Study of a novel agent for TCA precipitated proteins washing - comprehensive insights into the role of ethanol/HCl on molten globule state by multi-spectroscopic analyses.

Sample preparation for mass spectrometry-based proteomics is a key step for ensuring reliable data. In gel-free experimental workflows, protein purification often starts with a precipitation stage using trichloroacetic acid (TCA). In presence of TCA, proteins precipitate in a stable molten globule state making the pellet difficult to solubilize in aqueous buffer for proteolytic digestion and MS analysis. In this context, the objective of this work was to study the suitability of a novel agent, ethanol/HCl, for the washing of TCA-precipitated proteins. This method optimized the recovery of proteins in aqueous buffer (50 to 96%) while current organic solvents led to losses of material. Following a mechanistic study, the effect of ethanol/HCl on the conformation of TCA-precipitated proteins was investigated. It was shown that the reagent triggered the unfolding of TCA-stabilized molten globule into a reversible intermediate, characterized by a specific Raman signature, which favored protein subsequent resolubilization. Finally, the efficiency of ethanol/HCl for the washing of TCA-precipitated proteins extracted from a biofilm, a soil or a mouse liver was demonstrated (data available via ProteomeXchange with identifier PXD008110). Being versatile and simple, it could be of great interest to include an ethanol/HCl wash-step to produce high-quality protein extracts. SIGNIFICANCE: In mass spectrometry-based proteomics workflows, proteins precipitation and/or washing usually involves the use of acetone. In fact, this solvent is effective for removing both biological interferences (e.g. lipids) and chemicals employed in protein extraction/purification protocols (e.g. TCA, SDS). However, the use of acetone can lead to significant protein losses. Moreover, when proteins are precipitated with TCA, the acetone-treated precipitate remains hard to disperse, leading to poor resolubilization of proteins in aqueous buffers. Here, we investigated the use of ethanol/HCl for washing TCA-precipitated proteins, with the aim to produce high-quality protein extracts which can be directly analyzed by LC-MS. An opening study on standard solutions showed that ethanol/HCl led to reduced losses of proteins compared to usual solvents (i.e. acetone and ethanol). This reagent also enabled a better solubilization of proteins in aqueous buffer that is necessary for their direct trypsin digestion and LC-HRMS analysis. A mechanistic study, performed through several spectroscopic analyses (LC-HRMS, Raman, spectrofluorometry), showed that treatment with ethanol/HCl induced conformational changes of TCA-precipitated proteins. Finally, we compared the efficiency of ethanol/HCl to published protocols for the washing of protein extracts from three different complex samples (i.e. soil, biofilm, and mouse liver). Our results demonstrated that ethanol/HCl is a valuable alternative to previous protein washing methods and, therefore could become a useful tool in mass spectrometry-based proteomics workflows for various applications (e.g. clinical research, chemical biology, environmental metaproteomics…).

TCA precipitation and ethanol/HCl single-step purification evaluation: One-dimensional gel electrophoresis, bradford assays, spectrofluorometry and Raman spectroscopy data on HSA, Rnase, lysozyme - Mascots and Skyline data.

The data presented here are related to the research paper entitled "Study of a Novel Agent for TCA Precipitated Proteins Washing - Comprehensive Insights into the Role of Ethanol/HCl on Molten Globule State by Multi-Spectroscopic Analyses" (Eddhif et al., submitted for publication) [1]. The suitability of ethanol/HCl for the washing of TCA-precipitated proteins was first investigated on standard solution of HSA, cellulase, ribonuclease and lysozyme. Recoveries were assessed by one-dimensional gel electrophoresis, Bradford assays and UPLC-HRMS. The mechanistic that triggers protein conformational changes at each purification stage was then investigated by Raman spectroscopy and spectrofluorometry. Finally, the efficiency of the method was evaluated on three different complex samples (mouse liver, river biofilm, loamy soil surface). Proteins profiling was assessed by gel electrophoresis and by UPLC-HRMS.

Unusual microbial mat-related structural diversity 2.1 billion years ago and implications for the Francevillian biota.

