stroma associated with PCa progression. Translational and posttranslational regulation of collagen protein structure has potential for new markers to understand PCa progression and outcomes.


Assuntos
Colágeno/metabolismo , Neoplasias da Próstata/metabolismo , Neoplasias da Próstata/patologia , Processamento de Proteína Pós-Traducional , Idoso , Sequência de Aminoácidos , Autoantígenos , Colágeno Tipo I/metabolismo , Colágeno Tipo III/metabolismo , Colágeno Tipo IV/metabolismo , Colágeno Tipo VIII/metabolismo , Progressão da Doença , Colágenos Fibrilares/metabolismo , Humanos , Hidroxilação , Masculino , Pessoa de Meia-Idade , Proteínas de Neoplasias/metabolismo , Colágenos não Fibrilares , Prolina/metabolismo , Próstata/metabolismo , Prostatectomia , Neoplasias da Próstata/diagnóstico por imagem , Proteômica/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Espectroscopia de Infravermelho com Transformada de Fourier/métodos
8.
Proc Natl Acad Sci U S A ; 117(24): 13261-13266, 2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32482866

RESUMO

Modern organic reaction discovery and development relies on the rapid assessment of large arrays of hypothesis-driven experiments. The time-intensive nature of reaction analysis presents the greatest practical barrier for the execution of this iterative process that underpins the development of new bioactive agents. Toward addressing this critical bottleneck, we report herein a high-throughput analysis (HTA) method of reaction mixtures by photocapture on a 384-spot diazirine-terminated self-assembled monolayer, and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) analysis. This analytical platform has been applied to the identification of a single-electron-promoted reductive coupling of acyl azolium species.


Assuntos
Ensaios de Triagem em Larga Escala/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Benzimidazóis/síntese química , Benzimidazóis/química , Diazometano/química , Oxirredução , Raios Ultravioleta
9.
Food Chem ; 329: 127165, 2020 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-32504919

RESUMO

Biogenic amines are the important markers for food spoilage, thus, an on-package sensor for biogenic amine detection is crucial for food quality control. A dual detection platform including colorimetry and LDI-MS was developed for screening and quantitative determining of biogenic amines. Porous PLA film, was fabricated using calcium carbonate nanoparticles to enhance film porosity leading to increased surface area of colorimetric sensor. The color intensity significantly increases depending upon the enhanced analyte concentration with a linear range of 2.0-10.0 mg/mL for putrescine, and 0.1-6.0 mg/mL for cadaverine. On another layer, graphene oxide paper was applied as an LDI-MS substrate for sensitive quantification of biogenic amines. LOD values measured on graphene oxide coated side by LDI-MS were found to be 0.07 pM and 0.02 pM for putrescine and cadaverine, respectively. This platform was successfully applied for the detection of biogenic amines in pork samples with satisfactory results.


Assuntos
Aminas Biogênicas/análise , Colorimetria/métodos , Análise de Alimentos/métodos , Carne de Porco/análise , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Animais , Cadaverina/análise , Qualidade dos Alimentos , Grafite , Limite de Detecção , Nanopartículas/química , Poliésteres/química , Porosidade , Putrescina/análise , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/instrumentação
10.
PLoS Negl Trop Dis ; 14(5): e0008145, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32401760

RESUMO

Schistosomes are human pathogens causing the neglected tropical disease schistosomiasis, which occurs worldwide in (sub-)tropical regions. This infectious disease is often associated with poverty, and more than 700 million people are at risk of infection. Exploitation of novel habitats and limited therapeutic options brought schistosomes into research focus. Schistosomes are the only trematodes that have evolved separate sexes. They are covered by their metabolically active tegument, a surface area representing the interface between male and female in their permanent mating contact but also between parasite and host. The tegument comprises, besides others, numerous specific lipid compounds. Limited information is available on the exact lipid composition and its spatial distribution. We used atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization (AP-SMALDI) mass spectrometry imaging (MSI) to characterize the Schistosoma mansoni tegument surface in comparison to tissue sections of whole worms or couples. We found that phosphatidylcholines (PC) and specific phosphatidylethanolamines (PE) are significantly more abundant inside the worm body compared to the tegument. On the other hand, the latter was found to be enriched in sphingomyelins (SM), phosphatidylserines (PS), lysophosphatidylcholines (LPC), and specific PE species. We further investigated lipid classes concerning number of carbon atoms in fatty acyl chains as well as the degree of unsaturation and found pronounced differences between the tegument and whole-worm body. Furthermore, differences between male and female teguments were found. The lipid composition of S. mansoni tissues has been investigated in an untargeted, spatially resolved manner for the first time.


