ClinProtools

PURPOSE: Early diagnosis is crucial to improve outcomes for pancreatic cancer patients (PC). The present study is designed to identify differently expressed peptides involved in PC as potential biomarkers. EXPERIMENTAL DESIGN: The serum proteome of 22 PC patients, 12 pancreatitis patients (PP), and 45 healthy controls (HC) are analyzed using magnetic bead-based weak cation exchange (MB-WCX) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)...

Cases of newly developed advanced schistosomiasis (NDAS) have occurred in areas where schistosomiasis transmission has been blocked for more than 25 years. The causes and pathogenesis of NDAS are still unknown. Diagnosis of NDAS relies on historical investigation and clinical symptoms, such as liver fibrosis, hepatic ascites and abnormal biochemical indexes in serum. It is important but difficult at this stage to develop a new tool for early screening and rapid diagnosis. In this study, serum peptides from thirty patients with NDAS and thirty healthy controls were captured with weak cation exchange magnetic beads, and subjected to MALDI-TOF mass spectrometry and ClinProTools analysis...

The Bacillus (B.) cereus group consists of nine recognized species which are present worldwide. B. cereus play an important role in food-borne diseases by producing different toxins. Yet, only a small percentage of B. cereus strains are able to produce the heat stable cereulide, the causative agent of emetic food poisoning. To minimize the entry of emetic B. cereus into the food chain, food business operators are dependent on efficient and reliable methods enabling the differentiation between emetic and non-emetic strains...

Objective: The present study aimed to determine peptidome patterns in breast cancer (BC). Methods: We analyzed the plasma proteomic profiling of 80 BC patients and 50 healthy controls, using hydrophobic interaction chromatography magnetic beads (MB-HIC8) separation followed by Matrix assisted laser desorption ionization/ time of flight mass spectrometry (MALDI-TOF MS). Results: ClinProTools software identified 92 peaks that differed among the analyzed groups, 33 peaks were significantly different (P < 0...

Background: The accurate and rapid preliminarily identification of the types of methicillin-resistant Staphylococcus aureus (MRSA) is crucial for infection control. Currently, however, expensive, time-consuming, and labor-intensive methods are used for MRSA typing. By contrast, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a potential tool for preliminary lineage typing. The approach has not been standardized, and its performance has not been analyzed in some regions with geographic barriers (e...

Staphylococcus aureus encompasses 2 subspecies ( aureus and anaerobius) with significant differences in their epidemiology and pathogenicity. We evaluated the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the rapid identification of both subspecies using a panel of 52 S. aureus isolates (30 subsp. anaerobius and 22 subsp. aureus) recovered from different origins, countries, and years. The on-board library identification system correctly identified 42 of 52 (81%) S...

Lactobacillus casei, Lactobacillus paracasei , and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA-DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories...

AIM: We evaluated a Staphylococcus argenteus-specific diagnostic profile of matrix-assisted laser desorption/ionization time-of-flight mass spectrometer for accurate identification of this novel bacterium. MATERIALS & METHODS: Staphylococcus argenteus was identified based on negative crtM gene and presence of specific sequence types. A classification model was generated by cluster analysis of matrix-assisted laser desorption/ionization time-of-flight mass spectrometer results and ClinProTools software for 25 S...

AIM: Distinction of species within the Candida glabrata complex (i.e., C. glabrata sensu stricto, Candida nivariensis and Candida bracarensis) is relevant for epidemiological purposes and antifungal management. MATERIALS & METHODS: Two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems were comprehensively evaluated for the identification of fungi within this complex. RESULTS: None of the species (C...

Background: The development of clinically accessible biomarkers is critical for the early diagnosis of gastric cancer (GC) in patients. High-throughput proteomics techniques could not only effectively generate a serum peptide profile but also provide a new approach to identify potentially diagnostic and prognostic biomarkers for cancer patients. Methods: In this study, we aim to identify potentially discriminating serum biomarkers for GC. In the discovery cohort, we screened potential biomarkers using magnetic-bead-based purification and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in 64 samples from 32 GC patients that were taken both pre- and post-operatively and 30 healthy volunteers that served as controls...

Matrix Assisted Laser Desorption/Ionization and Time of Flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the identification of bacteria through the detection and analysis of their proteins or fragments derived from ribosomes. Slight sequence variations in conserved ribosomal proteins distinguish microorganisms at the subspecies and strain levels. Characterization of Leptospira spp. by 16S RNA sequencing is costly and time-consuming, and recent studies have shown that closely related species (e...

