scholarly journals Optimized Preparation of Urine Samples from Acute Melioidosis Patients for In-Solution Proteomic Studies using LCMS QTOF or MALDI TOF MS

2021 ◽  
Vol 20 (3) ◽  
Author(s):  
Aniza Pakeer ◽  
Mohammed Imad A. Mustafa Mahmud ◽  
Nosrihah Ismail ◽  
Vanitha Mariappan
Keyword(s):  
Biomarker Discovery ◽  
Acute Phase Proteins ◽  
Protein Precipitation ◽  
Urine Samples ◽  
Precipitation Method ◽  
Cell Mediated Immunity ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Culture Positive ◽  
Tof Ms

Introduction: Investigation of urine proteome in patients with acute melioidosis may reveal potential disease markers, from either bacterial or human proteins. We used an in-solution gel-free method instead of 2-DE to detect human and Burkholderia pseudomallei proteins in urine of patients with acute melioidosis. Here, we propose a simpler, economical method for preparing urine samples directly from melioidosis patients, for in-solution proteomic analysis using LCMS-QTOF MS/MS or MALDI-TOF MS/MS. Material and Methods: We adapted an acetone-TCA based protein precipitation method with LCMS-QTOF MS to detect the B. pseudomallei proteins directly from urine of acute melioidosis patients (culture positive and negative). This process involves protein precipitation, desalting, trypsin digestion, and optimization for the mass spectrometry. Results: A total of 3,866 human peptides were detected across 11 urine samples from clinically suspected acute melioidosis patients. Among them were three Burkholderia specific proteins detected in 75% of culture positive samples. Large amounts of acute phase proteins, cell mediated immunity proteins, complement pathway proteins and inflammatory mediators were seen upon gene ontology (GO) annotation and GO enrichment analysis. Conclusions: This simple in-solution sample preparation method can be replicated easily for LCMS/MS-QTOF and MALDI-TOF proteomic analyses, avoiding tedious optimization steps in 2-DE. This method is cost effective and can be done in centres without specialized 2-DE or MS equipment and elutes can be easily transported for analysis and bioinformatics. This is the first study to analyse urine samples directly for B. pseudomallei proteins. Discovery of the entire proteome as a whole is important in leading to biomarker discovery.

scholarly journals Relationships among intramammary health, udder and teat characteristics, and productivity of extensively managed ewes

2021 ◽  
Vol 99 (4) ◽  
Author(s):  
Ryan M Knuth ◽  
Whitney C Stewart ◽  
Joshua B Taylor ◽  
Bledar Bisha ◽  
Carl J Yeoman ◽  
...  
Keyword(s):  
Future Research ◽  
Morphometric Traits ◽  
Maldi Tof Ms ◽  
Microbial Species ◽  
Maldi Tof ◽  
Microbial Invasion ◽  
Lactation Stage ◽  
The Impact ◽  
Culture Positive ◽  
Tof Ms

Abstract Mastitis is an economically important disease and its subclinical state is difficult to diagnose, which makes mitigation more challenging. The objectives of this study were to screen clinically healthy ewes in order to 1) identify cultivable microbial species in milk, 2) evaluate somatic cell count (SCC) thresholds associated with intramammary infection, and 3) estimate relationships between udder and teat morphometric traits, SCC, and ewe productivity. Milk was collected from two flocks in early (<5 d) and peak (30 to 45 d) lactation to quantify SCC (n = 530) and numerate cultivable microbial species by culture-based isolation followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS; n = 243) identification. Within flock and lactation stage, 11% to 74% (mean = 36%) of samples were culture positive. More than 50 unique identifications were classified by MALDI-TOF MS analysis, and Bacillus licheniformis (18% to 27%), Micrococcus flavus (25%), Bacillus amyloliquefaciens (7% to 18%), and Staphylococcus epidermidis (26%) were among the most common within flock and across lactation stage. Optimum SCC thresholds to identify culture-positive samples ranged from 175 × 103 to 1,675 × 103 cells/mL. Ewe productivity was assessed as total 120-d adjusted litter weight (LW120) and analyzed within flock with breed, parity, year, and the linear covariate of log10 SCC (LSCC) at early or peak lactation. Although dependent on lactation stage and year, each 1-unit increase in LSCC (e.g., an increase in SCC from 100 × 103 to 1,000 × 103 cells/mL) was predicted to decrease LW120 between 9.5 and 16.1 kg when significant. Udder and teat traits included udder circumference, teat length, teat placement, and degree of separation of the udder halves. Correlations between traits were generally low to moderate within and across lactation stage and most were not consistently predictive of ewe LSCC. Overall, the frequencies of bacteria-positive milk samples indicated that subclinical mastitis (SCM) is common in these flocks and can impact ewe productivity. Therefore, future research is warranted to investigate pathways and timing of microbial invasion, genomic regions associated with susceptibility, and husbandry to mitigate the impact of SCM in extensively managed ewes.

