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1.
J Cardiovasc Pharmacol ; 81(1): 85-92, 2023 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-36027482

RESUMO

ABSTRACT: Salidroside has anti-inflammatory and antiatherosclerotic effects, and mitochondrial homeostasis imbalance is closely related to cardiovascular disease. The aim of this study was to investigate the effect of salidroside on mitochondrial homeostasis after macrophage polarization and elucidate its possible mechanism against atherosclerosis. RAW264.7 cells were stimulated with 1 µg·mL -1 Lipopolysaccharide and 50 ng·mL -1 IFN-γ establish M1 polarization and were also pretreated with 400 µM salidroside. The relative expression of proinflammatory genes was detected by RT-PCR whereas that of mitochondrial homeostasis-related proteins and nuclear factor kappa-B (NF-κB) was detected by WB. Levels of intracellular reactive oxygen species (ROS), mitochondrial membrane potential, and mass were measured by chemifluorescence whereas that of NF-κB nuclear translocation was detected by immunofluorescence. Compared with the Mφ group, the M1 group demonstrated increased mRNA expression of interleukin-1ß , inductible nitric oxide synthase (iNOS), and tumor necrosis factor-α ; increased protein expression of iNOS, NOD-like receptor protein 3, putative kinase 1 , and NF-κB p65 but decreased protein expression of MFN2, Tom20, and PGC-1α; decreased mitochondrial membrane potential and mass; and increased ROS levels and NF-κB p65 nuclear translocation. Salidroside intervention decreased mRNA expression of interleukin-1ß and tumor necrosis factor-α compared with the M1 group but did not affect that of iNOS. Furthermore, salidroside intervention prevented the changes in protein expression, mitochondrial membrane potential and mass, ROS levels, and NF-κB p65 nuclear translocation observed in the M1 group. In summary, salidroside ultimately inhibits M1 macrophage polarization and maintains mitochondrial homeostasis after macrophage polarization by increasing mitochondrial membrane potential, decreasing ROS levels, inhibiting NF-κB activation, and in turn regulating the expression of proinflammatory factors and mitochondrial homeostasis-associated proteins.


Assuntos
NF-kappa B , Fator de Necrose Tumoral alfa , NF-kappa B/metabolismo , Interleucina-1beta/metabolismo , Fator de Necrose Tumoral alfa/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Macrófagos , Lipopolissacarídeos/farmacologia , Óxido Nítrico Sintase/metabolismo , Homeostase , RNA Mensageiro/metabolismo
2.
Biochem Biophys Res Commun ; 614: 153-160, 2022 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-35597152

RESUMO

Previous studies have demonstrated that Neu5Gc is highly expressed in breast, ovarian, prostate, colon and lung cancers, but not in normal human cells. The presence of Neu5Gc is important for prognosis and is associated with aggressiveness, metastasis, and tumor grade. However, increased Neu5Gc in bladder cancer remains unclear. LIP from lamprey binds the carbohydrate receptor of N-glycolylneuraminic acid (Neu5Gc). The combination of Neu5Gc and LIP suggested that it might be used as a diagnostic tool for the detection of Neu5Gc tumor antigen. Here, the classical animal model of bladder cancer was successfully induced by MNU bladder perfusion. The ELISA results showed that the expression level of Neu5Gc in the urine of normal rats was 94.96 ± 21.01ng/mg, and that of bladder cancer rats was 158.28 ± 34.86 ng/mg. In addition, the results of SNA and LIP immunohistochemistry demonstrated the high expression of Neu5Gc in bladder cancer. After the addition of Neu5Gc to BIU-87 and SV-HUC-1 cells, transcriptomic sequencing and real-time quantitative PCR analysis demonstrated that the gene expression of Neu5Gc synthesis pathway was significantly increased. These data suggest that LIP provides a new tool for the detection of biological samples, especially urine from patients with bladder cancer or suspected cancer, and that revealing the mechanism of abnormal glycosylation can provide theoretical basis for clinical studies.


