EuPA Open Proteomics最新文献

An MS/MS based analytical strategy was followed to solve the complete sequence of two new peptides from frog (Odorrana schmackeri) skin secretion. This involved reduction and alkylation with two different alkylating agents followed by high resolution tandem mass spectrometry. De novo sequencing was achieved by complementary CID and ETD fragmentations of full-length peptides and of selected tryptic fragments. Heavy and light isotope dimethyl labeling assisted with annotation of sequence ion series. The identified primary structures are GCD[I/L]STCATHN[I/L]VNE[I/L]NKFDKSKPSSGGVGPESP-NH₂ and SCNLSTCATHNLVNELNKFDKSKPSSGGVGPESF-NH₂, i.e. two carboxyamidated 34 residue peptides with an aminoterminal intramolecular ring structure formed by a disulfide bridge between Cys₂ and Cys₇. Edman degradation analysis of the second peptide positively confirmed the exact sequence, resolving I/L discriminations. Both peptide sequences are novel and share homology with calcitonin, calcitonin gene related peptide (CGRP) and adrenomedullin from other vertebrates. Detailed sequence analysis as well as the 34 residue length of both O. schmackeri peptides, suggest they do not fully qualify as either calcitonins (32 residues) or CGRPs (37 amino acids) and may justify their classification in a novel peptide family within the calcitonin gene related peptide superfamily. Smooth muscle contractility assays with synthetic replicas of the S–S linked peptides on rat tail artery, uterus, bladder and ileum did not reveal myotropic activity.

Glycation represents the first stage in the development of diabetic complications. Aspirin was shown to prevent sugars reacting with proteins, but the exact mechanism of this interaction was not well defined. We performed a quantitative analysis to calculate the levels of acetylation and glycation of haemoglobin, among others red blood cell (RBC) proteins, using a label free approach. After glucose incubation, increases in the acetylation levels were seen for several haemoglobin subunits, while a parallel decrease of their glycation levels was observed after aspirin incubation. These results suggest that, a mutual influence between these two modifications, occur at protein level.

In non-cancerous cells, transforming growth factor-β (TGFβ) regulates cellular responses primarily through Smad signaling. However, during cancer progression (including colorectal) TGFβ promotes tumoral growth via Smad-independent mechanisms and is involved in crosstalk with various pathways like the mitogen-activated protein kinases (MAPK) and Wnt. Crosstalk between these pathways following activation by TGFβ and subsequent downstream signaling activity can be referred to as a crosstalk signaling signature. This review highlights the progress in understanding TGFβ signaling crosstalk involving various MAPK pathway members (e.g., extracellular signal-regulated kinase (Erk) 1/2, Ras, c-Jun N-terminal kinases (JNK) and p38) and the Wnt signaling pathway.

The complete characterization of the snake venom protein components is a requirement for a systems-wide understanding of their biological context. In this work, we provide a deep proteomic characterization of Crotalus durissus terrificus venom using different bottom-up approaches. We identified more than five times more protein families than the sum of all identifications previously reported. For the first time in this sub-species, we report the identification of three new toxin families: CRISP, phospholipase-B, and SVVEGF. This work also describes proteins involved in regulation of toxin synthesis and processing that are present in venom.

Bone marrow-derived human mesenchymal stem cells (BM-hMSCs) show promise as cell-based delivery vehicles for anti-glioma therapeutics, due to innate tropism for gliomas. However, in clinically relevant human-in-mouse glioma stem cell xenograft models, BM-hMSCs tropism is variable. We compared the proteomic profile of cancer and stromal cells in GSCXs that attract BM-hMSCs (“attractors”) with those to do not (“non-attractors”) to identify pathways that may modulate BM-hMSC homing, followed by targeted transcriptomics. The results provide the first link between fatty acid metabolism, glucose metabolism, ROS, and N-glycosylation patterns in attractors. Reciprocal expression of these pathways in the stromal cells suggests microenvironmental cross-talk.

The reproducibility of plasma protein quantitation between laboratories and between instrument types was examined in a large-scale international study involving 16 laboratories and 19 LC–MS/MS platforms, using two kits designed to evaluate instrument performance and one kit designed to evaluate the entire bottom-up workflow. There was little effect of instrument type on the quality of the results, demonstrating the robustness of LC/MRM-MS with isotopically labeled standards. Technician skill was a factor, as errors in sample preparation and sub-optimal LC–MS performance were evident. This highlights the importance of proper training and routine quality control before quantitation is done on patient samples.

Ten years ago, the first public proteomics repositories became available online. This anniversary is therefore an excellent occasion to look back on the past decade and evaluate what has changed in this time period. At the same time however, one should also dare to look forward, and therefore prepare for the next 10 years of proteomics data sharing.

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.

The Proteopathogen database was the first proteomics online resource focused on experiments related to Candida albicans and other fungal pathogens and their interaction with the host. Since then, the HUPO-PSI standards were implemented and settled, and the first large scale C. albicans proteomics resource appeared as a C. albicans PeptideAltas. This has enabled the remodeling of Proteopathogen to take advantage and benefit from the use of the HUPO-PSI adopted format for peptide and protein identification mzIdentML and continue offering a centralized resource for C. albicans, other fungal pathogens and different cell lines proteomics data.