Proteomic changes driven by urban pollution suggest particulate matter as a deregulator of energy metabolism, mitochondrial activity, and oxidative pathways in the rat brain.

The adverse effects of air pollution have been long studied in the lung and respiratory systems, but the molecular changes that this causes at the central nervous system level have yet to be fully investigated and understood. To explore the evolution with time of protein expression levels in the brain of rats exposed to particulate matter of different sizes, we carried out two-dimensional gel electrophoresis followed by determination of dysregulated proteins through Coomassie blue staining-based densities (SameSpots software) and subsequent protein identification using MALDI-based mass spectrometry. Expression differences in dysregulated proteins were found to be statistically significant with p-value <0.05. A systems biology-based approach was utilized to determine critical biochemical pathways involved in the rats' brain response. Our results suggest that rats' brains have a particulate matter size dependent-response, being the mitochondrial activity and the astrocyte function severely affected. Our proteomic study confirms the dysregulation of different biochemical pathways involving energy metabolism, mitochondrial activity, and oxidative pathways as some of the main effects of PM exposure on the rat brain. SIGNIFICANCE: Rat brains exposed to particulate matter with origin in car engines are affected in two main areas: mitochondrial activity, by the dysregulation of many pathways linked to the respiratory chain, and neuronal and astrocytic function, which stimulates brain changes triggering tumorigenesis and neurodegeneration.

Pulmonary nodules in a patient with Giant Cell Arteritis.

Giant Cell Arteritis (GCA) is a common systemic vasculitis that involves medium and large arteries, most frequently extracranial branches of the carotid artery. Prompt diagnosis and treatment is essential to prevent devastating complications, such as blindness, stroke and aortic aneurysm or dissection. Typical symptoms include headache, temporal artery tenderness and jaw claudication. On rare occasions patients present with complaints related to pulmonary involvement. These include interstitial infiltration, pulmonary nodules, pleural effusion and pulmonary haemorrhage. The authors report the case of a 74-year-old man who presented with symptoms compatible with GCA confirmed by temporal biopsy, and pulmonary nodules. These lesions were biopsied and histological exam confirmed features compatible with systemic vasculitis. The lesions resolved after two months of steroid treatment. This case shows that we should be aware of atypical GCA manifestations.

Label-free protein quantification after ultrafast digestion of complex proteomes using ultrasonic energy and immobilized-trypsin magnetic nanoparticles.

The ultimate high-throughput, high robustness and easy-to-handling sample treatment method for label-free shotgun proteomics is presented in this work. It is based on joining the effectiveness of immobilized trypsin at the nanoscale level with the latest technology to deliver ultrasonic energy. The new method can be used to reduce sample preparation time comprising the steps of reduction, alkylation and digestion time to just 15 min without compromising shotgun label-free protein quantification. It is demonstrated that trypsin immobilized at the nano-scale performs better than the commercially available counterpart macroparticles. Considering the current advances in (i) ultrasonic energy delivery that allows 96 samples to be treated at once in 30 min, and (ii) chromatography and mass spectrometry for shotgun proteomics, that allow to analyze complex proteomes in 5 min, we envision this methodology as the universal one to digest complex proteomes as it allows to profile quantitatively more than 200 samples per day.

Modulating the protein content of complex proteomes using acetonitrile.

In this work we present acetonitrile as a tool to modulate the dynamic range of the proteome of complex samples. Different concentrations of acetonitrile ranging from 15% v/v to 65% v/v were used to modulate the protein content of serum samples from healthy people and patients with lymphoma and myeloma. We show that the proteome above 70 kDa is pelleted as a function of the concentration of acetonitrile and that profiling with PCA or Clustering is only possible using the supernatants obtained for concentrations of acetonitrile higher than 45% v/v or the pellets for concentrations of acetonitrile of 35% and 45%. The differentiation and classification of the three groups of sera samples (healthy, lymphoma and myeloma) were possible using acetonitrile at 55% v/v concentration. This work opens new avenues for the application of acetonitrile as a cost-effective tool in proteomics applications.

