Charrier jean-philippe

• BioMérieux

Rapid and reliable pathogen identification is compulsory to confirm ventilator-associated pneumonia (VAP) in order to initiate appropriate antibiotic treatment. In the present proof of concept, the effectiveness of rapid microorganism identification with a targeted bottom-up proteomics approach was investigated in endotracheal aspirate (ETA) sample...

Introduction: Within less than a decade, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has entered clinical diagnostics and is today a generally accepted and appreciated integral part of the workflow for microbial identification. MALDI-TOF MS identification systems received approval from national and in...

Background: Thanks to a reasonable cost and simple sample preparation procedure, linear MALDI-ToF spectrometry is a growing technology for clinical microbiology. With appropriate spectrum databases, this technology can be used for early identification of pathogens in body fluids. However, due to the low resolution of linear MALDI-ToF instruments,...

Background: In the field of biomarker validation with mass spectrometry, controlling the technical variability is a critical issue. In selected reaction monitoring (SRM) measurements, this issue provides the opportunity of using variance component analysis to distinguish various sources of variability. However, in case of unbalanced data (unequal...

Resistance to β-lactams in Acinetobacter baumannii involves various mechanisms. To decipher them, whole genome sequencing (WGS) and real-time quantitative polymerase chain reaction (RT-qPCR) were complemented by mass spectrometry (MS) in selected reaction monitoring mode (SRM) in 39 clinical isolates. The targeted label-free proteomic approach enab...

This paper addresses the question of biomarker discovery in proteomics. Given clinical data regarding a list of proteins for a set of individuals, the tackled problem is to extract a short subset of proteins the concentrations of which are an indicator of the biological status (healthy or pathological). In this paper, it is formulated as a specific...

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoptio...

Protein biomarker discovery has inherent challenges linked to the validation of the analytical method used or to the impact of biological matrices. To guarantee the reliability of the identified biomarkers to monitor human diseases, matrix influences must be mastered. In this study, multiplexed mass spectrometry assays in selected reaction monitori...

Ribosomal proteins (r-proteins) are increasingly used as an alternative to ribosomal rRNA for prokaryotic systematics. However, their routine use is difficult because r-proteins are often not or wrongly annotated in complete genome sequences, and there is currently no dedicated exhaustive database of r-proteins. RiboDB aims at fulfilling this gap....

Mass spectrometry (MS) in Selected Reaction Monitoring (SRM) mode is proposed for in-depth characterisation of microorganisms in a multiplexed analysis. Within 60-80 minutes, the SRM method performs microbial identification (I), antibiotic-resistance detection (R), virulence assessment (V) and it provides epidemiological typing information (T). Thi...

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been introduced as an identification procedure for bacteria and fungi. The MALDI-TOF MS-based analysis of resistance to β-lactam antibiotics has been applied to detect hydrolysis of carbapenems by different bacterial strains. However, the detection of...

Both acquired and intrinsic mechanisms play a crucial role in Pseudomonas aeruginosa antibiotic resistance. Many clinically relevant resistance mechanisms result from changes in gene expression, namely multidrug efflux pump overproduction, AmpC β-lactamase induction or derepression, and inactivation or repression of the carbapenem-specific porin Op...

The paper proposes a variable selection method for proteomics. It aims at selecting, among a set of proteins, those (named biomarkers) which enable to discriminate between two groups of individuals (healthy and pathological). To this end, data is available for a cohort of individuals: the biological state and a measurement of concentrations for a l...

The cells in an organism emit different amounts of proteins according to their clinical state (healthy/pathological, for instance). The resulting proteomic profile can be used for early detection, diagnosis, and therapy planning. In this paper, we study the classification of a proteomic sample from the point of view of an inverse problem with a joi...

We present a combined theoretical and experimental study of the stability of ions in a linear ion trap under the application of one or two auxiliary radiofrequency (RF) fields, in order to perform simultaneous resonant excitation/ejection of several different ions. The influence of the amplitude and frequency of the auxiliary field is addressed thr...

Quantification and classification are key points for differential analysis of proteomic studies and diagnostic tests. A MRM analytical chain is a cascade of molecular events depicted by a graph structure, each node being associated to a molecular state such as protein, peptide or ion and each branch to a molecular processing. Each protein is associ...

A method for the in vitro diagnosis of colorectal cancer by determining the presence of Aminoacylase 1 tumor marker in a biological sample taken from a patient suspected of having colorectal cancer. Said method can be used for early diagnosis, screening, therapeutic follow-up and prognosis, and also for relapse diagnosis in relation to colorectal c...

LC ESI MS

The aim of the present study was to detect the Staphylococcus aureus delta-toxin using Whole-Cell (WC) Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDI-TOF) mass spectrometry (MS), correlate delta-toxin expression with accessory gene regulator (agr) status, and assess the prevalence of agr deficiency in clinical isolates with and w...

