Bertrand Rochat

Ultra-high pressure liquid chromatography–mass spectrometry for plant metabolomics: A systematic comparison of high-resolution quadrupole-time-of-flight and single stage Orbitrap mass spectrometers

The response of Arabidopsis to stress caused by mechanical wounding was chosen as a model to compare the performances of high resolution quadrupole-time-of-flight (Q-TOF) and single stage Orbitrap (Exactive Plus) mass spectrometers in untargeted metabolomics. Both instruments were coupled to ultra-high pressure liquid chromatography (UHPLC) systems set under identical conditions. The experiment was divided in two steps: the first analyses involved sixteen unwounded plants, half of which were spiked with pure standards that are not present in Arabidopsis. The second analyses compared the metabolomes of mechanically wounded plants to unwounded plants. Data from both systems were extracted using the same feature detection software and submitted to unsupervised and supervised multivariate analysis methods. Both mass spectrometers were compared in terms of number and identity of detected features, capacity to discriminate between samples, repeatability and sensitivity. Although analytical variability was lower for the UHPLC-Q-TOF, generally the results for the two detectors were quite similar, both of them proving to be highly efficient at detecting even subtle differences between plant groups. Overall, sensitivity was found to be comparable, although the Exactive Plus Orbitrap provided slightly lower detection limits for specific compounds. Finally, to evaluate the potential of the two mass spectrometers for the identification of unknown markers, mass and spectral accuracies were calculated on selected identified compounds. While both instruments showed excellent mass accuracy (<2.5ppm for all measured compounds), better spectral accuracy was recorded on the Q-TOF. Taken together, our results demonstrate that comparable performances can be obtained at acquisition frequencies compatible with UHPLC on Q-TOF and Exactive Plus MS, which may thus be equivalently used for plant metabolomics.

Kinetic study of neuropeptide Y (NPY) proteolysis in blood and identification of NPY3-35: a new peptide generated by plasma kallikrein.

There is little information on how neuropeptide Y (NPY) proteolysis by peptidases occurs in serum, in part because reliable techniques are lacking to distinguish different NPY immunoreactive forms and also because the factors affecting the expression of these enzymes have been poorly studied. In the present study, LC-MS/MS was used to identify and quantify NPY fragments resulting from peptidolytic cleavage of NPY1–36 upon incubation with human serum. Kinetic studies indicated that NPY1–36 is rapidly cleaved in serum into 3 main fragments with the following order of efficacy: NPY3–36 ≫ NPY3–35 > NPY2–36. Trace amounts of additional NPY forms were identified by accurate mass spectrometry. Specific inhibitors of dipeptidyl peptidase IV, kallikrein, and aminopeptidase P prevented the production of NPY3–36, NPY3–35, and NPY2–36, respectively. Plasma kallikrein at physiological concentrations converted NPY3–36 into NPY3–35. Receptor binding assays revealed that NPY3–35 is unable to bind to NPY Y1, Y2, and Y5 receptors; thus NPY3–35 may represent the major metabolic clearance product of the Y2/Y5 agonist, NPY3–36.

Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data

AbstractHigh-resolution (HR) MS instruments recording HR-full scan allow analysts to go further beyond pre-acquisition choices. Untargeted acquisition can reveal unexpected compounds or concentrations and can be performed for preliminary diagnosis attempt. Then, revealed compounds will have to be identified for interpretations. Whereas the need of reference standards is mandatory to confirm identification, the diverse information collected from HRMS allows identifying unknown compounds with relatively high degree of confidence without reference standards injected in the same analytical sequence. However, there is a necessity to evaluate the degree of confidence in putative identifications, possibly before further targeted analyses. This is why a confidence scale and a score in the identification of (non-peptidic) known-unknown, defined as compounds with entries in database, is proposed for (LC-) HRMS data. The scale is based on two representative documents edited by the European Commission (2007/657/EC) and the Metabolomics Standard Initiative (MSI), in an attempt to build a bridge between the communities of metabolomics and screening labs. With this confidence scale, an identification (ID) score is determined as [a number, a letter, and a number] (e.g., 2D3), from the following three criteria: I, a General Identification Category (1, confirmed, 2, putatively identified, 3, annotated compounds/classes, and 4, unknown); II, a Chromatography Class based on the relative retention time (from the narrowest tolerance, A, to no chromatographic references, D); and III, an Identification Point Level (1, very high, 2, high, and 3, normal level) based on the number of identification points collected. Three putative identification examples of known-unknown will be presented. Graphical Abstractᅟ

SIMPLE MEASUREMENT OF TESTOSTERONE IN MALE SALIVA SAMPLES USING DISPERSIVE LIQUID–LIQUID MICROEXTRACTION FOLLOWED BY LIQUID CHROMATOGRAPHY–TANDEM MASS SPECTROMETRY DETECTION

A simple method for the measurement of testosterone in male saliva samples using liquid chromatography coupled with a triple-quadrupole mass spectrometer was developed here. Testosterone and its d-3-labeled internal standard (IS) were extracted from 0.5 mL of the saliva sample after pretreatment with acetonitrile (ACN) + 1% formic acid (FA). After centrifugation, the supernatant was diluted and underwent a dispersive liquid–liquid microextraction (DLLME) treatment. The resulting sedimented phase was then dried under a gentle steam of nitrogen gas followed by a reconstitution step before liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. Testosterone and its IS were ionized via electrospray in the positive ionization mode. Testosterone and the IS [M + H]+ parent ions (m/z 289.2 and 292.2, respectively) and the same product ions (m/z 97.1) were used for the ion transitions in the selected reaction monitoring (SRM) mode. The calibration curve was linear over the concentration range of 0.15 to 5.0 nM. Intra-day accuracy was in the range of 82% to 107%. Intra- and inter-day precision varied in the range of 1.9% to 8.7% and 7.0% to 17.5%, respectively. Finally, testosterone in male saliva samples taken from four healthy adult volunteers was successfully measured and quantified.

Generic approach for the sensitive absolute quantification of large undigested peptides in plasma using a particular liquid chromatography–mass spectrometry setup

A generic LC-MS approach for the absolute quantification of undigested peptides in plasma at mid-picomolar levels is described. Nine human peptides namely, brain natriuretic peptide (BNP), substance P (SubP), parathyroid hormone 1-34 (PTH), C-peptide, orexines A and B (Orex-A and -B), oxytocin (Oxy), gonadoliberin-1 (gonadothropin releasing-hormone or luteinizing hormone-releasing hormone, LHRH) and α-melanotropin (α-MSH) were targeted. Plasma samples were extracted via a 2-step procedure: protein precipitation using 1vol of acetonitrile followed by ultrafiltration of supernatants on membranes with a MW cut-off of 30 kDa. By applying a specific LC-MS setup, large volumes of filtrates (e.g., 2×750 μL) were injected and the peptides were trapped on a 1mm i.d.×10 mm length C8 column using a 10× on-line dilution. Then, the peptides were back-flushed and a second on-line dilution (2×) was applied during the transfer step. The refocalized peptides were resolved on a 0.3mm i.d. C18 analytical column. Extraction recovery, matrix effect and limits of detection were evaluated. Our comprehensive protocol demonstrates a simple and efficient sample preparation procedure followed by the analysis of peptides with limits of detection in the mid-picomolar range. This generic approach can be applied for the determination of most therapeutic peptides and possibly for endogenous peptides with latest state-of-the-art instruments.