UNLABELLED: Crayfish spermatophores are deposited on the body surface of the female during mating and remain there for a period of time before fertilization ensues. Post-mating changes in protein expression level in the noble crayfish Astacus astacus spermatophore were quantified. In-gel digestion and high resolution mass spectrometry were used for label-free protein quantification. One hundred twelve proteins were identified in the spermatophore of noble crayfish. After 7 days of storage on the body of the female, 6 proteins were identified in the post-mating spermatophore that showed significant up-regulation and 4 significant down-regulations (p < 0.05, fold change ≥ 2). The highest rate of up-regulation was observed in sodium/hydrogen exchanger, which may indicate the importance of intracellular pH adjustment for final maturation of the crayfish spermatozoon. The highest rate of down-regulation was observed in histone H2A. This may increase chromatin flexibility and facilitate its transfer into the oocyte during fertilization. The vitellogenin protein was identified in the crayfish spermatophore and its level changed during storage on the body surface of female. Extensive proteomic modification of male gametes during storage on the body surface of the female suggests post-mating final maturation of the crayfish spermatozoon. BIOLOGICAL SIGNIFICANCE: Freshwater crayfish comprise a large and diverse group of ecologically and commercially important animals. Molecular studies of gametes in the crayfish can provide insight into the complex process of reproduction in this diverse group of animals. The results of such studies can be used for development of new techniques for artificial reproduction of these economically important species.

• MeSH
• alfa-makroglobuliny metabolismus   MeSH
• chromatografie kapalinová MeSH
• hemokyanin metabolismus   MeSH
• histony metabolismus   MeSH
• hmotnostní spektrometrie MeSH
• kapacitace spermií MeSH
• Na(+)-H(+) antiport metabolismus   MeSH
• proteomika metody   MeSH
• ryanodinový receptor vápníkového kanálu metabolismus   MeSH
• severní raci fyziologie   MeSH
• sexuální faktory MeSH
• spermatogonie fyziologie   MeSH
• spermie fyziologie   MeSH
• upregulace MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Surface plasmon resonance sensors have made vast advancements in the sensing technology and the number of applications achievable. New developments in surface plasmon resonance sensors have gained considerable momentum promoted by the urgent needs of fast, reliable and label-free methods for detection and quantification of analytes in molecular biology, medicine and other life sciences. However, even if enormous improvements in the limits of detections have been achieved, this technology still faces important challenges to be translated to clinical practice or in-field measurements. This paper reviews the important recent advances of this technology for the label-free detection in real biological samples and we discussed the key challenges to be overcome to transit from prototypes to commercial biosensors.

• MeSH
• biologie přístrojové vybavení   metody   MeSH
• diagnóza MeSH
• lidé MeSH
• povrchová plasmonová rezonance přístrojové vybavení   metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.

• MeSH
• analýza dat MeSH
• benchmarking * MeSH
• proteiny MeSH
• proteomika * MeSH
• průběh práce MeSH
• software MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Eggs of sterlet are discharged outside into ambient aquatic environment where egg activation and fertilization occur. Effects of different activation media including freshwater and clay suspension on protein abundances of egg were quantified in sterlet Acipenser ruthenus. In-gel digestion and high resolution mass spectrometry were used for label-free protein quantification in the eggs of five females. No significant (p > 0.05) difference was found between protein abundances in eggs activated with different media. However, results showed significant (p < 0.05, fold change ≥2) reduction in the abundances of nine proteins including six glycoproteins, enolase and heat shock protein in activated groups compared to freshly ovulated eggs as control. The fact that abundance of proteasome subunit alpha significantly reduced only in eggs which were activated by clay suspension suggests that activation medium can somehow intervene with protein regulation during fertilization. In conclusion, external fertilization in sturgeon egg is accompanied by huge release of proteins into the external environment that may participate in the construction of a transient microenvironment around egg for attraction and protection of spermatozoa to ensure ensuing fertilization. Data are available via ProteomeXchange with identifier PXD006232.

• MeSH
• fertilizace * MeSH
• fosfopyruváthydratasa metabolismus   MeSH
• glykoproteiny metabolismus   MeSH
• ovum metabolismus   MeSH
• proteiny teplotního šoku metabolismus   MeSH
• proteom metabolismus   MeSH
• ryby metabolismus   MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Morphine- and Concanavalin A-induced changes of protein composition of rat spleen lymphocytes were determined by high-resolution proteomic analysis, gel-free, label-free quantification, MaxLFQ. Stimulation by Con A resulted in a major reorganization of spleen cell protein composition evidenced by increased expression level of 94 proteins; 101 proteins were down-regulated (>2-fold). Interestingly, among proteins that were up-regulated to the largest extent were the prototypical brain proteins as a neuron specific enolase, synapsin-1, brain acid-soluble protein-1 and myelin basic protein. Morphine-induced change was limited to no more than 5 up-regulated and 18 down-regulated proteins (>2-fold).

