by Keyword: Ims

Oller-Moreno, S, Mallafré-Muro, C, Fernandez, L, Caballero, E, Blanco, A, Gumà, J, Marco, S, Pardo, A, (2023). GCIMS: An R package for untargeted gas chromatography - Ion mobility spectrometry data processing Chemometrics And Intelligent Laboratory Systems 241, 104938

Gas-Chromatography coupled to Ion Mobility Spectrometry (GC-IMS) based metabolomics is an emerging technique for obtaining fast, reliable untargeted metabolic fingerprints of biofluids. The generated raw data is highly dimensional and complex, suffers from baseline problems, misalignments, long peak tails and strong nonlinearities that must be corrected to extract chemically relevant features from samples. In this work, we present our GCIMS R package, which includes spectra loading, metadata handling, denoising, baseline correction, spectral and chromatographic alignment, peak detection, integration, and peak clustering to produce a peak table ready for multivariate data analysis. We discuss package design decisions, and, for illustration purposes, we show a case study of sex discrimination on the basis of the volatile compounds in urine samples. The GCIMS package provides a user-friendly workflow for non-code developers to process their raw data samples.

JTD Keywords: Breath analysis, Headspace, Ims, Urine

Mallafre-Muro, C, Cruz, M, Borrego, ABI, Romero, LF, Martinez, AP, Colas, SM, (2022). Study of quality controls for stability check of the ROIs of a ketones mixture in different GC-IMS measurement campaigns 2022 Ieee International Symposium On Olfaction And Electronic Nose (Isoen 2022)

GC-IMS is a very good complementary technique to traditional GC-MS, that presents some advantages, but also, some disadvantages such as misalignments produced by many parameters affecting the equipment stability. The reproducibility of the measures has been studied in two different measurement campaigns with a set of automatized quality control parameters. Figures of merit from one region of interest present in the samples show that the saturation and asymmetry do not change between measurement campaigns, but the volume and area of the total ion spectra change. A correction of these changes between batches should be developed.

JTD Keywords: Batches, Figures of merit, Gc-ims, Reproducibility, Rois

Fernandez, L, Blanco, A, Mallafre-Muro, C, Marco, S, (2022). Towards batch correction for GC-IMS data 2022 Ieee International Symposium On Olfaction And Electronic Nose (Isoen 2022)

Gas Chromatography Ion Mobility Spectrometry (GC-IMS) is a fast, non-expensive analytical technique that allows obtaining relevant chemical information from vapor mixtures. However, the technique presents some difficulties that should be solved to ensure reliable and reproducible results, namely: 1) data exhibits simultaneously high dimensionality and sparsity on their chemical information content, 2) data samples must usually be corrected even within a batch because of baseline and misalignment problems, 3) additional data corrections must be performed to prevent from chemical fingerprinting variations among batches. In this work, we have acquired data from two different batches (A and B) of ketone mixtures (2-Butanone, 2-Pentanone, 2-Hexanone, and 2-Heptanone). The analytical method for batch A and B was the same, except for the value of carrier gas flow parameter, which was approximately doubled for batch B. We have addressed problems 1) and 2) independently for each batch, obtaining as a result two peak tables. 3). Common peaks present in batches A and B were found after scaling the retention time axis of batch B and perform k-medoids clustering. Using this information, test data from batch B has been corrected through a linear transformation.

JTD Keywords: Batch correction, Batch effect, Gc-ims

Freire, R, Fernandez, L, Mallafré-Muro, C, Martín-Gómez, A, Madrid-Gambin, F, Oliveira, L, Pardo, A, Arce, L, Marco, S, (2021). Full workflows for the analysis of gas chromatography—ion mobility spectrometry in foodomics: Application to the analysis of iberian ham aroma Sensors 21, 6156

Gas chromatography—ion mobility spectrometry (GC-IMS) allows the fast, reliable, and inexpensive chemical composition analysis of volatile mixtures. This sensing technology has been successfully employed in food science to determine food origin, freshness and preventing alimentary fraud. However, GC-IMS data is highly dimensional, complex, and suffers from strong non-linearities, baseline problems, misalignments, peak overlaps, long peak tails, etc., all of which must be corrected to properly extract the relevant features from samples. In this work, a pipeline for signal pre-processing, followed by four different approaches for feature extraction in GC-IMS data, is presented. More precisely, these approaches consist of extracting data features from: (1) the total area of the reactant ion peak chromatogram (RIC); (2) the full RIC response; (3) the unfolded sample matrix; and (4) the ion peak volumes. The resulting pipelines for data processing were applied to a dataset consisting of two different quality class Iberian ham samples, based on their feeding regime. The ability to infer chemical information from samples was tested by comparing the classification results obtained from partial least-squares discriminant analysis (PLS-DA) and the samples’ variable importance for projection (VIP) scores. The choice of a feature extraction strategy is a trade-off between the amount of chemical information that is preserved, and the computational effort required to generate the data models.