Dithiothreitol-based protein equalization technology to unravel biomarkers for bladder cancer.

This study aimed to assess the benefits of dithiothreitol (DTT)-based sample treatment for protein equalization to assess potential biomarkers for bladder cancer. The proteome of plasma samples of patients with bladder carcinoma, patients with lower urinary tract symptoms (LUTS) and healthy volunteers, was equalized with dithiothreitol (DTT) and compared. The equalized proteomes were interrogated using two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry. Six proteins, namely serum albumin, gelsolin, fibrinogen gamma chain, Ig alpha-1 chain C region, Ig alpha-2 chain C region and haptoglobin, were found dysregulated in at least 70% of bladder cancer patients when compared with a pool of healthy individuals. One protein, serum albumin, was found overexpressed in 70% of the patients when the equalized proteome of the healthy pool was compared with the equalized proteome of the LUTS patients. The pathways modified by the proteins differentially expressed were analyzed using Cytoscape. The method here presented is fast, cheap, of easy application and it matches the analytical minimalism rules as outlined by Halls. Orthogonal validation was done using western-blot. Overall, DTT-based protein equalization is a promising methodology in bladder cancer research.

Unparalleled sample treatment throughput for proteomics workflows relying on ultrasonic energy.

We report on the new microplate horn ultrasonic device as a powerful tool to speed proteomics workflows with unparalleled throughput. 96 complex proteomes were digested at the same time in 4min. Variables such as ultrasonication time, ultrasonication amplitude, and protein to enzyme ratio were optimized. The "classic" method relying on overnight protein digestion (12h) and the sonoreactor-based method were also employed for comparative purposes. We found the protein digestion efficiency homogeneously distributed in the entire microplate horn surface using the following conditions: 4min sonication time and 25% amplitude. Using this approach, patients with lymphoma and myeloma were classified using principal component analysis and a 2D gel-mass spectrometry based approach. Furthermore, we demonstrate the excellent performance by using MALDI-mass spectrometry based profiling as a fast way to classify patients with rheumatoid arthritis, systemic lupus erythematosus, and ankylosing spondylitis. Finally, the speed and simplicity of this method were demonstrated by clustering 90 patients with knee osteoarthritis disease (30), with a prosthesis (30, control group) and healthy individuals (30) with no history of joint disease. Overall, the new approach allows profiling a disease in just one week while allows to match the minimalism rules as outlined by Halls.

Ultrasonic-based membrane aided sample preparation of urine proteomes.

A new ultrafast ultrasonic-based method for shotgun proteomics as well as label-free protein quantification in urine samples is developed. The method first separates the urine proteins using nitrocellulose-based membranes and then proteins are in-membrane digested using trypsin. The enzymatic digestion process is accelerated from overnight to four minutes using a sonoreactor ultrasonic device. Overall, the sample treatment pipeline comprising protein separation, digestion and identification is done in just 3h. The process is assessed using urine of healthy volunteers. The method shows that male can be differentiated from female using the protein content of urine in a fast, easy and straightforward way. 232 and 226 proteins are identified in urine of male and female, respectively. From this, 162 are common to both genders, whilst 70 are unique to male and 64 to female. From the 162 common proteins, 13 are present at levels statistically different (p < 0.05). The method matches the analytical minimalism concept as outlined by Halls, as each stage of this analysis is evaluated to minimize the time, cost, sample requirement, reagent consumption, energy requirements and production of waste products.

A selective emissive chromogenic and fluorogenic seleno-coumarin probe for Cu2+ detection in aprotic media.

