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Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods are performed for the purpose of improving D. pulex proteome exploration. Benefits for employing both in‐gel and in‐solution methods of trypsin digestion are observed. Furthermore, acquisition methods employing ion mobility separation greatly increase peptide identification and more than doubled the proteome coverage. Bioinformatic analysis suggests that mitochondrial and hydrolytic activities are enriched in D. pulex compared to closely related invertebrates or Homo sapiens. Also, novel D. pulex proteins possessing putative genome modifying functional domains are identified. Data are available via ProteomeXchange with identifier PXD008455.  相似文献   

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The polyanion Li7V15O36(CO3) is a nanosized molecular cluster (≈1 nm in size), that has the potential to form an open host framework with a higher surface‐to‐bulk ratio than conventional transition metal oxide electrode materials. Herein, practical rechargeable Na‐ion batteries and symmetric Li‐ion batteries are demonstrated based on the polyoxovanadate Li7V15O36(CO3). The vanadium centers in {V15O36(CO3)} do not all have the same VIV/V redox potentials, which permits symmetric devices to be created from this material that exhibit battery‐like energy density and supercapacitor‐like power density. An ultrahigh specific power of 51.5 kW kg?1 at 100 A g?1 and a specific energy of 125 W h kg?1 can be achieved, along with a long cycling life (>500 cycles). Moreover, electrochemical and theoretical studies reveal that {V15O36(CO3)} also allows the transport of large cations, like Na+, and that it can serve as the cathode material for rechargeable Na‐ion batteries with a high specific capacity of 240 mA h g?1 and a specific energy of 390 W h kg?1 for the full Na‐ion battery. Finally, the polyoxometalate material from these electrochemical energy storage devices can be easily extracted from spent electrodes by simple treatment with water, providing a potential route to recycling of the redox active material.  相似文献   

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We report automated and time‐efficient (2 h per sample) profiling of muscle using ultra‐performance LC coupled directly with high‐definition MS (HDMSE). Soluble proteins extracted from rat gastrocnemius (n = 10) were digested with trypsin and analyzed in duplicate using a 90 min RPLC gradient. Protein identification and label‐free quantitation were performed from HDMSE spectra analyzed using Progenesis QI for Proteomics software. In total 1514 proteins were identified. Of these, 811 had at least three unique peptides and were subsequently used to assess the dynamic range and precision of LC‐HDMSE label‐free profiling. Proteins analyzed by LC‐HDMSE encompass the entire complement of glycolytic, β‐oxidation, and tricarboxylic acid enzymes. In addition, numerous components of the electron transport chain and protein kinases involved in skeletal muscle regulation were detected. The dynamic range of protein abundances spanned four orders of magnitude. The correlation between technical replicates of the ten biological samples was R2 = 0.9961 ± 0.0036 (95% CI = 0.9940 – 0.9992) and the technical CV averaged 7.3 ± 6.7% (95% CI = 6.87 – 7.79%). This represents the most sophisticated label‐free profiling of skeletal muscle to date.  相似文献   

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The use of ultra performance liquid chromatography coupled to data independent tandem mass spectrometry with traveling wave ion mobility for detection and structural identification of ether‐linked glycerophosphoethanolamine is described. The experimental design generates 4D data (chromatographic retention time, precursor accurate mass, drift time with associated calculated collisional cross‐section, and time‐aligned accurate mass diagnostic product ions) for each ionization mode. Confident structure identification depends on satisfying 4D data confirmation in both positive and negative ion mode. Using this methodology, a number of ether‐linked glycerophosphoethanolamine lipids are structurally elucidated from mouse brain lysosomes. It is further determined that several ether‐linked glycerophosphoethanolamine structures are differentially abundant between lysosomes isolated from mouse cortex following traumatic brain injury as compared to that of sham animals. The combined effort of aligning multi‐dimensional mass spectrometry data with a well‐defined traumatic brain injury model lays the foundation for gaining mechanistic insight in the role lysosomal membrane damage plays in neuronal cell death following brain injury.  相似文献   

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Lipids are involved in many biological processes and their study is constantly increasing. To identify a lipid among thousand requires of reliable methods and techniques. Ion Mobility (IM) can be coupled with Mass Spectrometry (MS) to increase analytical selectivity in lipid analysis of lipids. IM-MS has experienced an enormous development in several aspects, including instrumentation, sensitivity, amount of information collected and lipid identification capabilities. This review summarizes the latest developments in IM-MS analyses for lipidomics and focuses on the current acquisition modes in IM-MS, the approaches for the pre-treatment of the acquired data and the subsequent data analysis. Methods and tools for the calculation of Collision Cross Section (CCS) values of analytes are also reviewed. CCS values are commonly studied to support the identification of lipids, providing a quasi-orthogonal property that increases the confidence level in the annotation of compounds and can be matched in CCS databases. The information contained in this review might be of help to new users of IM-MS to decide the adequate instrumentation and software to perform IM-MS experiments for lipid analyses, but also for other experienced researchers that can reconsider their routines and protocols.  相似文献   