Assuntos
Neoplasias da Bexiga Urinária , Animais , Antígenos de Neoplasias , Ensaio de Imunoadsorção Enzimática , Humanos , Imuno-Histoquímica , Lampreias , Ratos , Neoplasias da Bexiga Urinária/diagnóstico
3.
Cell Mol Biol Lett ; 27(1): 64, 2022 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-35907821

RESUMO

Progranulin (PGRN) is an autocrine growth factor that regulates cell proliferation, migration, wound healing, and tissue repair in mammals. Lamprey is the most primitive of the extant vertebrates and is regarded as the survivor of a once flourishing group of paleozoic vertebrates, with a history of more than 500 million years. To date, the evolutionary dynamics and the underlying function of the PGRNs remain largely unclear in lamprey. Here, we screened four genes encoding PGRNs from the genomes of Lethenteron reissneri and Petromyzon marinus, including one long form (named Lr-PGRN-L) and three short forms (named Lr-PGRN-S1, Lr-PGRN-S2, and Lr-PGRN-S3), and performed phylogenetic tree, functional domain, and synteny analyses to identify the evolutionary history of the four Lr-PGRNs. In addition, the expressions of the four Lr-pgrn family genes and the immune response against various pathogenic challenges were also investigated. We found that these genes were widely distributed in various tissues of lamprey and performed a variety of functions. Moreover, our results suggest that Lr-PGRN-S1 induces cell migration and proliferation, and is involved in repair after skin and spinal cord injury under appropriate conditions. Our findings are valuable because they improve the understanding of the evolutionary relationship of vertebrate pgrn genes, as well as providing new insights into the diverse and important roles of Lr-PGRNs.


Assuntos
Evolução Molecular , Petromyzon , Animais , Proliferação de Células/genética , Granulinas/genética , Granulinas/metabolismo , Mamíferos , Petromyzon/genética , Petromyzon/metabolismo , Filogenia
4.
J Proteome Res ; 19(9): 3867-3876, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32786689

RESUMO

Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.


Assuntos
Proteômica , Software , Algoritmos , Espectrometria de Massas , Proteoma
5.
J Proteome Res ; 18(5): 2185-2194, 2019 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-30990045

RESUMO

Although thousands of intact proteins have been feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99.2% for complex intact protein samples extracted from HeLa cells. Further, the pTop 2.0 software is developed for automated quantification of intact proteoforms in a high-throughput manner. The high quantification accuracy and reproducibility of this strategy have been demonstrated for both standard and complex cellular protein samples. A total of 2283 intact proteoforms originated from 660 protein accessions are successfully quantified under anaerobic and aerobic conditions and the differentially expressed proteins are observed to be involved in the important biological processes such as stress response.


Assuntos
Misturas Complexas/química , Marcação por Isótopo/métodos , Proteoma/isolamento & purificação , Proteômica/métodos , Sequência de Aminoácidos , Hipóxia Celular , Cromatografia Líquida , Escherichia coli/química , Escherichia coli/genética , Escherichia coli/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Células HeLa , Humanos , Espectrometria de Massas , Proteoma/classificação , Proteoma/genética , Proteoma/metabolismo , Reprodutibilidade dos Testes , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Software , Espectrometria de Massas em Tandem/métodos
6.
Anal Chem ; 90(9): 5857-5864, 2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29624053