BACKGROUND Papillary thyroid cancer (PTC) is currently the most commonly diagnosed endocrine malignancy. In addition, the sex- and age-adjusted incidence of PTC has exhibited a greater increase over the last 2 decades than in many other malignancies. Thus, discovering noninvasive specific serum biomarker to distinguish PTC from cancer-free controls in its early stages remains an important goal. MATERIAL AND METHODS Serum samples from 88 PTC patients and 80 cancer-free controls were randomly allocated into training or validation sets...

BACKGROUND: Chronic alcohol use disorders (AUD) are associated with white matter (WM) degeneration with altered myelin integrity. Matrix assisted laser desorption ionization-imaging mass spectrometry (MALDI-IMS) enables high throughput analysis of myelin lipid biochemical histopathology to help characterize disease mechanisms. PURPOSE: This study utilized MALDI-IMS to investigate frontal lobe WM myelin lipid abnormalities in AUD. METHODS: Standardized cores of formalin-fixed WM from Brodmann Area 4 (BA4) and BA8/9 of 20 postmortem AUD and 19 control adult human brains were embedded in carboxymethyl-cellulose, cryo-sectioned (8 μm), thaw-mounted onto indium tin oxide (ITO) -coated glass slides, and sublimed with 2,5-dihydroxybenzxoic acid (DHB) matrix...

Using common taxonomic methods such as 16S rDNA sequencing and physiological and biochemical analysis to identify members of the Lactobacillus casei group (LCG) is time-consuming, expensive and inaccurate. In this study, we applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to rapid discriminate LCG strains by creating an analytical in-house database (IHDB) and to develop a classification model for subspecies-level differentiation based on MS biomarkers using ClinProTools bioinformatics software (Bruker Daltonics, Billerica, MA)...

Haemophilus influenzae is associated with severe invasive disease, while Haemophilus haemolyticus is considered part of the commensal flora in the human respiratory tract. Although the addition of a custom mass spectrum library into the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system could improve identification of these two species, the establishment of such a custom database is technically complicated and requires a large amount of resources, which most clinical laboratories cannot afford...

BACKGROUND: Although pemetrexed plus cis/carboplatin has become the most effective chemotherapy regimen for patients with advanced lung adenocarcinoma, predictive biomarkers are not yet available, and new tools to identify chemosensitive patients who would likely benefit from this treatment are desperately needed. In this study, we constructed and validated predictive peptide models using the serum peptidome profiles of two datasets. METHODS: One hundred eighty-three patients treated with first-line platinum-based pemetrexed treatment for advanced lung adenocarcinoma were retrospectively enrolled and randomized into the training (n = 92) or validation (n = 91) set, and pre-treatment serum samples were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and ClinProTools software...

Besides food quality control of fish or cephalopods, the novel mass spectrometry (MS) approaches could be effective and beneficial methods for the investigation of biodiversity in ecological research. Our aims were to verify the applicability of MALDI-TOF MS in the rapid identification of closely related species, and to further develop it for sex determination in phenotypically similar fish focusing on the low mass range. For MALDI-TOF MS spectra analysis, ClinProTools software was applied, but our observed classification was also confirmed by Self Organizing Map...

BACKGROUND: Treatment options for patients with squamous cell carcinoma of the lung (SCC) are limited in chemotherapy. However, not all patients could benefit form standard platinum regimen. Considering the dismal prognosis of patients with advanced SCC, a greater focus on selecting sensitive chemotherapy regimens remains of upmost importance to improve outcomes in this disease. In this study, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to detect pre-chemotherapy serum peptides in advanced lung squamous cell carcinoma patients accepting paclitaxel combined with platinum chemotherapy and to analyze the correlation between serum peptides and chemotherapy efficacy...

Background. Diagnoses of malignant pleural effusion (MPE) are a crucial problem in clinics. In our study, we compared the peptide profiles of MPE and tuberculosis pleural effusion (TPE) to investigate the value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in diagnosis of MPE. Material and Methods. The 46 MPE and 32 TPE were randomly assigned to training set and validation set. Peptides were isolated by weak cation exchange magnetic beads and peaks in the m/z range of 800-10000 Da were analyzed...

AIMS: Carbapenem resistance in Bacteroides fragilis is emerging and is mainly attributed to insertion sequence (IS)-mediated activation of the carbapenemase gene cfiA. We investigated the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and the CarbaNP assay for the rapid identification of these strains. METHODS: This study used the Bruker MALDI Biotype system and the mass spectra models generated by 20 B. fragilis reference strains (10 cfiA-positive and 10 cfiA-negative) in the ClinProTools software to identify 404 B...