EuPA Open Proteomics最新文献

A relatively simple combination of Schirmer strip sampling with straightforward sensitive nanoLC quadrupole-Orbitrap tandem mass spectrometry after a minimum of sample processing steps allows for replicate proteomic analysis of single human tears, i.e., without the requirement for sample pooling. This opens the way to clinical applications of the analytical workflow, e.g., to monitor disease progression or treatment efficacy within individual patients. Proof of concept is provided by triplicate analyses of a singular sampling of tears of a dry eye patient, before and one and two months after minor salivary gland transplantation. To facilitate comparison with the outcome of previously reported analytical protocols, we also include the data from a typical healthy young adult tear sample as obtained by our streamlined method.

With 375 confidently identified proteins in the healthy adult tear, the obtained results are comprehensive and in large agreement with previously published observations on pooled samples of multiple patients. We conclude that, to a limited extent, bottom–up tear protein identifications from individual patients may have clinical relevance.

Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein identifications and 12.2% of reliable quantification were obtained. A 61 times lower limit of protein quantitation was reached compared to protein concentrations observed in raw serum. The concentrations of detected proteins were confronted to estimated reference values.

Propionibacterium acnes, plays an important role in acne vulgaris and other diseases. However, understanding of the exact mechanisms of P. acnes pathogenesis is limited. Few studies have investigated its proteome, which is essential for vaccine development. Here, we comprehensively investigate the proteome of P. acnes strain ATCC 6919, including secreted, cell wall, membrane, and cytosolic fractions in three types of growth media. A total of 531 proteins were quantified using an Orbitrap mass spectrometer and bioinformatically categorized for localization and function. Several, including PPA1939, a highly expressed surface and secreted protein, were identified as potential vaccine candidates.

Gel-free liquid chromatography mass spectrometry coupled to chemical proteomics is a powerful approach for characterizing cellular target profiles of small molecules. We have previously described a fast and efficient elution protocol; however, altered target profiles were observed. We hypothesised that elution conditions critically impact the effectiveness of disrupting drug-protein interactions. Thus, a number of elution conditions were systematically assessed with the aim of improving the recovery of all classes of proteins whilst maintaining compatibility with immunoblotting procedures. A double elution with formic acid combined with urea emerged as the most efficient and generically applicable elution method for chemical proteomics

The phytochemical sulforaphane can induce cell cycle arrest and apoptosis in metastatic prostate cancer cells, though the mechanism of action is not fully known. We conducted a global proteome analysis in LNCaP metastatic prostate cancer cells to characterize how global protein signature responds to sulforaphane. We conducted parallel analyses to evaluate semi-quantitative 1-dimensional versus 2-dimensional liquid chromatography tandem mass spectrometry (LC–MS/MS) and their utility in characterizing whole cell lysate. We show that 2-dimensional LC–MS/MS can be a useful tool for characterizing global protein profiles and identify TRIAP1 as a novel regulator of cell proliferation in LNCaP metastatic prostate cancer cells.

Changes of abundance that occur in the repertoire of low abundance milk proteins after cessation of milk removal have not been characterised. Skimmed milk and whey from cows sampled at day 0 and either day 3 or day 8 after drying off were subjected to three untargeted proteomics techniques; 2-D gel electrophoresis, GeLC-MS, and dimethyl isotopic labelling of tryptic peptides. The changes observed included 45 fragments of abundant milk proteins and 36 host-defence proteins, suggesting activation of proteolysis and inflammation. The findings form a basis for adding value to dairy production.