RESUMO

3- and 4-Hydroxyprolines (HyP) are regioisomers that play different roles in various species and organs. Despite their distinct functions inside cells, they are generally considered indistinguishable using mass spectrometry due to their identical masses. Here, we demonstrate, for the first time, that characteristic w ions can be produced by electron-transfer/higher energy collision dissociation (EThcD) dual fragmentation technique to confidently discriminate 3-HyP/4-HyP isomers. An integrated and high throughput strategy was developed which combined online LC separation with EThcD for large-scale differentiation of 3-HyP/4-HyP in complex samples. An automated algorithm was developed for charge state dependent characterization of 3-HyP/4-HyP isomers. Using this combined discrimination approach, we identified 108 3-HyP sites and 530 4-HyP sites from decellularized pancreas, allowing more than 5-fold increase of both 3-HyP and 4-HyP identifications compared to previous reports. This approach outperformed ETD and HCD in the analysis of HyP-containing peptides with unique capacity to generate w ions for HyP discrimination, improved fragmentation of precursor ions, as well as unambiguous localization of modifications. A high content of 3-HyP was observed in the C-terminal (GPP)n domain of human CO1A1, which was previously only identified in vertebrate fibrillar collagens from tendon. Unexpectedly, some unusual HyP sites at Xaa position in Gly-HyP-Ala, Gly-HyP-Val, Gly-HyP-Gln, Gly-HyP-Ser, and Gly-HyP-Arg were also confirmed to be 3-hydroxylated, whose functions and enzymes are yet to be discovered. Overall, this novel discrimination strategy can be readily implemented into de novo sequencing or other proteomic search engines.


Assuntos
Hidroxiprolina/análise , Transporte de Elétrons , Humanos , Espectrometria de Massas , Pâncreas/química , Pâncreas/citologia , Proteínas/química , Estereoisomerismo
7.
Nat Methods ; 12(4): 329-31, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25664544

RESUMO

We developed a high-throughput mass spectrometry method, pLink-SS (http://pfind.ict.ac.cn/software/pLink/2014/pLink-SS.html), for precise identification of disulfide-linked peptides. Using pLink-SS, we mapped all native disulfide bonds of a monoclonal antibody and ten standard proteins. We performed disulfide proteome analyses and identified 199 disulfide bonds in Escherichia coli and 568 in proteins secreted by human endothelial cells. We discovered many regulatory disulfide bonds involving catalytic or metal-binding cysteine residues.


Assuntos
Dissulfetos/química , Espectrometria de Massas , Proteoma/química , Proteômica/métodos , Sequência de Aminoácidos , Escherichia coli/química , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Biblioteca de Peptídeos , Ribonucleases/química
8.
J Proteome Res ; 16(2): 645-654, 2017 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-28019094

RESUMO

De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by ∼300 times, Open-pNovo is close to or even ∼10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5-87% more peptides, including 14-250% more modified peptides. On a high-quality simulated data set, ∼85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.


Assuntos
Sequência de Aminoácidos/genética , Peptídeos/genética , Processamento de Proteína Pós-Traducional/genética , Algoritmos , Bases de Dados de Proteínas , Análise de Sequência de Proteína , Software , Espectrometria de Massas em Tandem
10.
Anal Chem ; 88(6): 3082-90, 2016 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-26844380

RESUMO

There has been tremendous progress in top-down proteomics (TDP) in the past 5 years, particularly in intact protein separation and high-resolution mass spectrometry. However, bioinformatics to deal with large-scale mass spectra has lagged behind, in both algorithmic research and software development. In this study, we developed pTop 1.0, a novel software tool to significantly improve the accuracy and efficiency of mass spectral data analysis in TDP. The precursor mass offers crucial clues to infer the potential post-translational modifications co-occurring on the protein, the reliability of which relies heavily on its mass accuracy. Concentrating on detecting the precursors more accurately, a machine-learning model incorporating a variety of spectral features was trained online in pTop via a support vector machine (SVM). pTop employs the sequence tags extracted from the MS/MS spectra and a dynamic programming algorithm to accelerate the search speed, especially for those spectra with multiple post-translational modifications. We tested pTop on three publicly available data sets and compared it with ProSight and MS-Align+ in terms of its recall, precision, running time, and so on. The results showed that pTop can, in general, outperform ProSight and MS-Align+. pTop recalled 22% more correct precursors, although it exported 30% fewer precursors than Xtract (in ProSight) from a human histone data set. The running speed of pTop was about 1 to 2 orders of magnitude faster than that of MS-Align+. This algorithmic advancement in pTop, including both accuracy and speed, will inspire the development of other similar software to analyze the mass spectra from the entire proteins.