A new selenium containing coumarin (compound 7) was designed and synthesized from the amide linkage between coumarin-519 (6) and 2-(butylselanyl)ethanamine (5). The molecular structure of 7 was accurately characterized, and its photophysical properties in acetonitrile, ethanol and chloroform solutions were studied by absorption, stationary and time-resolved fluorescence spectroscopies. Changes in the solvent polarity affected the Stokes shift, quantum yields and lifetime of the excited states. The spectroscopic behavior of compound 7 was evaluated in the presence of different monovalent, divalent and trivalent metallic cations (Na+, K+, Ca2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Pb2+, Hg2+, Hg+, Ag+, Al3+, Fe3+, Ga3+ and Cr3+) in acetonitrile solution. Among the tested cations, 7 exhibited high selective interaction with Cu2+, which was evidenced by the not expected absorption hypsocromic shift (usually coumarin-519 gives red-shifted complexes) and intense chelation-enhanced fluorescence quenching (CHEQ). We performed spectrophotometric and spectrofluorimetric titrations of 7 upon addition of Cu2+. From these data, the minimal detectable and quantifiable amounts were calculated and found to be 0.2 and 0.4 µmol L-1 by absorption and 0.6 and 1.0 µmol L-1 by emission, respectively. The 7-Cu2+ compound presented the 1 : 1 stoichiometry and the stability constant values of absorption and emission were found to be log ß = 5.78 and log ß = 6.32 respectively. Taking into account the high selectivity of the 7-Cu2+ compound in organic solvent systems, and considering the role of copper in organic transformations, it can be regarded as a promising fluorescent sensor for studies concerning the determination of oxidation-dependent transient entities in organic reactions like those involving cuprates. Additionally, it can be used for the detection and quantification of this metal cation in vitro in aprotic biological systems.

The interaction of Hg(2+) and trivalent ions with two new fluorescein bio-inspired dual colorimetric/fluorimetric probes.

Two new luminescent compounds containing fluorescein-amino acid units have been designed and synthesized via an ester linkage between a fluorescein ethyl ester and Boc-Ser(TBDMS)-OH or Boc-Cys(4-MeBzl)-OH, and their photophysical properties have been explored. The optical response of both compounds (2 and 3) towards the metal ions Na(+), K(+), Hg(+), Ag(+), Ca(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Pb(2+), Hg(2+), Al(3+), Fe(3+), Ga(3+)and Cr(3+) was investigated in pure acetonitrile and in acetonitrile/water mixtures. A strong CHEF (Chelation-Enhanced Fluorescence) effect was observed with all the trivalent metals and Hg(2+) ions in both solvents. UV-vis absorption, steady state and time resolved emission spectroscopy methods were employed. The results show the formation of mononuclear complexes with Al(3+), Fe(3+), Ga(3+), Cr(3+), and Hg(2+). Theoretical calculation using Density Functional Theory was performed in order to obtain atomistic insights into the coordination geometry of Al(3+) and Hg(2+) to the fluorescein 3, which is in accordance with the experimental stoichiometry results obtained in the Job's plot method. Among the active cations, the minimum detectable amount is under 1 µM for most of the cases in both absorption and fluorescence spectroscopy methods.

A cost-effective method to get insight into the peritoneal dialysate effluent proteome.