The 2.1-billion-year-old (Ga) Francevillian series in Gabon hosts some of the oldest reported macroscopic fossils of various sizes and shapes, stimulating new debates on the origin, evolution and organization of early complex life. Here, we document ten representative types of exceptionally well-preserved mat-related structures, comprising "elephant-skin" textures, putative macro-tufted microbial mats, domal buildups, flat pyritized structures, discoidal microbial colonies, horizontal mat growth patterns, wrinkle structures, "kinneyia" structures, linear patterns and nodule-like structures. A combination of petrographic analyses, scanning electron microscopy, Raman spectroscopy and organic elemental analyses of carbon-rich laminae and microtexture, indicate a biological origin for these structures. The observed microtextures encompass oriented grains, floating silt-sized quartz grains, concentrated heavy minerals, randomly oriented clays, wavy-crinkly laminae and pyritized structures. Based on comparisons with modern analogues, as well as an average δ13 C organic matter (Corg ) composition of -32.94 ± 1.17‰ (1 standard deviation, SD) with an outlier of -41.26‰, we argue that the mat-related structures contain relicts of multiple carbon pathways including heterotrophic recycling of photosynthetically derived Corg . Moreover, the relatively close association of the macroscopic fossil assemblages to the microbial mats may imply that microbial communities acted as potential benthic O2 oases linked to oxyphototrophic cyanobacterial mats and grazing grounds. In addition, the mat's presence likely improved the preservation of the oldest large colonial organisms, as they are known to strongly biostabilize sediments. Our findings highlight the oldest community assemblage of microscopic and macroscopic biota in the aftermath of the "Great Oxidation Event," widening our understanding of biological organization during Earth's middle age.

Confocal microprobe Raman imaging of urban tropospheric aerosol particles.

Particulate matter with aerodynamic diameters of < 1, 1-2.5, and 2.5-10 microm were collected during two seasons in two urban zones situated northeast and southwest, respectively, of a lead/zinc smelter located in a former mining region of northern France. We demonstrate the effectiveness of the combined use of computer-controlled Raman mapping and multivariate curve resolution (MCR) of the Raman images to determine heterogeneous chemistry at the level of aerosol particle. The resulting molecular images of major species were found to be in accurate agreement with elemental images obtained by WDS X-ray-mapping. Environmental SEM was very useful to localize spare metal-rich particles before Raman mapping. Some spare particles containing pyromorphite (Pb5(PO4)3OH) and franklinite (ZnxFe3-xO4) mixed with mineral dust were detected at the northeast (NE) sampling site, when the wind was blowing from the west (W) sector. These particles were probably suspended in the troposphere by the action of wind or by mechanical disturbance of polluted top soils. The most abundantly encountered particles in the 10-2.5 and 2.5-1 microm fractions were found to be aggregates of NaCl, CaCO3, CaSO4 x 2H2O, CaMg(CO3)2, SiO2, feldspar, clay minerals, alpha-Fe2O3, NaNO3, and Ca(NO3)2 x 4H20. Black carbon and (NH4)2SO4 particles were observed predominantly in the finest fraction. It was not rare to detect Pb and Zn-rich particles in the 10-2.5 and 2.5-1 microm fractions collected at the southwest (SW) sampling site, when the wind was blowing from the NE sector. Most of these mixed particles probably result from the aggregation between PbSO4, PbO x PbSO4, and ZnS particles emitted by the smelters and hydroscopic mineral dust during transport in the troposphere.

Combined use of conventional and second-derivative data in the SIMPLISMA self-modeling mixture analysis approach.

