EuPA Open Proteomics最新文献

Archiving of biological specimens is important due to the importance of reanalysis of already prepared MALDI MS samples or simultaneuous analysis of a sample series. Proteins/peptides and digests were prepared for measurement on a polymer-based metal nano-coated MALDI target and subjected to various storage conditions (−80 °C to RT) in a vacuum-sealed pouch and at atmosphere for 6 months. The MS data gathered from these preparations illustrate trends in the aging of different samples and to find optimal storage conditions (−20 or −80 °C in low oxygen environment). The disposable/low cost target proved to be a suitable platform for storage and MALDI MS.

Relative and absolute quantification of proteins in biological and clinical samples are common approaches in proteomics. Until now, targeted protein quantification is mainly performed using a combination of HPLC-based peptide separation and selected reaction monitoring on triple quadrupole mass spectrometers. Here, we show for the first time the potential of absolute quantification using a direct infusion strategy combined with single ion monitoring (SIM) on a Q Exactive mass spectrometer. By using complex membrane fractions of Escherichia coli, we absolutely quantified the recombinant expressed heterologous human cytochrome P450 monooxygenase 3A4 (CYP3A4) comparing direct infusion-SIM with conventional HPLC-SIM. Direct-infusion SIM revealed only 14.7% (±4.1 (s.e.m.)) deviation on average, compared to HPLC-SIM and a decreased processing and analysis time of 4.5 min (that could be further decreased to 30 s) for a single sample in contrast to 65 min by the LC–MS method. Summarized, our simplified workflow using direct infusion-SIM provides a fast and robust method for quantification of proteins in complex protein mixtures.

MS-based proteomic methods were utilised for the first time in the discovery of novel penile cancer biomarkers. MALDI MS imaging was used to obtain the in situ biomolecular MS profile of squamous cell carcinoma of the penis which was then compared to benign epithelial MS profiles. Spectra from cancerous and benign tissue areas were examined to identify MS peaks that best distinguished normal epithelial cells from invasive squamous epithelial cells, providing crucial evidence to suggest S100A4 to be differentially expressed. Verification by immunohistochemistry resulted in positive staining for S100A4 in a sub-population of invasive but not benign epithelial cells.

We investigated to which extent polymorphisms of an individual affect the proteomic network. Consomic mouse strains (CS) were used to study the trans-effect of the cis-variant (polymorphic) proteins of the strain PWD/Ph on the proteins of the host strain C57BL/6J. The cardiac proteome of ten CSs was analyzed by 2-DE and MS. Cis-variant PWD proteins altered a high number of C57BL/6J proteins, but the number of trans-variant proteins differed considerably between different CSs. Cardiac hypertrophy was induced in CSs. We found that high variability of the proteome, as induced by polymorphisms in CS14, acts protective against the complex disease.

Metabolism is the consortium of reactions within a cell which directs a variety of processes including energy synthesis, signalling and the behaviour of a biological system. Metabolic networks, and more specifically the activity of enzymes within them, provide an accurate status of how cellular information is being executed. The performance of these networks and their ability to siphon metabolites in a number of directions may be the difference between a healthy and diseased state. Blue native polyacrylamide gel electrophoresis (BN-PAGE), owing to its simplicity and wide-ranging applications, permits the inspection of these nodules. The separation of proteins and enzyme complexes in their native format enables the exploration of enzymatic activity in metabolic networks via in-gel assays. These are quick, specific, and amenable to further studies. This electrophoretic technology not only enables the visualization of enzymatic efficacy but reveals the crosstalk among enzymes and their interactions with other organellar partners.

We review and demonstrate how an empirical Bayes method, shrinking a protein's sample variance towards a pooled estimate, leads to far more powerful and stable inference to detect significant changes in protein abundance compared to ordinary t-tests. Using examples from isobaric mass labelled proteomic experiments we show how to analyze data from multiple experiments simultaneously, and discuss the effects of missing data on the inference. We also present easy to use open source software for normalization of mass spectrometry data and inference based on moderated test statistics.

More than 90% of polycythemia vera (PV) patients have a mutation in the protein JAK2, which is closely associated with the erythrocyte membrane. With the comparison of 1-D gels of erythrocyte membranes obtained from PV patients treated with hydroxycarbamide and those of untreated controls we observed significant differences in the region of 40–55 kDa. On the basis of the LC–MS/MS analysis of this region we report up-regulation of four protein disulfide isomerases, which was subsequently confirmed by targeted mass spectrometric analysis. In further studies it will be prudent to compare this in patients both treated and not treated with hydroxycarbamide.

This study focuses on meat protein degradation by different starter cultures. Sausage models inoculated with Lactobacillus curvatus CRL705 and Staphylococcus vitulinus GV318 alone and as a mixture were incubated 10 days at 22 °C. Low molecular weight peptides (<3 kDa) derived from sarcoplasmic proteins were analyzed by a peptidomic approach. A diverse number of protein fragments were identified. The greatest peptides diversity was obtained when the mixed starter culture was present. Peptides mainly arose from myoglobin, creatine-kinase, glyceraldehyde-3-phosphate-dehydrogenase and fructose-biphosphate-aldolase (ALDOA). ALDOA hydrolysis was attributed to the mixed starter culture; the released peptides could act as biomarkers for a specific sausage technology.

Significance

The selection of a specific autochthonous starter culture guarantees the hygiene and typicity of fermented sausages. The identification of new peptides as well as new target proteins by means of peptidomics represents a significant step toward the elucidation of the role of microorganisms in meat proteolysis. Moreover, these peptides may be further used as biomarkers capable to certify the use of the applied autochthonous starter culture described here.

Defining alterations in signalling pathways in normal and malignant cells is becoming a major field in proteomics. A number of different approaches have been established to isolate, identify and quantify phosphorylated proteins and peptides. In the current report, a comparison between SCX prefractionation versus an antibody based approach, both coupled to TiO₂ enrichment and applied to TMT labelled cellular lysates, is described. The antibody strategy was more complete for enriching phosphopeptides and allowed the identification of a large set of proteins known to be phosphorylated (715 protein groups) with a minimum number of not previously known phosphorylated proteins (2).

Liver plays a key role in metabolism and detoxification, therefore analysis of its proteome is relevant for toxicology and drug discovery studies. To optimize for high proteome coverage, protein and peptide-level ion exchange fractionation were assessed using rat liver microsomes and S9 fractions. 2D-(SCX-RP)-LC–MS/MS analysis with peptide fractionation was subsequently employed for rat, mouse and human samples, yielding between 1400 and 1939 identified proteins, 58% of which were shared between species, and with relatively high sequence coverage. This rich dataset is specifically interesting for the toxicology community, and could serve as an excellent source for targeted assay development.