Assuntos
Bases de Dados de Proteínas , Armazenamento e Recuperação da Informação , Proteínas/análise , Algoritmos , Aprendizado de Máquina , Software
11.
Mol Cell Proteomics ; 13(1): 360-71, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24187338

RESUMO

The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of researchers and their results were collectively analyzed. The results from the twenty-four participants, who represented a broad spectrum of experience levels with this type of data analysis, produced several important observations. First, there is significantly more variability in the ability to assess whether a results is significant than there is to determine the correct answer. Second, labile post-translational modifications, particularly tyrosine sulfation, present a challenge for most researchers. Finally, for modification site localization there are many tools being employed, but researchers are currently unsure of the reliability of the results these programs are producing.


Assuntos
Peptídeos/isolamento & purificação , Processamento de Proteína Pós-Traducional/genética , Proteoma , Sequência de Aminoácidos/genética , Misturas Complexas/química , Misturas Complexas/genética , Biologia Computacional , Humanos , Peptídeos/química , Peptídeos/metabolismo , Análise de Sequência de Proteína
13.
Anal Chem ; 86(11): 5286-94, 2014 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-24799117

RESUMO

In relative protein abundance determination from peptide intensities recorded in full mass scans, a major complication that affects quantitation accuracy is signal interference from coeluting ions of similar m/z values. Here, we present pQuant, a quantitation software tool that solves this problem. pQuant detects interference signals, identifies for each peptide a pair of least interfered isotopic chromatograms: one for the light and one for the heavy isotope-labeled peptide. On the basis of these isotopic pairs, pQuant calculates the relative heavy/light peptide ratios along with their 99.75% confidence intervals (CIs). From the peptides ratios and their CIs, pQuant estimates the protein ratios and associated CIs by kernel density estimation. We tested pQuant, Census and MaxQuant on data sets obtained from mixtures (at varying mixing ratios from 10:1 to 1:10) of light- and heavy-SILAC labeled HeLa cells or (14)N- and (15)N-labeled Escherichia coli cells. pQuant quantitated more peptides with better accuracy than Census and MaxQuant in all 14 data sets. On the SILAC data sets, the nonquantified "NaN" (not a number) ratios generated by Census, MaxQuant, and pQuant accounted for 2.5-10.7%, 1.8-2.7%, and 0.01-0.5% of all ratios, respectively. On the (14)N/(15)N data sets, which cannot be quantified by MaxQuant, Census and pQuant produced 0.9-10.0% and 0.3-2.9% NaN ratios, respectively. Excluding these NaN results, the standard deviations of the numerical ratios calculated by Census or MaxQuant are 30-100% larger than those by pQuant. These results show that pQuant outperforms Census and MaxQuant in SILAC and (15)N-based quantitation.


Assuntos
Peptídeos/química , Proteínas/química , Escherichia coli/química , Células HeLa/química , Humanos , Isótopos , Espectrometria de Massas , Isótopos de Nitrogênio , Radioisótopos de Nitrogênio , Software
14.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 36(4): 415-421, 2024 Apr.
Artigo em Zh | MEDLINE | ID: mdl-38813638