Simple-to-use interactive self-modeling mixture analysis (SIMPLISMA) is a successful pure variable approach to resolve spectral mixture data. A pure variable (e.g., wavenumber, frequency number, etc.) is defined as a variable that has significant contributions from only one of the pure components in the mixture data set. For spectral data with highly overlapping pure components or significant baselines, the pure variable approach has limitations; however, in this case, second-derivative spectra can be used. In some spectroscopies, very wide peaks of components of interest are overlapping with narrow peaks of interest. In these cases, the use of conventional data in SIMPLISMA will not result in proper pure variables. The use of second-derivative data will not be successful, since the wide peaks are lost. This paper describes a new SIMPLISMA approach in which both the conventional spectra (for pure variables of wide peaks) and second-derivative spectra (for pure variables of narrow peaks, overlapping with the wide peaks) are used. This new approach is able to properly resolve spectra with wide and narrow peaks and minimizes baseline problems by resolving them as separate components. Examples will be given of NMR spectra of surfactants and Raman imaging data of dust particle samples taken from a lead and zinc factory's ore stocks that were stored outdoors.

Speciation of PM10 sources of airborne nonferrous metals within the 3-km zone of lead/zinc smelters.

The purpose of this study was to estimate the speciation of PM10 sources of airborne Pb, Zn, and Cd metals (PM10 is an aerosol standard of aerodynamic diameter less than 10 microm.) in the atmosphere of a 3 km zone surrounding lead/zinc facilities in operation for a century. Many powdered samples were collected in stacks of working units (grilling, furnace, and refinery), outdoor storages (ores, recycled materials), surrounding waste slag (4 Mt), and polluted topsoils (3 km). PM10 samples were generated from the raw powders by using artificial resuspension and collection devices. The bulk PM10 multielemental analyses were determined by inductively coupled plasma-atomic emission spectrometry (ICP-AES). The proportions in mass of Pb (50%), Zn (40%), and Cd (1%) contents and associated metals (traces) reach the proportions of corresponding raw powdered samples of ores, recycled materials, and fumesize emissions of plants without specific enrichment. In contrast, Pb (8%) and Zn (15%) contents of PM10 of slag deposit were found to be markedly higher than those of raw dust, Pb (4%), and Zn (9%), respectively. In the same way, Pb (0.18%), Zn (0.20%), and Cd (0.004%) were enriched by 1.7, 2.1, and 2.3 times, respectively, in PM10 as compared with raw top-soil corresponding values. X-ray wavelength dispersive electron-microprobe (EM-WDS) microanalysis did not indicate well-defined phases or simple stoichiometries of all the PM10 samples atthe level of the spatial resolution (1 microm3). X-ray photoelectron spectroscopy (XPS) indicated that minor elements such as Cd, Hg, and C are more concentrated on the particle surface than in the bulk of PM10 generated by the smelting processes. (XPS) provided also the average speciation of the surface of PM10; Pb is mainly represented as PbSO4, Zn as ZnS, and Cd as CdS or CdSO4, and small amounts of coke were also detected. The speciation of bulk PM10 crystallized compounds was deduced from XRD diffractograms with a raw estimation of the relative quantities. PbS and ZnS were found to be the major phases in PM10 generated by the smelting facilities with PbSO4, PbSO4 x PbO, PbSO4 x 4PbO, Pb metal, and ZnO as minor phases. The slag waste PM10 was found to contain some amounts of PbCO3, PbSO4 x PbO, and ZnFe2O4 phases. The large heterogeneity at the level of the individual particle generates severe overlap of chemical information even at the microm scale using electron microprobe (WDS) and Raman microprobe techniques. Fortunately, scanning Raman microspectrometry combined with SIMPle-to-use Interactive Self-modeling Mixture Analysis (SIMPLISMA) performed the PM10 speciation at the level of individual particles. The speciation of major Pb, Zn, and Cd compounds of PM10 stack emissions and wind blown dust of ores and recycled materials were found to be PbSO4, PbSO4 x PbO, PbSO4 x 4PbO, PbO, metallic Pb, ZnS, ZnO, and CdS. The PM10 dust of slag waste was found to contain PbCO3, Pb(OH)2 x 2PbCO3, PbSO4 x PbO, and ZnS, while PM10-bound Pb, Zn of the top-soils contain Pb5(PO4)3Cl, ZnFe2O4 as well as Pb(II) and Zn(II) compounds adsorbed on Fe(III) oxides and in association with clays.