• MeSH
• aktivace lymfocytů účinky léků   genetika   MeSH
• konkanavalin A farmakologie   MeSH
• krysa rodu rattus MeSH
• lymfocyty účinky léků   metabolismus   MeSH
• morfin farmakologie   MeSH
• potkani Wistar MeSH
• proteom účinky léků   MeSH
• proteomika metody   MeSH
• regulace genové exprese účinky léků   MeSH
• slezina cytologie   MeSH
• stanovení celkové genové exprese MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

• MeSH
• klinické laboratorní techniky MeSH
• molekulární biologie MeSH
• polymerázová řetězová reakce MeSH
• Publikační typ
• monografie MeSH

• Konspekt
• Biologické vědy
• NLK Obory
• biologie

The increased risk of acute large-scale radiological exposure for the world's population underlines the need for optimal radiation biomarkers. Ionizing radiation triggers a complex response by the genome, proteome, and metabolome, all of which have been reported as suitable indicators of radiation-induced damage in vivo. This study analyzed peripheral blood samples from total-body irradiation (TBI) leukemia patients through mass spectrometry (MS) to identify and quantify differentially regulated proteins in plasma before and after irradiation. In brief, samples were taken from 16 leukemic patients prior to and 24 h after TBI (2 × 2.0 Gy), processed with Tandem Mass Tag isobaric labelling kit (TMTpro-16-plex), and analyzed by MS. In parallel, label-free relative quantification was performed with a RP-nanoLC-ESI-MS/MS system in a Q-Exactive mass spectrometer. Protein identification was done in Proteome Discoverer v.2.2 platform (Thermo). Data is available via ProteomeXchange with identifier PXD043516. Using two different methods, we acquired two datasets of up-regulated (ratio ≥ 1.2) or down-regulated (ratio ≤ 0.83) plasmatic proteins 24 h after irradiation, identifying 356 and 346 proteins in the TMT-16plex and 285 and 308 label-free analyses, respectively (P ≤ 0.05). Combining the two datasets yielded 15 candidates with significant relation to gamma-radiation exposure. The majority of these proteins were associated with the inflammatory response and lipid metabolism. Subsequently, from these, five proteins showed the strongest potential as radiation biomarkers in humans (C-reactive protein, Alpha amylase 1A, Mannose-binding protein C, Phospholipid transfer protein, and Complement C5). These candidate biomarkers might have implications for practical biological dosimetry.

• MeSH
• biologické markery krev   MeSH
• celotělové ozáření * škodlivé účinky   MeSH
• dospělí MeSH
• krevní proteiny analýza   metabolismus   MeSH
• leukemie * krev   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové biomarkery krev   MeSH
• proteom analýza   MeSH
• senioři MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

PURPOSE: Doxorubicin is an anthracycline drug which inhibits the growth of breast cancer cell lines. However, a major factor limiting its use is a cumulative, dose-dependent cardiotoxicity, resulting in a permanent loss of cardiomyocytes. Vitamin C was found to potentiate the cytotoxic effects of a variety of chemotherapeutic drugs including doxorubicin. The aim of the study was to describe the changes in protein expression and proliferation of the MCF-7 cells induced by the vitamin C applied with doxorubicin. METHODS: Label-free quantitative proteomics and real-time cell analysis methods were used to search for proteome and cell proliferation changes. These changes were induced by the pure DOX and by DOX combined with vitamin C applied on the MCF-7 cell line. RESULTS: From the real-time cell analysis experiments, it is clear that the highest anti-proliferative effect occurs with the addition of 200 µM of vitamin C to 1 µM of doxorubicin. By applying both the label-free protein quantification method and total ion current assay, we found statistically significant changes (p ≤ 0.05) of 26 proteins induced by the addition of vitamin C to doxorubicin on the MCF-7 cell line. These differentially expressed proteins are involved in processes such as structural molecule activity, transcription and translation, immune system process and antioxidant, cellular signalling and transport. CONCLUSION: The detected proteins may be capable of predicting response to DOX therapy. This is a key tool in the treatment of breast cancer, and the combination with vit C seems to be of particular interest due to the fact that it can potentiate anti-proliferative effect of DOX.