RESUMO

OBJECTIVE: To investigate the establishment method, coordination points and safe transport management strategy of vena-arterial extracorporeal membrane oxygenation (VA-ECMO) in patients with downtime difficulties during cardiopulmonary bypass (CPB). METHODS: A observation study was conducted. The patients admitted to the department of critical care medicine of the First Affiliated Hospital of Wannan Medical College (Yijishan Hospital) from January 2020 to October 2022 were enrolled. These patients could not be separated from CPB and received VA-ECMO-assisted CPB surgery. The clinical data of the patients were recorded, including the basic information of the patients, the data of VA-ECMO establishment and transport process, the clinical indicators before and after VA-ECMO installation, the operation data of VA-ECMO and clinical outcomes. The experience was summarized from the aspects of extracorporeal membrane oxygenation (ECMO) establishment, transport process, team cooperation, and adverse events during transport. The clinical indicators before and after ECMO operation were compared. According to whether ECMO was successfully weaned, the patients were divided into a successful weaning group and a failure weaning group, and the clinical data between the two groups were compared. RESULTS: Eighteen patients who underwent VA-ECMO-assisted CPB were enrolled, including 10 males and 8 females. The average age was (56.7±12.3) years old. Preoperative left ventricular ejection fraction (LVEF) was 0.46±0.10, and the main reasons for switching to VA-ECMO assistance included right ventricular systolic weakness in 6 cases, total cardiac systolic weakness in 5 cases, left ventricular systolic weakness in 4 cases, high pulmonary arterial pressure in 2 cases, and intractable ventricular fibrillation in 1 case. Among the 18 patients transferred from CPB to VA-ECMO, 10 cases were successfully weaned and 8 cases failed. In ICU, 8 cases survived, 5 cases died, and 5 cases gave up treatment and discharged. The average time for successful CPB to VA-ECMO establishment was (24.6±7.4) minutes, initial blood flow was (3.3±0.4) L/min, and transit time was (8.4±1.5) minutes. ECMO-assisted duration averaged (82.0±69.3) hours. Adverse events occurred in 9 patients during ECMO establishment and transfer. Post-ECMO onboarding for 4 hours, significant improvements were noted in blood lactic acid (Lac), pH value, mean arterial pressure (MAP), central venous oxygen saturation (ScvO2) as compared with pre-ECMO onboarding [Lac (mmol/L): 10.5±7.0 vs. 15.2±6.8, pH value: 7.38±0.92 vs. 7.26±0.87, MAP (mmHg, 1 mmHg ≈ 0.133 kPa): 74.9±13.7 vs. 58.4±17.0, ScvO2: 0.678±0.065 vs. 0.611±0.061, all P < 0.01], and vasoactive-inotropic score (VIS) was also decreased (39.8±29.8 vs. 68.9±64.4, P < 0.01). Compared with successful weaning group, the patients in the failed weaning group exhibited higher pre-machine Lac (mmol/L: 18.8±7.8 vs. 12.3±4.3, P < 0.05), longer CPB time [minutes: 238.0 (208.8, 351.2) vs. 200.0 (185.8, 217.0), P < 0.05], and shorter ECMO-assisted time [hours: 19.5 (11.0, 58.8) vs. 94.5 (65.8, 179.8), P < 0.01]. However, there was no statistically significant difference in pre-machine pH value, ScvO2, MAP, VIS score, and initial blood flow and establishment time of ECMO between the two groups. CONCLUSIONS: VA-ECMO is an effective circulatory aid for CPB surgery that cannot be weaned after CPB. The establishment and transfer of CPB "bridge" to ECMO aid depends on multi-disciplinary treatment (MDT) cooperation. The success rate of ECMO weaning is related to the Lac and CPB duration. If it is not possible to detach from the CPB successfully, VA-ECMO should be initiated as early as possible.


Assuntos
Ponte Cardiopulmonar , Oxigenação por Membrana Extracorpórea , Humanos , Oxigenação por Membrana Extracorpórea/métodos , Ponte Cardiopulmonar/métodos , Feminino , Masculino , Pessoa de Meia-Idade
15.
Life (Basel) ; 14(5)2024 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-38792619

