A mesofluidic platform integrating on-chip probe ultrasonication for multiple sample pretreatment involving denaturation, reduction, and digestion in protein identification assays by mass spectrometry.

The integration of ultrasound (US)-assisted sample processing on-chip in a lab-on-a-valve (LOV) format for automated high-throughput shotgun proteomic assays is herein presented for the first time. The proof of concept of this system was demonstrated with the analysis of three proteins and sera from patients with lymphoma or myeloma.

A new approach to bacterial colony morphotyping by matrix-assisted laser desorption ionization time of flight-based mass spectrometry.

Matrix assisted laser desorption ionization time of flight mass spectrometry has been explored as a tool to bacterial colony morphotyping. To this end, four colony morphotypes of Pseudomonas aeruginosa and four of Staphylococcus aureus were analysed using intact bacteria. Results suggest that mass spectrometry of intact bacteria could, in some extent, be used to complement the classical morphological classification of bacteria.

Mass spectrometry-based fingerprinting of proteins & peptides in wine quality control: a critical overview.

In this work we have critically revised and updated the literature dealing with wine quality control based on protein or peptide mass spectrometry-based fingerprinting. A number of pitfalls in the experimental design of most work dealing with this subject are highlighted along with recommendations on how to circumvent them. As a general trend, the conclusions reported to date in the literature of the topic are inconclusive mainly due to the (i) low number of representative samples, (ii) lack of basic analytical concepts, and (iii) lack of adequate statistical and software tools. In addition, we have critically revised the sample treatments commonly used to separate proteins from wines, emphasizing that the majority of literature is devoted to white wines, probably because of difficulties in isolating the protein content in red wines.

Direct matrix assisted laser desorption ionization mass spectrometry-based analysis of wine as a powerful tool for classification purposes.

The variables affecting the direct matrix assisted laser desorption ionization mass spectrometry-based analysis of wine for classification purposes have been studied. The type of matrix, the number of bottles of wine, the number of technical replicates and the number of spots used for the sample analysis have been carefully assessed to obtain the best classification possible. Ten different algorithms have been assessed as classification tools using the experimental data collected after the analysis of fourteen types of wine. The best matrix was found to be α-Cyano with a sample to matrix ratio of 1:0.75. To correctly classify the wines, profiling a minimum of five bottles per type of wine is suggested, with a minimum of three MALDI spot replicates for each bottle. The best algorithm to classify the wines was found to be Bayes Net.

Decision peptide-driven: a free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry.

The decision peptide-driven tool implements a software application for assisting the user in a protocol for accurate protein quantification based on the following steps: (1) protein separation through gel electrophoresis; (2) in-gel protein digestion; (3) direct and inverse (18)O-labeling and (4) matrix assisted laser desorption ionization time of flight mass spectrometry, MALDI analysis. The DPD software compares the MALDI results of the direct and inverse (18)O-labeling experiments and quickly identifies those peptides with paralleled loses in different sets of a typical proteomic workflow. Those peptides are used for subsequent accurate protein quantification. The interpretation of the MALDI data from direct and inverse labeling experiments is time-consuming requiring a significant amount of time to do all comparisons manually. The DPD software shortens and simplifies the searching of the peptides that must be used for quantification from a week to just some minutes. To do so, it takes as input several MALDI spectra and aids the researcher in an automatic mode (i) to compare data from direct and inverse (18)O-labeling experiments, calculating the corresponding ratios to determine those peptides with paralleled losses throughout different sets of experiments; and (ii) allow to use those peptides as internal standards for subsequent accurate protein quantification using (18)O-labeling. In this work the DPD software is presented and explained with the quantification of protein carbonic anhydrase.