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Data‐independent acquisition (DIA) is an emerging technology for quantitative proteomics. Current DIA focusses on the identification and quantitation of fragment ions that are generated from multiple peptides contained in the same selection window of several to tens of m/z. An alternative approach is WiSIM‐DIA, which combines conventional DIA with wide‐SIM (wide selected‐ion monitoring) windows to partition the precursor m/z space to produce high‐quality precursor ion chromatograms. However, WiSIM‐DIA has been underexplored; it remains unclear if it is a viable alternative to DIA. We demonstrate that WiSIM‐DIA quantified more than 24 000 unique peptides over five orders of magnitude in a single 2 h analysis of a neuronal synapse‐enriched fraction, compared to 31 000 in DIA. There is a strong correlation between abundance values of peptides quantified in both the DIA and WiSIM‐DIA datasets. Interestingly, the S/N ratio of these peptides is not correlated. We further show that peptide identification directly from DIA spectra identified >2000 proteins, which included unique peptides not found in spectral libraries generated by DDA.  相似文献   

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Data‐independent acquisition (DIA) generates comprehensive yet complex mass spectrometric data, which imposes the use of data‐dependent acquisition (DDA) libraries for deep peptide‐centric detection. Here, it is shown that DIA can be redeemed from this dependency by combining predicted fragment intensities and retention times with narrow window DIA. This eliminates variation in library building and omits stochastic sampling, finally making the DIA workflow fully deterministic. Especially for clinical proteomics, this has the potential to facilitate inter‐laboratory comparison.  相似文献   

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Amyloidosis is a group of diseases caused by extracellular accumulation of fibrillar polypeptide aggregates. So far, diagnosis is performed by Congo red staining of tissue sections in combination with polarization microscopy. Subsequent identification of the causative protein by immunohistochemistry harbors some difficulties regarding sensitivity and specificity. Mass spectrometry based approaches have been demonstrated to constitute a reliable method to supplement typing of amyloidosis, but still depend on Congo red staining. In the present study, we used matrix‐assisted laser desorption/ionization mass spectrometry imaging coupled with ion mobility separation (MALDI‐IMS MSI) to investigate amyloid deposits in formalin‐fixed and paraffin‐embedded tissue samples. Utilizing a novel peptide filter method, we found a universal peptide signature for amyloidoses. Furthermore, differences in the peptide composition of ALλ and ATTR amyloid were revealed and used to build a reliable classification model. Integrating the peptide filter in MALDI‐IMS MSI analysis, we developed a bioinformatics workflow facilitating the identification and classification of amyloidosis in a less time and sample‐consuming experimental setup. Our findings demonstrate also the feasibility to investigate the amyloid's protein composition, thus paving the way to establish classification models for the diverse types of amyloidoses and to shed further light on the complex process of amyloidogenesis.  相似文献   

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Antibody–drug conjugates (ADCs) are antibody‐based therapeutics that have proven to be highly effective cancer treatment platforms. They are composed of monoclonal antibodies conjugated with highly potent drugs via chemical linkers. Compared to cysteine‐targeted chemistries, conjugation at native lysine residues can lead to a higher degree of structural heterogeneity, and thus it is important to evaluate the impact of conjugation on antibody conformation. Here, we present a workflow involving native ion mobility (IM)‐MS and gas‐phase unfolding for the structural characterization of lysine‐linked monoclonal antibody (mAb)–biotin conjugates. Following the determination of conjugation states via denaturing Liquid Chromatography‐Mass Spectrometry (LC–MS) measurements, we performed both size exclusion chromatography (SEC) and native IM‐MS measurements in order to compare the structures of biotinylated and unmodified IgG1 molecules. Hydrodynamic radii (Rh) and collision cross‐sectional (CCS) values were insufficient to distinguish the conformational changes in these antibody–biotin conjugates owing to their flexible structures and limited instrument resolution. In contrast, collision induced unfolding (CIU) analyses were able to detect subtle structural and stability differences in the mAb upon biotin conjugation, exhibiting a sensitivity to mAb conjugation that exceeds native MS analysis alone. Destabilization of mAb–biotin conjugates was detected by both CIU and differential scanning calorimetry (DSC) data, suggesting a previously unknown correlation between the two measurement tools. We conclude by discussing the impact of IM‐MS and CIU technologies on the future of ADC development pipelines.  相似文献   

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Artemisia annua is well known for biosynthesizing the antimalarial drug artemisinin. Here, a global proteomic profiling of A. annua is conducted with identification of a total of 13 403 proteins based on the genome sequence annotation database. Furthermore, a spectral library is generated to perform quantitative proteomic analysis using data independent acquisition mass spectrometry. Specifically, proteins between two chemotypes that produce high (HAP) and low (LAP) artemisinin content, respectively, are comprehensively quantified and compared. 182 proteins are identified with abundance significantly different between these two chemotypes means after the statistic use the p‐value and fold change it is found 182 proteins can reach the demand conditions which represent the expression are significantly different between the high artemisnin content plants (HAPs) and the low artemisnin content plants (LAPs). Data are available via ProteomeXchange with identifier PXD015547. Overall, this current study globally identifies the proteome of A. annua and quantitatively compares the targeted sub‐proteomes between the two cultivars of HAP and LAP, providing systematic information on metabolic pathways of A. annua.  相似文献   