RESUMO

The carbon-to-nitrogen (C/N) ratio in the cultivation medium significantly influences the growth rate, vigor of mycelium, yield of fruiting bodies, and their nutritional composition. Recently, agricultural and forestry wastes have been increasingly used in cultivating Flammulina velutipes. However, systematic research on how these materials affect the nutritional and functional properties of the fruiting bodies is lacking. This study investigated the effects of different C/N ratios on F. velutipes cultivation. We evaluated the agronomic traits, nutritional composition, and flavor compounds of the fruiting bodies. Our findings reveal that an optimal C/N ratio of 27:1 in the composted substrates enhances the total yield of fruiting bodies, with 25.1% soybean straw as the primary raw material. This ratio also significantly increases the levels of crude protein, total amino acids, and essential amino acids in the fruiting bodies (p < 0.05). Fruiting bodies from the high-nitrogen (HN) treatment showed the highest content of umami amino acids and equivalent umami concentration value. Additionally, we employed an untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics approach to analyze the metabolite profiles of fruiting bodies cultivated in high-nitrogen (HN), medium-nitrogen (MN), and low-nitrogen (LN) substrates. We found that the carbon-nitrogen ratio can affect the flavor and quality of fruiting bodies by regulating amino acid biosynthesis and metabolism and other related pathways. Our results suggest that a C/N ratio of 27:1 offers numerous benefits for the cultivation of F. velutipes with comprehensive analyses and has promising application prospects.

16.
J Proteome Res ; 12(2): 615-25, 2013 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-23272783

RESUMO

De novo peptide sequencing is the only tool for extracting peptide sequences directly from tandem mass spectrometry (MS) data without any protein database. However, neither the accuracy nor the efficiency of de novo sequencing has been satisfactory, mainly due to incomplete fragmentation information in experimental spectra. Recent advancement in MS technology has enabled acquisition of higher energy collisional dissociation (HCD) and electron transfer dissociation (ETD) spectra of the same precursor. These spectra contain complementary fragmentation information and can be collected with high resolution and high mass accuracy. Taking these advantages, we have developed a new algorithm called pNovo+, which greatly improves the accuracy and speed of de novo sequencing. On tryptic peptides, 86% of the topmost candidate sequences deduced by pNovo+ from HCD + ETD spectral pairs matched the database search results, and the success rate reached 95% if the top three candidates were included, which was much higher than using only HCD (87%) or only ETD spectra (57%). On Asp-N, Glu-C, or Elastase digested peptides, 69-87% of the HCD + ETD spectral pairs were correctly identified by pNovo+ among the topmost candidates, or 84-95% among the top three. On average, it takes pNovo+ only 0.018 s to extract the sequence from a spectrum or spectral pair on a common personal computer. This is more than three times as fast as other de novo sequencing programs. The increase of speed is mainly due to pDAG, a component algorithm of pNovo+. pDAG finds the k longest paths in a directed acyclic graph without the antisymmetry restriction. We have verified that the antisymmetry restriction is unnecessary for high resolution, high mass accuracy data. The extensive use of HCD and ETD spectral information and the pDAG algorithm make pNovo+ an excellent de novo sequencing tool.


Assuntos
Algoritmos , Peptídeos/isolamento & purificação , Análise de Sequência de Proteína/normas , Espectrometria de Massas em Tandem/normas , Sequência de Aminoácidos , Animais , Bases de Dados de Proteínas , Humanos , Metaloendopeptidases/química , Dados de Sequência Molecular , Elastase Pancreática/química , Peptídeos/química , Sensibilidade e Especificidade , Análise de Sequência de Proteína/métodos , Serina Endopeptidases/química , Tripsina/química
17.
Mol Cell Proteomics ; 10(5): M110.000455, 2011 May.
Artigo em Inglês | MEDLINE | ID: mdl-21321130

RESUMO

Identification of proteins and their modifications via liquid chromatography-tandem mass spectrometry is an important task for the field of proteomics. However, because of the complexity of tandem mass spectra, the majority of the spectra cannot be identified. The presence of unanticipated protein modifications is among the major reasons for the low spectral identification rate. The conventional database search approach to protein identification has inherent difficulties in comprehensive detection of protein modifications. In recent years, increasing efforts have been devoted to developing unrestrictive approaches to modification identification, but they often suffer from their lack of speed. This paper presents a statistical algorithm named DeltAMT (Delta Accurate Mass and Time) for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. The algorithm is based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample and their spectra are correlated with each other in precursor masses and retention times. By representing each pair of spectra as a delta mass and time vector, bivariate Gaussian mixture models are used to detect modification-related spectral pairs. Unlike previous approaches to unrestrictive modification identification that mainly rely upon the fragment information and the mass dimension in liquid chromatography-tandem mass spectrometry, the proposed algorithm makes the most of precursor information. Thus, it is highly efficient while being accurate and sensitive. On two published data sets, the algorithm effectively detected various modifications and other interesting events, yielding deep insights into the data. Based on these discoveries, the spectral identification rates were significantly increased and many modified peptides were identified.