Protein depletion with acetonitrile and protein equalization with dithiothreitol have been assessed with success as proteomics tools for getting insight into the peritoneal dialysate effluent proteome. The methods proposed are cost-effective, fast and easy of handling, and they match the criteria of analytical minimalism: low sample volume and low reagent consumption. Using two-dimensional gel electrophoresis and peptide mass fingerprinting, a total of 72 unique proteins were identified. Acetonitrile depletes de PDE proteome from high-abundance proteins, such as albumin, and enriches the sample in apolipo-like proteins. Dithiothreitol equalizes the PDE proteome by diminishing the levels of albumin and enriching the extract in immunoglobulin-like proteins. The annotation per gene ontology term reveals the same biological paths being affected for patients undergoing peritoneal dialysis, namely that the largest number of proteins lost through peritoneal dialysate are extracellular proteins involved in regulation processes through binding. SIGNIFICANCE: Renal failure is a growing problem worldwide, and particularly in Europe where the population is getting older. Up-to-date there is a focus of interest in peritoneal dialysis (PD), as it provides a better quality of life and autonomy of the patients than other renal replacement therapies such as haemodialysis. However, PD can only be used during a short period of years, as the peritoneum lost its permeability through time. Therefore to make a breakthrough in PD and consequently contribute to better healthcare system it is urgent to find a group of biomarkers of peritoneum degradation. Here we report on two cost-effective methods for protein depletion in peritoneal dialysate effluent (PDE). The use of ACN and DTT over PDE to deplete high abundant proteins or to equalize the concentration of proteins, respectively, performs well and with similar protein profiles than when the same chemicals are used in human plasma samples. ACN depletes de PDE proteome from large proteins, such as albumin, and enriches the sample in apolipoproteins. DTT equalizes the PDE proteome by diminishing the levels of large proteins such as albumin and enriching the extract in immunoglobulins. Although the number and type of proteins identified are different, the annotation per gene ontology term reveals the same biological paths being affected for patients undergoing peritoneal dialysate. Thus, the largest number of proteins lost through peritoneal dialysate belongs to the group of extracellular proteins involved in regulation processes through binding. As for the searching of biomarkers, DTT seems to be the most promising of the two methods because acts as an equalizer and it allows interrogating more proteins in the same sample.

Ocean warming alters cellular metabolism and induces mortality in fish early life stages: A proteomic approach.

Climate change has pervasive effects on marine ecosystems, altering biodiversity patterns, abundance and distribution of species, biological interactions, phenology, and organisms' physiology, performance and fitness. Fish early life stages have narrow thermal windows and are thus more vulnerable to further changes in water temperature. The aim of this study was to address the sensitivity and underlying molecular changes of larvae of a key fisheries species, the sea bream Sparus aurata, towards ocean warming. Larvae were exposed to three temperatures: 18°C (control), 24°C (warm) and 30°C (heat wave) for seven days. At the end of the assay, i) survival curves were plotted for each temperature treatment and ii) entire larvae were collected for proteomic analysis via 2D gel electrophoresis, image analysis and mass spectrometry. Survival decreased with increasing temperature, with no larvae surviving at 30°C. Therefore, proteomic analysis was only carried out for 18°C and 24°C. Larvae up-regulated protein folding and degradation, cytoskeletal re-organization, transcriptional regulation and the growth hormone while mostly down-regulating cargo transporting and porphyrin metabolism upon exposure to heat stress. No changes were detected in proteins related to energetic metabolism suggesting that larval fish may not have the energetic plasticity needed to sustain cellular protection in the long-term. These results indicate that despite proteome modulation, S. aurata larvae do not seem able to fully acclimate to higher temperatures as shown by the low survival rates. Consequently, elevated temperatures seem to have bottleneck effects during fish early life stages, and future ocean warming can potentially compromise recruitment's success of key fisheries species.

Classifying patients in peritoneal dialysis by mass spectrometry-based profiling.

Protein equalization with dithiothreitol, protein depletion with acetonitrile and the entire proteome were assessed in conjunction with matrix assisted laser desorption ionization time of flight mass spectrometry-based profiling for a fast and effective classification of patients with renal insufficiency. Two case groups were recruited as proof of concept, patients with chronic glomerulonephritis and diabetic nephropathy. Two key tools were used to develop this approach: protein concentration with centrifugal concentrator tubes with 10 KDa cut-off membranes and chemical assisted protein equalization with dithiothreitol or chemical assisted protein depletion with acetonitrile. In-house developed software was used to apply principal component analysis and hierarchical clustering to the profiles obtained. The results suggest that chemical assisted protein equalization with dithiothreitol is a methodology more robust than the other two ones, as the patients were well grouped by principal component analysis or by hierarchical clustering.

A methodological approach based on gold-nanoparticles followed by matrix assisted laser desorption ionization time of flight mass spectrometry for the analysis of urine profiling of knee osteoarthritis.

