SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis

In Depth Exploration of the Alternative Proteome of Drosophila melanogaster

Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins.

Cell metabolomics to study the cytotoxicity of carbon black nanoparticles on A549 cells using UHPLC-Q/TOF-MS and multivariate data analysis

Carbon black nanoparticles (CBNPs) are core component of fine particulate matter (PM2.5) in the atmosphere. It was reported that the particle in the atmosphere with smaller size and the larger the specific surface area are easier to reach the deep respiratory tract or even the alveoli through the respiratory barrier and cause lung injury. Therefore, it has been believed that ultrafine or nanometer particles with more toxic than those with larger particle sizes. Moreover, it was confirmed that CBNPs could induce inflammation, oxidative stress and changes in cell signaling and gene expression in mammalian cells and organs. However, the cytotoxicity mechanism of them has been uncertain so far. The aim of the present study was to explore the underlying mechanism of cytotoxicity induced by CBNPs on A549 cells. In the current research, the viabilities of A549 cells were detected by Cell Counting Kit-8 (CCK-8) assay. The further metabolomics studies were conducted to detect the cytotoxic effect of CBNPs on A549 cells with an IC50 value of 70 μg/mL for 48 h. Potential differential compounds were identified and quantified using a novel on-line acquisition method based on ultra-liquid chromatography quadrupole time-of-flight mass spectrometry(UHPLC-Q-TOF/MS). The cytotoxicity mechanism of CBNPs on A549 cells was evaluated by multivariate data analysis and statistics. As a result, a total of 32 differential compounds were identified between CBNPs exposure and control groups. In addition, pathway analysis showed the metabolic changes were involved in the tricarboxylic acid (TCA) cycle, alanine, aspartate and glutamate metabolism, histidine metabolism and so on. It is also suggested that CBNPs may induce cytotoxicity by affecting the normal process of energy metabolism and disturbing several vital signaling pathways and finally induce cell apoptosis.

SWATH mass spectrometry as a tool for quantitative profiling of the matrisome

Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to the inherent complexity and insolubility of these proteins. Here we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins in both non-enriched and ECM enriched tissue without the need for prior fractionation. Utilising a spectral library containing 201 matrisomal proteins, we compared the performance and reproducibility of SWATH MS over conventional data-dependent analysis mass spectrometry (DDA MS) in unfractionated murine lung and liver. SWATH MS conferred a 15-20% increase in reproducible peptide identification across replicate experiments in both tissue types and identified 54% more matrisomal proteins in the liver versus DDA MS. We further use SWATH MS to evaluate the quantitative changes in matrisome content that accompanies ECM enrichment. Our data shows that ECM enrichment led to a systematic increase in core matrisomal proteins but resulted in significant losses in matrisome-associated proteins including the cathepsins and proteins of the S100 family. Our proof-of-principle study demonstrates the utility of SWATH MS as a versatile tool for in-depth characterisation of the matrisome in unfractionated and non-enriched tissues. SIGNIFICANCE: The matrisome is a complex network of extracellular matrix (ECM) and ECM-associated proteins that provides scaffolding function to tissues and plays important roles in the regulation of fundamental cellular processes. However, due to its inherent complexity and insolubility, proteomic studies of the matrisome typically require the application of enrichment workflows prior to MS analysis. Such enrichment strategies often lead to losses in soluble matrisome-associated components. In this study, we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins. We show that SWATH MS provides a more reproducible coverage of the matrisome compared to data-dependent analysis (DDA) MS. We also demonstrate that SWATH MS is capable of accurate quantification of matrisomal proteins without prior ECM enrichment and fractionation, which may simplify sample handling workflows and avoid losses in matrisome-associated proteins commonly linked to ECM enrichment.