Assuntos
Algoritmos , Cromatografia Líquida/métodos , Processamento de Proteína Pós-Traducional , Proteoma/química , Espectrometria de Massas em Tandem/métodos , Cromatografia Líquida/normas , Interpretação Estatística de Dados , Bases de Dados de Proteínas , Proteínas Fúngicas/química , Células HeLa , Humanos , Peso Molecular , Padrões de Referência , Espectrometria de Massas em Tandem/normas
18.
J Am Soc Mass Spectrom ; 34(8): 1598-1608, 2023 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-37463304

RESUMO

Mass spectrometry (MS)-based analysis of RNA oligonucleotides (oligos) plays an increasingly important role in the development of RNA therapeutics and epitranscriptomics research. However, MS fragmentation behaviors of RNA oligomers are understood insufficiently. Herein, we characterized the negative-ion-mode fragmentation behaviors of 26 synthetic RNA oligos containing four to eight nucleotides using collision-induced dissociation (CID) on a high-resolution, accurate-mass instrument. We found that in CID spectra acquired under the normalized collision energy (NCE) of 35%, approximately 70% of the total peak intensity was attributed to sequencing ions (a-B, a, b, c, d, w, x, y, z), around 25% of the peak intensity came from precursor ions that experienced complete or partial loss of a nucleobase in the form of either a neutral or an anion, and the remainder were internal ions and anionic nucleobases. The top five sequencing ions were the y, c, w, a-B, and a ions. Furthermore, we observed that CID fragmentation behaviors of RNA oligos were significantly impacted by their precursor charge. Specifically, when the precursors had a charge from 1- to 5-, the fractional intensity of sequencing ions decreased, while that of precursors that underwent either neutral or charged losses of a nucleobase increased. Additionally, we found that RNA oligos containing 3'-U tended to produce precursors with HNCO and/or NCO- losses, which presumably corresponded to isocyanic acid and cyanate anion, respectively. These findings provide valuable insights for better comprehending the mechanism behind RNA fragmentation by MS/MS, thereby facilitating the future automated identification of RNA oligos based on their CID spectra in a more efficient manner.


Assuntos
Oligonucleotídeos , Espectrometria de Massas em Tandem , Oligonucleotídeos/química , Espectrometria de Massas em Tandem/métodos , RNA , Íons/química , Ânions , Espectrometria de Massas por Ionização por Electrospray
19.
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue ; 35(10): 1080-1084, 2023 Oct.
Artigo em Zh | MEDLINE | ID: mdl-37873714