JTD Keywords: authenticity, classification, electronic-nose, feature extraction, food analysis, gc-ims, headspace, least-squares, models, pld-da, pre-processing, quality, sensory analysis, wine, Feature extraction, Food analysis, Gc-ims, Hs-gc-ims, Pld-da, Pre-processing

Fernandez, L., Martin-Gomez, A., Mar Contreras, M., Padilla, M., Marco, S., Arce, L., (2017). Ham quality evaluation assisted by gas chromatography ion mobility spectrometry IEEE Conference Publications ISOCS/IEEE International Symposium on Olfaction and Electronic Nose (ISOEN) , IEEE (Montreal, Canada) , 1-3

In recent years, Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) has been successfully employed in food science as a control technique for the prevention of fraud according to food and labeling regulations. In this work, we propose the use of GC-IMS technique to assess the quality of Iberian ham with regard to the Iberian Pig's diet (either nourished with feed or with acorns). For this purpose, we have acquired a dataset composed of 53 samples of Iberian ham from different food providers using a commercial GC-IMS (FlavourSpec, from G.A.S. Dortmund, Germany). Intensive signal pre-processing for GC-IMS was applied to the raw data. This dataset was employed to create four Partial Least Squares Discriminant Analysis (PLSDA) models corresponding to different train/test partitions of the dataset. Nearly perfect classification rates (above 91 %) were obtained for each partition of the dataset, denoting the high power of GC-IMS to characterize food samples.

JTD Keywords: Classification, Food Science, GC-IMS, Ham quality, PLSDA

Michiardi, A., Helary, G., Nguyen, P. C. T., Gamble, L. J., Anagnostou, F., Castner, D. G., Migonney, V., (2010). Bioactive polymer grafting onto titanium alloy surfaces Acta Biomaterialia 6, (2), 667-675

Bioactive polymers bearing sulfonate (styrene sodium sulfonate, NaSS) and carboxylate (methylacrylic acid, MA) groups were grafted onto Ti6Al4V alloy surfaces by a two-step procedure. The Ti alloy surfaces were first chemically oxidized in a piranha solution and then directly subjected to radical polymerization at 70 °C in the absence of oxygen. The grafted surfaces were characterized by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and the toluidine blue colorimetric method. Toluidine blue results showed 1-5 μg cm-2 of polymer was grafted onto the oxidized Ti surfaces. Grafting resulted in a decrease in the XPS Ti and O signals from the underlying Ti substrate and a corresponding increase in the XPS C and S signals from the polymer layer. The ToF-SIMS intensities of the S- and SO- ions correlated linearly with the XPS atomic percent S concentrations and the ToF-SIMS intensity of the TiO3H2- ion correlated linearly with the XPS atomic per cent Ti concentration. Thus, the ToF-SIMS S-, SO- and TiO3H2- intensities can be used to quantify the composition and amount of grafted polymer. ToF-SIMS also detected ions that were more characteristic of the polymer molecular structure (C6H4SO3- and C8H7SO3- from NaSS, C4H5O2- from MA), but the intensity of these peaks depended on the polymer thickness and composition. An in vitro cell culture test was carried out with human osteoblast-like cells to assess the influence of the grafted polymers on cell response. Cell adhesion after 30 min of incubation showed significant differences between the grafted and ungrafted surfaces. The NaSS grafted surfaces showed the highest degree of cell adhesion while the MA-NaSS grafted surfaces showed the lowest degree of cell adhesion. After 4 weeks in vivo in rabbit femoral bones, bone was observed to be in direct contact with all implants. The percentage of mineralized tissue around the implants was similar for NaSS grafted and non-grafted implants (59% and 57%). The MA-NaSS grafted implant exhibited a lower amount of mineralized tissue (47%).

JTD Keywords: Bioactive polymers, Osteointegration, Titanium alloy, ToF-SIMS, XPS

Marco, S., Pomareda, V., Pardo, A., Kessler, M., Goebel, J., Mueller, G., (2009). Blind source separation for ion mobility spectra Olfaction and Electronic Nose: Proceedings of the 13th International Symposium on Olfaction and Electronic Nose 13th International Symposium on Olfaction and the Electronic Nose (ed. Pardo, M., Sberveglieri, G.), Amer Inst Physics (Brescia, Italy) 1137, 551-553

Miniaturization is a powerful trend for smart chemical instrumentation in a diversity of applications.. It is know that miniaturization in IMS leads to a degradation of the system characteristics. For the present work, we are interested in signal processing solutions to mitigate limitations introduced by limited drift tube length that basically involve a loss of chemical selectivity. While blind source separation techniques (BSS) are popular in other domains, their application for smart chemical instrumentation is limited. However, in some conditions, basically linearity, BSS may fully recover the concentration time evolution and the pure spectra with few underlying hypothesis. This is extremely helpful in conditions where non-expected chemical interferents may appear, or unwanted perturbations may pollute the spectra. SIMPLISMA has been advocated by Harrington et al. in several papers. However, more modem methods of BSS for bilinear decomposition with the restriction of positiveness have appeared in the last decade. In order to explore and compare the performances of those methods a series of experiments were performed.