Assuntos
Lipidômica/métodos , Lipídeos/química , Schistosoma mansoni/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Animais , Feminino , Metabolismo dos Lipídeos , Masculino , Schistosoma mansoni/metabolismo
11.
BMC Bioinformatics ; 21(1): 129, 2020 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-32245392

RESUMO

BACKGROUND: Imaging mass spectrometry (imaging MS) is an enabling technology for spatial metabolomics of tissue sections with rapidly growing areas of applications in biology and medicine. However, imaging MS data is polluted with off-sample ions caused by sample preparation, particularly by the MALDI (matrix-assisted laser desorption/ionization) matrix application. Off-sample ion images confound and hinder statistical analysis, metabolite identification and downstream analysis with no automated solutions available. RESULTS: We developed an artificial intelligence approach to recognize off-sample ion images. First, we created a high-quality gold standard of 23,238 expert-tagged ion images from 87 public datasets from the METASPACE knowledge base. Next, we developed several machine and deep learning methods for recognizing off-sample ion images. The following methods were able to reproduce expert judgements with a high agreement: residual deep learning (F1-score 0.97), semi-automated spatio-molecular biclustering (F1-score 0.96), and molecular co-localization (F1-score 0.90). In a test-case study, we investigated off-sample images corresponding to the most common MALDI matrix (2,5-dihydroxybenzoic acid, DHB) and characterized properties of matrix clusters. CONCLUSIONS: Overall, our work illustrates how artificial intelligence approaches enabled by open-access data, web technologies, and machine and deep learning open novel avenues to address long-standing challenges in imaging MS.


Assuntos
Aprendizado de Máquina , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Aprendizado Profundo , Gentisatos/química
12.
Exp Parasitol ; 213: 107890, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32272128

RESUMO

The foodborne zoonotic nematode Trichinella spp. can cause human trichinellosis when raw or undercooked contaminated meat is ingested. To date, twelve Trichinella species/genotypes have been described. According to EU regulation any Trichinella larvae detected during mandatory routine examinations need to be identified at a species level by a competent laboratory. Currently, Trichinella species identification is performed using molecular biology tools such as multiplex PCR, PCR-sequencing or PCR-RFLP. These techniques require high level of skills for good interpretation of the results. Due to its rapidness and ease of use a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protocol was previously developed for the identification of Trichinella species. Using this method, spectra from different Trichinella species and strains were acquired allowing to generate new Main Spectra (MSP). Finally a new MSP database from Trichinella spp. Samples of different countries (France, Germany and Poland), including field samples, was generated. Comparing the different main spectra, Trichinella worms were identified at the species level and differences in the genetic diversities within the different species are discussed. In conclusion, using the previously described method on field samples is a reliable, rapid, easy-to-use and cheap tool for Trichinella species identification. The new Trichinella database could be incremented with new samples. It constitutes a tool, which could be used as an alternative method to replace the actual molecular methods for Trichinella species identification.


Assuntos
Doenças Transmitidas por Alimentos/veterinária , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/veterinária , Trichinella/isolamento & purificação , Triquinelose/veterinária , Animais , Doenças Transmitidas por Alimentos/parasitologia , França , Alemanha , Polônia , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Trichinella/classificação , Triquinelose/parasitologia
13.
PLoS One ; 15(4): e0231004, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32271809

RESUMO

Blood and serum N-glycans can be used as markers for cancer diagnosis, as alterations in protein glycosylation are associated with cancer pathogenesis and progression. We aimed to develop a platform for breast cancer (BrC) diagnosis based on serum N-glycan profiles using MALDI-TOF mass spectroscopy. Serum N-glycans from BrC patients and healthy volunteers were evaluated using NosQuest's software "NosIDsys." BrC-associated "NosID" N-glycan biomarkers were selected based on abundance and NosIDsys analysis, and their diagnostic potential was determined using NosIDsys and receiver operating characteristic curves. Results showed an efficient pattern recognition of invasive ductal carcinoma patients, with very high diagnostic performance [area under the curve (AUC): 0.93 and 95% confidence interval (CI): 0.917-0.947]. We achieved effective stage-specific differentiation of BrC patients from healthy controls with 82.3% specificity, 84.1% sensitivity, and 82.8% accuracy for stage 1 BrC and recognized hormone receptor-2 and lymph node invasion subtypes based on N-glycan profiles. Our novel technique supplements conventional diagnostic strategies for BrC detection and can be developed as an independent platform for BrC screening.