RESUMO

OBJECTIVE: To explore the predictive value of diaphragmatic thickening fraction (DTF) combined with Medical Research Council-score (MRC score) on the outcome of weaning from mechanical ventilation in ICU-acquired weakness (ICU-AW) patients. METHODS: A retrospective case-control study was conducted. The clinical data of mechanically ventilated patients with an MRC score of less than 48 admitted to the department of critical care medicine of the First Affiliated Hospital of Wannan Medical College from January 2022 to March 2023 were collected, including general information, ultrasound indicators, MRC scores, main clinical outcomes, and weaning outcomes. Patients were divided into successful weaning group and failed weaning group according to whether the patient could maintain effective autonomous breathing for at least 48 hours without using an invasive or non-invasive ventilator. The clinical data of the two groups were compared. Receiver operator characteristic curve (ROC curve) was plotted to analyze the predictive value of DTF and MRC score alone or in combination for successful weaning of patients. RESULTS: A total of 87 patients were enrolled, of which 58 were successful weaning and 29 were failed weaning. There were no statistically significant differences in general data such as gender, age, underlying disease, heart rate (HR), mean arterial pressure (MAP), pH value, blood lactic acid (Lac), oxygenation index (PaO2/FiO2), and severity scores between the two groups. Compared with the failed weaning group, the DTF and MRC scores of patients in the successful weaning group were significantly increased [DTF: (26.02±2.68)% vs. (22.79±5.40)%, MRC score: 38.90±2.78 vs. 33.24±3.78, both P < 0.05]. The duration of mechanical ventilation and the length of ICU stay of patients in the successful weaning group were significantly shorter than those in the failed weaning group [duration of mechanical ventilation (hours): 102.21±32.60 vs. 113.14±41.34, length of ICU stay (days): 6.48±2.18 vs. 10.11±4.01, both P < 0.05], and the re-intubation rate and ICU hospitalization cost were significantly lowered [re-intubation rate: 6.90% (4/58) vs. 27.59% (8/29), ICU hospitalization cost (10 000 RMB): 4.99±0.87 vs. 7.85±2.45, both P < 0.05]. ROC curve analysis showed that the area under the ROC curve (AUC) of DTF and MRC score for predicting successful weaning in ICU-AW mechanical ventilation patients was 0.839 [95% confidence interval (95%CI) was 0.746-0.931] and 0.799 (95%CI was 0.701-0.899), respectively. Using DTF ≥ 25.01% as the optimal cut-off value to predict successful weaning, the sensitivity was 82.76%, and the specificity was 72.41%. Predicting successful weaning based on an optimal cut-off value of MRC score of ≥ 35.50 had a sensitivity of 79.31% and a specificity of 70.69%. Based on the DTF ≥ 25.01% combined with MRC score ≥ 35.50, it was predicted that the weaning would be successful, with an AUC of 0.887 (95%CI was 0.812-0.962), sensitivity increased to 89.70%, and specificity increased to 79.30%. CONCLUSIONS: The DTF and MRC score have good guiding value for the selection of weaning timing and predicting the weaning outcomes in ICU-AW patients. Compared with independent DTF and MRC score, the combination of DTF and MRC score improves the predictive value of successful weaning in ICU-AW patients.


Assuntos
Respiração Artificial , Desmame do Respirador , Humanos , Estudos de Casos e Controles , Estudos Retrospectivos , Unidades de Terapia Intensiva
20.
Med Eng Phys ; 120: 104042, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37838396

RESUMO

Artificial implant materials may articulate against native articular cartilage in certain clinical scenarios and the selection of an implant material that results in the least wear on articular cartilage is preferred to maintain normal joint architecture and function. This project compared the wear on porcine femoral condyles induced by articulation against porcine patellae, titanium alloy (Ti6Al4V), ultra high molecular weight polyethylene (UHMWPE), and carbon fibre reinforced polyether-ether-ketone (CFR-PEEK) through an ex vivo experimental setup. A sinusoidal compressive load of 30-160 N, representing an approximate joint pressure of 0.19-1 MPa at a frequency of 3 Hz coupled with a rotational displacement of +/- 10° at 3 Hz was used to simulate physiological joint motion. Wear was characterized via gross examination and histologically using the OARSI scoring system after 43,200 cycles. CFR-PEEK resulted in the most significant wear on articular cartilage compared to titanium alloy and UHMWPE whereas titanium alloy and UHMWPE resulted in similar levels of wear. All materials caused more wear compared to cartilage-on-cartilage testing. The wear mechanism was characterized by progressive loss of proteoglycan content in cartilage in histology samples.


Assuntos
Cartilagem Articular , Titânio , Animais , Suínos , Fibra de Carbono , Projetos Piloto , Materiais Biocompatíveis/farmacologia , Teste de Materiais , Polietilenoglicóis , Polietilenos , Cetonas , Ligas , Éteres
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