JTD Keywords: Ion Mobility Spectrometry (IMS), Blind Source Separation (BSS), Multivariate Analysis, SIMPLISMA, MCR, Non-Negative Matrix Factorization (NMF)

Hernansanz, A., Amat, J., Casals, A., (2009). Optimization criterion for safety task transfer in cooperative robotics 14th International Conference on Advanced Robotics (ICAR) , IEEE (Munich, Germany) , 254-259

This paper presents a strategy for a cooperative multirobot system, constituting a virtual robot. The virtual robot is composed of a set of robotic arms acting as only one, transferring the execution of a teleoperated task from one to another when necessary. To decide which of the robots is the most suitable to execute the task at every instant, a multiparametric decision function has been defined. This function is based on a set of intrinsic and extrinsic evaluation indexes of the robot. Since the internal operation of the virtual robot must be transparent to the user, a control architecture has been developed.

JTD Keywords: Control engineering computing, Manipulators, Multi-robot systems, Optimsation, Telerobotics, Virtual reality

Montoliu, I., Pomareda, V., Kalms, A., Pardo, A., Gobel, J., Kessler, M., Muller, G., Marco, S., (2009). Resolution of ion mobility spectra for the detection of hazardous substances in real sampling conditions Olfaction and Electronic Nose: Proceedings of the 13th International Symposium on Olfaction and Electronic Nose 13th International Symposium on Olfaction and the Electronic Nose (ed. Pardo, M., Sberveglieri, G.), Amer Inst Physics (Brescia, Italy) 1137, 576-578

This work presents the possibilities offered by a blind source separation method such Multivariate Curve Resolution- Alternating Least Squares (MCR-ALS) in the analysis of Ion Mobility Spectra (IMS). Two security applications are analyzed in this context: the detection of TNT both in synthetic and real samples. Results obtained show the possibilities offered by the direct analysis of the drift time spectra when an appropriate resolution method is used.

JTD Keywords: Ion Mobility Spectrometry, Multivariate Curve Resolution, Security, LIMS, MCR-ALS

Sporer, C., Casal, L., Caballero, D., Samitier, J., Errachid, A., Perez-Garcia, L., (2009). Novel anionophores for biosensor applications: nano characterisation of SAMS based on amphiphilic imidazolium protophanes and cyclophanes on gold surfaces Sensor Letters 6th Maghreb-Europe Meeting on Materials and Their Applications for Devices and Physical, Chemical and Biological Sensors , AMER SCIENTIFIC PUBLISHERS (Rabat, Morocco) 7, (5), 757-764

Here we report on the results of surface deposition of the novel amphiphilic imidazolium heterocyclophanes and protophanes 1, 2, 3 onto gold electrodes by soft lithography and wet chemistry techniques. Depending on the specific functionalization conditions chosen, the surface properties and the pattern composition can vary widely. The formation of aggregates of monolayers or oligolayer structures and of rings with nano dimensioned wall widths has been investigated with Atomic Force Microscopy (AFM), Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) and Contact angle measurements.

JTD Keywords: Afm, Imidazolium anionophores, Microcontact printing, Tof-sims

Navarro, M., Benetti, E. M., Zapotoczny, S., Planell, J. A., Vancso, G. J., (2008). Buried, covalently attached RGD peptide motifs in poly(methacrylic acid) brush layers: The effect of brush structure on cell adhesion Langmuir 24, (19), 10996-11002

Iniferter-mediated surface-initiated photopolymerization was used to graft poly(methacrylic acid) (PMAA) brush layers obtained from surface-attached iniferters in self-assembled monolayers to a gold surface. The tethered chains were subsequently functionalized with the cell-adhesive arginine-glycine-aspartic acid (RGD) motif. The modified brushes were extended by reinitiating the polymerization to obtain an additional layer of PMAA, thereby burying the peptide-functionalized segments inside the brush structure. Contact angle measurements and Fourier transform infrared (FTIR) spectroscopy were employed to characterize the wettability and the chemical properties of these platforms. Time of flight secondary ion mass spectroscopy (TOF-SIMS) measurements were performed to monitor the chemical composition of the polymer layer as a function of the distance to the gold surface and obtain information concerning the depth of the RGD motifs inside the brush structure. The brush thickness was evaluated as a function of the polymerization (i.e.. UV-irradiation) time with atomic force microscopy (AFM) and ellipsometry. Cell adhesion tests employing human osteoblasts were performed on substrates with the RGD peptides exposed at the surface as well as covered by a PMAA top brush layer. Immunofluorescence studies demonstrated a variation of the cell morphology as a function of the position of the peptide units along the grafted chains.

JTD Keywords: Ion mass-spectrometry, Transfer radical polymerization, Asymmetric diblock copolymers, Arg-gly-asp, Swelling behaviour, Endothelial-cells, Thin-films, fibronectin, Surfaces, SIMS