scholarly journals Diagnostic accuracy of MALDI-TOF mass spectrometry for the direct identification of clinical pathogens from urine

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 266-273
Author(s):  
Min Tang ◽  
Jia Yang ◽  
Ying Li ◽  
Luhua Zhang ◽  
Ying Peng ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Likelihood Ratio ◽  
Meta Analysis ◽  
Positive Likelihood Ratio ◽  
Negative Likelihood Ratio ◽  
Urine Samples ◽  
Direct Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

AbstractMatrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid and cost-effective detection of clinical pathogenic microorganisms. This study aimed to evaluate and compare the diagnostic performance of MALDI-TOF MS with that of conventional approaches for the direct identification of pathogens from urine samples. A systematic review was conducted based on a literature search of relevant databases. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve of the combined studies were estimated. Nine studies with a total of 3920 subjects were considered eligible and included in the meta-analysis. The pooled sensitivity was 0.85 (95% CI 0.79-0.90), and the pooled specificity was 0.93 (95% CI 0.82-0.97). The PLR and NLR were 11.51 (95% CI 4.53-29.26) and 0.16 (95% CI 0.11-0.24), respectively. The area under the SROC curve was 0.93 (95% CI 0.91-0.95). Sensitivity analysis showed that the results of this meta-analysis were stable. MALDI-TOF MS could directly identify microorganisms from urine samples with high sensitivity and specificity.

Challenges in biomarker discovery with MALDI-TOF MS

2016 ◽  
Vol 458 ◽  
pp. 84-98 ◽  
Author(s):  
Joanna Hajduk ◽  
Jan Matysiak ◽  
Zenon J. Kokot
Keyword(s):  
Biomarker Discovery ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals An alternative for urine cultures: Direct identification of uropathogens from urine by MALDI-TOF MS

2020 ◽  
Author(s):  
Arzu Akşit İlki ◽  
Sevim Özsoy ◽  
Gulşen Gelmez ◽  
Burak Aksu ◽  
Güner Söyletir
Keyword(s):  
Flow Cytometry ◽  
Antibiotic Susceptibility ◽  
Clinical Microbiology ◽  
Urine Samples ◽  
Clinical Microbiology Laboratory ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Susceptibility Tests ◽  
Tract Infections ◽  
Tof Ms

AbstractUrinary tract infections are one of the most common bacterial infections and rapid diagnosis of the infection is essential for appropriate antibiotic therapy. The goal of our study was to identify urinary pathogens directly by MALDI-TOF MS and to perform antibiotic susceptibility tests in order to shorten the period spent for culturing.Urine samples submitted for culture to the Clinical Microbiology Laboratory were enrolled in this study. Urine samples were screened for leukocyte and bacteria amount by flow cytometry. Samples with bacterial load of 106–107/mL were tested directly by MALDI-TOF MS and antibiotic susceptibility tests (AST) were performed.In total, 538 positive urine samples were evaluated in our study. MALDI-TOF MS identified the microorganism directly from the urine sample in 91.8% of these samples and the concordance rate of conventional identification and direct detection was 95.8% for Gram-negatives at the genus and species level. Escherichia coli (n:401) was the most frequently isolated microorganism, followed by Klebsiella pneumoniae (n:57). AST results were generated for 111 of these urine samples and the concordance was 90% and 87% for E. coli and K. pneumoniae, respectively.Our results showed that screening of urine samples with flow cytometry to detect positive samples and identification of uropathogens directly by MALDI-TOF MS with an accuracy of over 90% can be a suitable method particularly for Gram-negative bacteria in clinical microbiology laboratories.

scholarly journals MALDI-TOF-MS Analysis in the Identification of Urine Proteomic Patterns of Gestational Trophoblastic Disease