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Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH‐MS is a specific variant of data‐independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH‐MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH‐MS data, a strategy based on peptide‐centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH‐MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH‐MS data using peptide‐centric scoring. Furthermore, concepts on how to improve SWATH‐MS data acquisition, potential trade‐offs of parameter settings and alternative data analysis strategies are discussed.  相似文献   

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Protein posttranslational modifications (PTMs) are of increasing interest in biomedical research, yet studies rarely examine more than one PTM. One barrier to multi‐PTM studies is the time cost for both sample preparation and data acquisition, which scale linearly with the number of modifications. The most prohibitive requirement is often the need for large amounts of sample, which must be increased proportionally with the number of PTM enrichment steps. Here, a streamlined, quantitative label‐free proteomic workflow—“one‐pot” PTM enrichment—that enables comprehensive identification and quantification of peptides containing acetylated and succinylated lysine residues from a single sample containing as little as 1 mg mitochondria protein is described. Coupled with a label‐free, data‐independent acquisition (DIA), 2235 acetylated and 2173 succinylated peptides with the one‐pot method are identified and quantified and peak areas are shown to be highly correlated between the one‐pot and traditional single‐PTM enrichments. The ‘one‐pot’ method makes possible detection of multiple PTMs occurring on the same peptide, and it is shown that it can be used to make unique biological insights into PTM crosstalk. Compared to single‐PTM enrichments, the one‐pot workflow has equivalent reproducibility and enables direct assessment of PTM crosstalk from biological samples in less time from less tissue.  相似文献   

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Despite experimental evidence supporting ICR-like interactions in biological systems, to date there is no reasonable theoretical explanation for this phenomenon. The parametric resonance approach introduced by Lednev has enjoyed limited success in predicting the response as a function of the ratio of AC magnetic intensity to that of the DC field, explaining the results in terms of magnetically induced changes in the transition probability of calcium binding states. In the present work, we derive an expression for the velocity of a damped ion with arbitrary q/m under the influence of the Lorentz force. Series solutions to the differential equations reveal transient responses as well as resonance-like terms. One fascinating result is that the expressions for ionic drift velocity include a somewhat similar Bessel function dependence as was previously obtained for the transition probability in parametric resonance. However, in the present work, not only is there an explicit effect due to damping, but the previous Bessel dependence now occurs as a subset of a more general solution, including not only the magnetic field AC/DC ratio as an independent variable, but also the ratio of the cyclotronic frequency Omega to the applied AC frequency omega. In effect, this removes the necessity to explain the ICR interaction as stemming from ion-protein binding sites. We hypothesize that the selectively enhanced drift velocity predicted in this model can explain ICR-like phenomena as resulting from increased interaction probabilities in the vicinity of ion channel gates.  相似文献   

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Oligodendrocytes stain more strongly for iron than any other cell in the CNS, and they require iron for the production of myelin. For most cell types transferrin is the major iron delivery protein, yet neither transferrin receptor protein nor mRNA are detectable in mature oligodendrocytes. Thus an alternative iron delivery mechanism must exist. Given the significant long term consequences of developmental iron deficiency and the iron requirements for normal myelination, identification of the iron delivery mechanism for oligodendrocytes is important. Previously we have reported that oligodendrocytes bind H‐ferritin and that H‐ferritin binds to white matter tracts in vivo. Recently, T cell immunoglobulin and mucin domain‐containing protein‐2 (Tim‐2) was shown to bind and internalize H‐ferritin. In the present study we show that Tim‐2 is expressed on oligodendrocytes both in vivo and in vitro. Further, the onset of saturable H‐ferritin binding in CG4 oligodendrocyte cell line is accompanied by Tim‐2 expression. Application of a blocking antibody to the extracellular domain of Tim‐2 significantly reduces H‐ferritin binding to the differentiated CG4 cells and primary oligodendrocytes. Tim‐2 expression on CG4 cells is responsive to iron; decreasing with iron loading and increasing with iron chelation. Taken together, these data provide compelling evidence that Tim‐2 is the H‐ferritin receptor on oligodendrocytes suggesting it is the primary mechanism for iron acquisition by these cells.  相似文献   

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The current state of proteomics requires a choice between targeted and global discovery methods. A method, that combines targeted and data‐independent acquisition for absolute quantification of all identified plasma proteins, in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run, using a panel of spike‐in standards (SIS), is established and optimized. The absolute quantification (AQ) of SWATH and multiple‐reaction monitoring‐high resolution (MRM‐HR) acquisition methods are compared using the 100 protein PlasmaDive SIS panel spiked into non‐depleted human plasma. SWATH provides equivalent quantification and differentially abundant protein profiles as MRM‐HR. Absolute quantities of the SIS peptides from the SWATH data are used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provide similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof‐of‐concept, the eAQ method is applied to 12 plasma samples from six non‐small cell lung cancer (NSCLC) patients and the performance of eAQ values versus peak area quantification is evaluated. There is a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. This eAQ method can provide quantitative data equivalent to AQ or peak area values.  相似文献   

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