The aim of this work is to develop a nanoparticle-based methodology to find out biomarkers of diagnostic for knee osteoarthritis, KOA, through the use of matrix assisted laser desorption ionization time-of-flight-based mass spectrometry profiling. Urine samples used for this study were obtained from KOA patients (42 patients), patients with prosthesis (58 patients), and controls (36 individuals) with no history of joint disease. Gold-nano particle MALDI-based urine profiling was optimized and then applied over the 136 individuals. Jaccard index and 10 different classifiers over MALDI MS datasets were used to find out potential biomarkers. Then, the specificity and sensitivity of the method were evaluated. The presence of ten m/z signals as potential biomarkers in the healthy versus non-healthy approach suggests that patients (KOA and prosthesis) are differentiable from the healthy volunteers through profiling. The automatic diagnostic study confirmed these preliminary conclusions. The sensitivity and the specificity for the urine profiling criteria here reported, achieved by the C4.5 classifier, is 97% and 69% respectively. Thus, it is confirmed the utility of the method proposed in this work as an additional fast, non-expensive and robust test for KOA diagnostic. When the proposed method is compared with those used in common practice it is found that sensitivity is the highest, thus with a low false negative rate for diagnostic KOA patients in the population studied. Specificity is lower but in the range accepted for diagnostic objectives.

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.

BACKGROUND: Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills. RESULTS: Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Mass-Up software allows data preprocessing, as well as subsequent analysis including (i) biomarker discovery, (ii) clustering, (iii) biclustering, (iv) three-dimensional PCA visualization and (v) classification of large sets of spectra data. CONCLUSIONS: Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at http://sing.ei.uvigo.es/mass-up.

Untangling interactions of a zinc(II) complex containing a coumarin-porphyrin unit with alkaloids in water solutions: a photophysical study.

A metal complex 1 derivative from a coumarin bearing a porphyrin unit was spectroscopically characterized and its sensing ability towards the alkaloids caffeine 2, nicotine 3 and cotinine 4 was evaluated in these studies. This probe shows to be sensitive to the alkaloids studied, where a detectable amount of 2.5 ± 0.3 µM of cotinine was determined in dam water from the Vigia Dam located in the Montoito village region, Alentejo district, Portugal. The interaction of 1 with cotinine was also verified by MALDI-TOF-MS, where it was found with peaks at 877.2 and 1053.3 m/z corresponding to the species [1H](+) and [1CotinineH](+), respectively.

A journey through PROTEOSONICS.

Ultrasonic energy is gaining momentum in Proteomics. It helps to shorten many proteomics workflows in an easy and efficient manner. Ultrasonic energy is nowadays used for protein extraction, solubilisation and cell disruption, to speed protein identification, protein quantification, peptide profiling, metal-protein complexes characterisation and imaging mass spectrometry. The present review gives a perspective of the latest achievements in ultrasonic-based sample treatment for proteomics as well as provides the basic concepts and the tools of the trade to efficiently implement this tool in proteomics labs.

A comprehensive factorial design study of variables affecting protein extraction from formalin-fixed kidney tissue samples.

Formalin-fixed tissues are an important source of biological samples for biomedical research. However, proteomics analysis of formalin-fixed tissues has been set aside by formalin-induced protein modifications, which reduce protein extraction efficiency. In this study, a two level full factorial experimental design (2(4)) was used to determine the effects of the extracting conditions in the efficiency of protein recovery from formalin-fixed kidney samples. The following variables were assessed: temperature of extraction, pH of extraction, composition of the extracting buffer and the use ultrasonic energy applied with probe. It is clearly demonstrated that when hating and ultrasonic energy are used in conjunction, a 7-fold increase (p < 0.05) in protein extraction is obtained if compared to extracting conditions for which neither heating nor ultrasonic energy are used. The optimization study was done following the amount of protein extracted by UV (Nanodrop(®) technology, protein ABS at 280 nm) and by 1D SDS-PAGE. Extracts obtained with the optimized conditions were subjected to LC-MALDI MS/MS. A total of 112 proteins were identified.

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.