Metabolites ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 30 ◽  
Author(s):  
Paulina Banach ◽  
Paweł Dereziński ◽  
Eliza Matuszewska ◽  
Jan Matysiak ◽  
Hubert Bochyński ◽  
...  
Keyword(s):  
Roc Curves ◽  
Gestational Trophoblastic Disease ◽  
Urine Samples ◽  
Maldi Tof Ms ◽  
Linear Mode ◽  
Trophoblastic Disease ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Pre Treatment ◽  
Tof Ms

Gestational trophoblastic disease (GTD) is a group of highly aggressive, rare tumors. Human chorionic gonadotropin is a common biomarker used in the diagnosis and monitoring of GTD. To improve our knowledge of the pathology of GTD, we performed protein-peptide profiling on the urine of patients affected with gestational trophoblastic neoplasm (GTN). We analyzed urine samples from patients diagnosed with GTN (n = 26) and from healthy pregnant and non-pregnant controls (n = 17) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Ions were examined in a linear mode over a m/z range of 1000–10,000. All GTN urine samples were analyzed before and after treatment and compared with those of the controls. The statistical analyses included multivariate classification algorithms as well as ROC curves. Urine sample analyses revealed there were significant differences in the composition of the ions between the evaluated groups. Comparing the pre-treatment and group with the pregnant controls, we identified two discriminatory proteins: hemoglobin subunit α (m/z = 1951.81) and complement C4A (m/z = 1895.43). Then, comparing urine samples from the post-treatment cases with those from the non-pregnant controls, we identified the peptides uromodulin fragments (m/z = 1682.34 and 1913.54) and complement C4A (m/z = 1895.43).

Nanostructured Affinity Surfaces for MALDI-TOF-MS–Based Protein Profiling and Biomarker Discovery

2009 ◽  
pp. 421-456
Author(s):  
R. M. Vallant ◽  
M. Rainer ◽  
M. Najam-Ul-Haq ◽  
R. Bakry ◽  
C. Petter ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Protein Profiling ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Rapid Discrimination and Authentication of Korean Farmstead Mozzarella Cheese through MALDI-TOF and Multivariate Statistical Analysis

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 333
Author(s):  
Sujatha Kandasamy ◽  
Jayeon Yoo ◽  
Jeonghee Yun ◽  
Han-Byul Kang ◽  
Kuk-Hwan Seol ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Multivariate Statistical Analysis ◽  
Biomarker Discovery ◽  
Geographical Location ◽  
Accurate Method ◽  
Multivariate Statistical ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Geographical origin and authenticity are the two crucial factors that propel overall cheese perception in terms of quality and price; therefore, they are of great importance to consumers and commercial cheese producers. Herein, we demonstrate a rapid, accurate method for discrimination of domestic and import mozzarella cheeses in the Republic of Korea by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The protein profiles’ data aided by multivariate statistical analysis successfully differentiated farmstead and import mozzarella cheeses according to their geographical location of origin. A similar investigation within domestic samples (farmsteads/companies) also showed clear discrimination regarding the producer. Using the biomarker discovery tool, we identified seven distinct proteins, of which two (m/z 7407.8 and 11,416.6) were specific in farmstead cheeses, acting as potential markers to ensure authentication and traceability. The outcome of this study can be a good resource in building a database for Korean domestic cheeses. This study also emphasizes the combined utility of MALDI-TOF MS and multivariate analysis in preventing fraudulent practices, thereby ensuring market protection for Korean farmstead cheeses.

scholarly journals Use of the MALDI-TOF MS for identification of microorganisms causing felis urine samples

2020 ◽  
Vol 64 (1) ◽  
pp. 11-13
Author(s):  
Hiroto Maeda ◽  
Takayuki Ishige ◽  
Toshifumi Watanabe ◽  
Kazuyuki Sogawa
Keyword(s):  
Urine Samples ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Capture and detection of urine bacteria using a microchannel silicon nanowire microfluidic chip coupled with MALDI-TOF MS

The Analyst ◽  
2021 ◽  
Vol 146 (4) ◽  
pp. 1151-1156
Author(s):  
Yuexin Li ◽  
Tao Wang ◽  
Jianmin Wu
Keyword(s):  
Microfluidic Chip ◽  
Silicon Nanowire ◽  
Urine Samples ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Identification Of Bacteria ◽  
Tof Ms

A microchannel silicon nanowire microfluidic chip coupled with a MALDI-TOF MS platform allows fast enrichment and identification of bacteria in urine samples.

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