Clinical characteristics of patients with chronic infections. (PDF)

Analysis of robustness and repeatability of the method under routine calibration conditions. Matrix Assisted Laser Desorption Ionization/Time-Of-Flight mass spectrometry analysis of 3 isogenic strains and 2 representative clinical isolates from the collection of 168. RN6390 (delta-toxin positive parental strain) showing 3005±5 Thomson (Th) peak, RN...

Genotyping of 7 couples of Staphylococcus aureus isolates using microarrays. (PDF)

The transfer of biomarkers from the discovery field to clinical use is still, despite progress, on a road filled with pitfalls. Since the emergence of proteomics, thousands of putative biomarkers have been published, often with overlapping diagnostic capacities. The strengthening of the robustness of discovery technologies, particularly in mass spe...

A hierarchical SRM acquisition chain model for improved protein quantification in serum samples. Poster + Poster Flash présenté à la conférence RECOMB-CP 2012

Colorectal cancer (CRC) is a major public health issue worldwide, and novel tumor markers may contribute to its efficient management by helping in early detection, prognosis or surveillance of disease. The aim of our study was to identify new serum biomarkers for CRC, and we followed a phased biomarker discovery and validation process to obtain an...

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Mass spectrometry-based strategies for the quantification of low-abundance putative protein biomarkers in human blood currently require extensive sample fractionation steps which hamper their implementation in a routine and robust way across clinical laboratories. We demonstrate that a technique using MS(3) reconstructed chromatograms on a signatur...

Proteomics discovery leads to a list of potential protein biomarkers that have to be subsequently verified and validated with a statistically viable number of patients. Although the most sensitive, the development of an ELISA test is time-consuming when antibodies are not available and need to be conceived. Mass spectrometry analysis driven in quan...

Proteomic approaches including high-resolution 2-DE are providing the tools needed to discover disease-associated biomarkers in complex biological samples. Although 2-DE is an extremely powerful approach to analyze the proteome, the separation of proteins with extreme molecular masses still remains an issue requiring improvement. Because high molec...

Many problems concerned with the production and the purification of recombinant proteins must be addressed prior to launching an industrial production process. Among these problems, attention is focused on low-level expression that complicates the purification step and can jeopardise the process. The expression of a membrane protein, rP30, of Toxop...

IntroductionMaterials and methodsResults and discussionConcluding remarksReferences

Cardiac troponin I (cTnI) is a specific marker of myocardial injury. In blood of patients with cardiovascular diseases, cTnI is released as a mixture of free, complexed and post-translationally modified forms. The cTnI forms present in the plasma from 8 patients with acute myocardial infarction (AMI) have been analysed by two-dimensional gel electr...

Prostate-specific antigen (PSA) is widely used as a serum marker for the diagnosis of prostate cancer. To evaluate two anti-free PSA monoclonal antibodies (mAbs) as potential tools in new generations of more relevant PSA assays, we report here their properties towards the recognition of specific forms of free PSA in seminal fluids, LNCaP supernatan...

Prostate specific antigen (PSA) is a protease which is characteristic of the prostate. It is widely used as a serum marker for the early diagnosis of prostate cancer (PCa). Nevertheless, for concentrations between 4 and 10 ng/mL, PSA does not enable PCa to be distinguished from benign diseases, such as benign prostate hyperplasia (BPH). In sera, th...

The synthetic peptides E30D and D10P that correspond to prostate specific antigen (PSA) sequences 60-91 and 78-89, respectively, and contain the kallikrein loop were used to immunize mice to obtain anti-PSA monoclonal antibodies (mAbs). Antipeptide mAb characteristics were studied using biosensor technology and enzyme-linked immunosorbent assay, an...

Prostate-specific antigen (PSA) is an important marker for the diagnosis and management of prostate cancer, and the free PSA/total PSA ratio has been shown to be efficient for distinguishing prostate cancer from benign prostatic hyperplasia. We report here the characterization of seven mouse monoclonal antibodies (mAbs) and the partial localization...

Prostate-specific antigen (PSA), the main marker for prostate cancer (PCa), is released from the prostate into the blood stream at nanogram level and may increase in PCa and nonmalignant disease such as benign prostate hyperplasia (BPH). More recently, advantage was taken of PSA's ability to bind to protease inhibitors in serum in order to improve...

For isolation of low soluble recombinant full-length (amino acids 1-191) core protein of hepatitis C virus (HCV) overexpressed in Escherichia coli, the advantage of combining two electrophoretic techniques, in comparison with chromatographic separation, is demonstrated. The protein extract was first solubilized in agents compatible with electrophor...

This paper presents a model of the combined ultrafiltration-diafiltration process used by plasma fractionation centers to prepare human albumin by Cohn's ethanol precipitation technique. This process consists of a predilution to lower the ethanol concentration Ca from 40 to 20%, a preconcentration phase to raise albumin concentration to ∼ 80 g/l, a...