Assuntos
Neoplasias da Mama/diagnóstico , Polissacarídeos/sangue , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Biomarcadores Tumorais/sangue , Neoplasias da Mama/sangue , Neoplasias da Mama/patologia , Carcinoma Ductal de Mama/sangue , Carcinoma Ductal de Mama/diagnóstico , Estudos de Casos e Controles , Feminino , Glicosilação , Humanos , Curva ROC , Sensibilidade e Especificidade
15.
J Vis Exp ; (157)2020 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-32176198

RESUMO

Desorption/Ionization Induced by Neutral SO2 Clusters (DINeC) is employed as a very soft and efficient desorption/ionization technique for mass spectrometry (MS) of complex molecules and their reactions on surfaces. DINeC is based on a beam of SO2 clusters impacting on the sample surface at low cluster energy. During cluster-surface impact, some of the surface molecules are desorbed and ionized via dissolvation in the impacting cluster; as a result of this dissolvation-mediated desorption mechanism, low cluster energy is sufficient and the desorption process is extremely soft. Both surface adsorbates and molecules of which the surface is composed of can be analyzed. Clear and fragmentation-free spectra from complex molecules such as peptides and proteins are obtained. DINeC does not require any special sample preparation, in particular no matrix has to be applied. The method yields quantitative information on the composition of the samples; molecules at a surface coverage as low as 0.1 % of a monolayer can be detected. Surface reactions such as H/D exchange or thermal decomposition can be observed in real-time and the kinetics of the reactions can be deduced. Using a pulsed nozzle for cluster beam generation, DINeC can be efficiently combined with ion trap mass spectrometry. The matrix-free and soft nature of the DINeC process in combination with the MSn capabilities of the ion trap allows for very detailed and unambiguous analysis of the chemical composition of complex organic samples and organic adsorbates on surfaces.


Assuntos
Angiotensina II/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Medição da Troca de Deutério , Cinética , Simulação de Dinâmica Molecular , Proteólise , Propriedades de Superfície , Temperatura , Vácuo
16.
PLoS One ; 15(2): e0228459, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32027671

RESUMO

BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a significant pathogen causing healthcare-associated infections. Matrix-assisted laser desorption/ionisation mass spectrometry time-of-flight mass spectrometry (MALDI-TOF MS) is used by clinical microbiology laboratories to address the need for rapid, cost-effective and accurate identification of microorganisms. We evaluated application of machine learning methods for differentiation of drug resistant bacteria from susceptible ones directly using the profile spectra of whole cells MALDI-TOF MS in 46 CRKP and 49 CSKP isolates. METHODS: We developed a two-step strategy for data preprocessing consisting of peak matching and a feature selection step before supervised machine learning analysis. Subsequently, five machine learning algorithms were used for classification. RESULTS: Random forest (RF) outperformed other four algorithms. Using RF algorithm, we correctly identified 93% of the CRKP and 100% of the CSKP isolates with an overall classification accuracy rate of 97% when 80 peaks were selected as input features. CONCLUSIONS: We conclude that CRKPs can be differentiated from CSKPs through RF analysis. We used direct colony method, and only one spectrum for an isolate for analysis, without modification of current protocol. This allows the technique to be easily incorporated into clinical practice in the future.


Assuntos
Algoritmos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Infecções por Klebsiella/diagnóstico , Klebsiella pneumoniae/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Aprendizado de Máquina Supervisionado , Antibacterianos/uso terapêutico , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Carbapenêmicos/uso terapêutico , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia , DNA Bacteriano/análise , DNA Bacteriano/isolamento & purificação , Humanos , Infecções por Klebsiella/tratamento farmacológico , Infecções por Klebsiella/microbiologia , Klebsiella pneumoniae/genética , Testes de Sensibilidade Microbiana , Valor Preditivo dos Testes , Técnica de Amplificação ao Acaso de DNA Polimórfico
17.
PLoS One ; 15(2): e0228935, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32101540

RESUMO

The objective of this study was to assess whether use of matrix assisted laser desorption ionization-time of flight (MALDI-TOF), through improvements in identification time, reduces time to directed antibiotic coverage. We therefore conducted a retrospective review of 377 blood cultures from hospitalized patients with gram negative bacteremia that underwent testing by MALDI-TOF compared to standard identification methods (VITEK 2) for blood cultures from January 2016 to December 2017. We found that MALDI significantly reduced time between blood culture collection to reach pathogen identification and was associated with a significantly reduced time to initiate more specific therapy, with a mean difference of 16.37 hours, 95% CI 10.05 to 22.69 (mean time 50.34 hours (+/- 21.21) vs VITEK: 66.71 hrs (+/- 27.12), p<0.001 as well as a reduced time to discontinue previous therapy (p = 0.004). In conclusion, in reducing time to identification of gram negative bacteremia, MALDI-TOF led to improvements in antibiotic coverage.


Assuntos
Bacteriemia/diagnóstico , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Antibacterianos/uso terapêutico , Bacteriemia/tratamento farmacológico , Hemocultura/métodos , Humanos , Estudos Retrospectivos
18.
Nat Microbiol ; 5(3): 498-510, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32015496

RESUMO

Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defence molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry to image host-microbe symbioses and their metabolic interactions. The metaFISH pipeline aligns and integrates metabolite and fluorescent images at the micrometre scale to provide a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts and variation in metabolic phenotypes within a single symbiont 16S rRNA phylotype, and enabled the discovery of specialized metabolites from the host-microbe interface. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ and is a powerful tool for microbiologists across fields.


Assuntos
Bivalves/microbiologia , Interações entre Hospedeiro e Microrganismos/fisiologia , Metabolômica/métodos , Microbiota/fisiologia , Animais , Bactérias/genética , Bactérias/metabolismo , Hibridização in Situ Fluorescente , Metaboloma , Microbiota/genética , RNA Ribossômico 16S/genética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Simbiose , Espectrometria de Massas em Tandem
19.
J Am Soc Mass Spectrom ; 31(2): 326-335, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-32031384

RESUMO

First results for a new atmospheric-pressure matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging source operating at 213 nm laser wavelength are presented. The activation of analytes in the 213 nm MALDI process at atmospheric pressure was evaluated and compared to results for 337 nm MALDI and electrospray ionization using thermometer molecules. Different sample preparation techniques for nicotinic acid, the matrix with the highest ionization efficiency at 213 nm of all tested matrices, were evaluated and optimized to obtain small crystal sizes, homogenous matrix layer sample coverage, and high ion signal gains. Mass spectrometry imaging experiments of phospholipids in mouse tissue sections in positive- and negative-ion mode with different lateral resolutions and the corresponding pre-/post-mass spectrometry imaging workflows are presented. The use of custom-made objective lenses resulted in sample ablation spot diameters of on average 2.9 µm, allowing mass spectrometry imaging experiments to be performed with 3 µm pixel size without oversampling. The ion source was coupled to an orbital trapping mass spectrometer offering high mass resolution (>100.000), high mass accuracy (≤ ±2 ppm), and high sensitivity (single pixel on-tissue tandem MS from 6.6 µm2 ablation area). The newly developed 213 nm atmospheric-pressure MALDI source combines the high mass resolution and high mass accuracy performance characteristics of orbital trapping mass spectrometers with high lateral resolution (pixel size ∼3 µm) mass spectrometry imaging.


Assuntos
Química Encefálica , Rim/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Animais , Pressão Atmosférica , Lasers , Camundongos , Fosfolipídeos/análise
20.
J Am Soc Mass Spectrom ; 31(2): 292-297, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-32031410

RESUMO

Mass spectrometry imaging as a field has pushed its frontiers to three dimensions. Most three-dimensional mass spectrometry imaging (3D MSI) approaches require serial sectioning that results in a loss of biological information between analyzed slices and difficulty in reconstruction of 3D images. In this contribution, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) was demonstrated to be applicable for 3D MSI that does not require sectioning because IR laser ablates material on a micrometer scale. A commercially available over-the-counter pharmaceutical was used as a model to demonstrate the feasibility of IR-MALDESI for 3D MSI. Depth resolution (i.e., z-resolution) as a function of laser energy levels and density of ablated material was investigated. The best achievable depth resolution from a pill was 2.3 µm at 0.3 mJ/pulse. 2D and 3D MSI were performed on the tablet to show the distribution of pill-specific molecules. A 3D MSI analysis on a region of interest of 15 × 15 voxels across 50 layers was performed. Our results demonstrate that IR-MALDESI is feasible with 3D MSI on a pill, and future work will be focused on analyses of biological tissues.


Assuntos
Imageamento Tridimensional/métodos , Preparações Farmacêuticas/química , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Comprimidos com Revestimento Entérico/química , Antiulcerosos/análise , Citratos/análise , Omeprazol/análise , Inibidores da Bomba de Prótons/análise , Espectrometria de Massas por Ionização por Electrospray/métodos , Amido/análise
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