• MeSH
• antioxidancia farmakologie   MeSH
• chemorezistence MeSH
• doxorubicin farmakologie   MeSH
• kyselina askorbová farmakologie   MeSH
• lidé MeSH
• MFC-7 buňky MeSH
• nádory prsu farmakoterapie   metabolismus   MeSH
• proliferace buněk MeSH
• proteom metabolismus   MeSH
• proteomika MeSH
• protinádorová antibiotika farmakologie   MeSH
• screeningové testy protinádorových léčiv MeSH
• synergismus léků MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

UNLABELLED: Proteomic analysis was performed in post-nuclear supernatant fraction (PNS) prepared from forebrain cortex of rats exposed to increasing doses of morphine (10-50mg/kg) for 10days and sacrificed 24h (group +M10) or 20days (group +M10/-M20) after the last dose of morphine. PNS fraction was resolved by 2D-ELFO and stained by CBB. Analysis of the difference between (+M10) and (-M10) samples of PNS by PDQuest accompanied by MALDI-TOF MS/MS indicated the significant change of 28 proteins. Importantly, the number of altered proteins was decreased to 14 after 20days of nurturing animals in the absence of morphine. This new and important finding indicating the ability of mammalian organism to return to physiological norm after removal of the drug was verified by an independent methodology - gel-free & label-free quantification and normalization procedure denominated as MaxLFQ. The 113 proteins were identified as altered by morphine in (+M10) samples when compared with (-M10) samples of PNS and this number was decreased to 19 after 20days of nurturing the animals in the absence of this drug. BIOLOGICAL SIGNIFICANCE: Forebrain cortex of rats exposed to morphine for 10days is severely altered as far as the overall protein composition is involved. Depending on the method used for protein detection and quantification, 28 (MALDI-TOF MS/MS) or 113 (MaxLFQ) altered proteins were identified. Importantly, in rats sacrificed 20days after the last dose of morphine, the number of altered proteins was decreased to 14 (MALDI-TOF MS/MS) and 19 (MaxLFQ), respectively. Our data indicate the high ability of living organism to oppose the drastic, morphine-induced change of the target tissue protein composition with the aim to return to the physiological norm after complete removal of the drug.

• MeSH
• abstinenční syndrom MeSH
• krysa rodu rattus MeSH
• morfin aplikace a dávkování   farmakologie   MeSH
• přední mozek chemie   účinky léků   MeSH
• proteiny analýza   MeSH
• proteomika metody   MeSH
• tandemová hmotnostní spektrometrie MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH

The goal of this study was to explore the plasma proteome of myelodysplastic syndrome (MDS) patients with refractory anemia with excess blasts subtype 2 (RAEB-2) in comparison to healthy controls. 20 plasma samples were separated with 2D electrophoresis and statistically processed with Progenesis SameSpots software. 47 significantly differing (P < 0.05) spots were observed, and 27 different proteins were identified by nano-LC-MS/MS. Mass spectrometry-based relative label-free quantification showed a 2-fold increase of the leucine-rich alpha-2-glycoprotein (LRAG) peptide levels in the RAEB-2 group. Changes in the fragments of the inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4) protein were observed. Western blot analysis showed no differences in albumin and ITIH4 levels, while increased expression was observed for LRAG in the RAEB-2 group. Quantification using ELISA showed decreased plasma level of alpha-2-HS glycoprotein in the RAEB-2 group. In conclusion, this is the first time that alpha-2-HS glycoprotein and LRAG were proposed as new biomarkers of RAEB-2 and advanced MDS, respectively. Alpha-2-HS glycoprotein, a protein involved in the bone marrow development and previously proposed as a MDS biomarker candidate, was significantly decreased in RAEB-2. Increased expression and changes in modification(s) were observed for LRAG, a protein involved in granulocytic and neutrophil differentiation, and angiogenesis.

• MeSH
• anotace sekvence MeSH
• biologické markery krev   chemie   MeSH
• dospělí MeSH
• krevní proteiny chemie   metabolismus   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• myelodysplastické syndromy krev   MeSH
• peptidové fragmenty chemie   MeSH
• proteom chemie   metabolismus   MeSH
• refrakterní anemie s nadbytkem blastů krev   MeSH
• sekvence aminokyselin MeSH
• senioři MeSH
• studie případů a kontrol MeSH
• tandemová hmotnostní spektrometrie MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH