Research on the Upper Limit of Accuracy for Predicting Theoretical Tandem Mass Spectrometry

In recent years, numerous theoretical tandem mass spectrometry prediction methods have been proposed, yet a systematic study and evaluation of their theoretical accuracy limits have not been conducted. If the accuracy of current methods approaches this limit, further exploration of new prediction techniques may become redundant. Conversely, a need for more precise prediction methods or models may be indicated. In this study, we have experimentally analyzed the limits of accuracy at different numbers of ions and parameters using repeated spectral pairs and integrating various similarity metrics. Results show significant achievements in accuracy for backbone ion methods with room for improvement. In contrast, full-spectrum prediction methods exhibit greater potential relative to the theoretical accuracy limit. Additionally, findings highlight the significant impact of normalized collision energy and instrument type on prediction accuracy, underscoring the importance of considering these factors in future theoretical tandem mass spectrometry predictions.

The Deconvolution Method for Obtaining Correspondence in Data-Independent Acquisition Mass Spectrometry Data

Although data-independent acquisition (DIA) shows powerful potential in achieving comprehensive peptide information acquisition, the difficulty in determining the precursor m/z and distinguishing fragment ions has posed challenges in DIA data analysis. To address this challenge, a common approach is to recover the correspondence between precursor ions and fragment ions, followed by peptide identification using traditional data-dependent acquisition (DDA) database searching. In this study, we propose a cosine similarity-based deconvolution method that rapidly establishes the correspondence between chromatographic profiles of precursor ions and fragment ions through matrix calculations. Experimental results demonstrate that our method, referred to as CosDIA, yields a peptide identification count close to that of DIA-umpire. However, compared to DIA-umpire, we can establish the correspondence between original MS/MS spectra and pseudo-MS/MS spectra. Furthermore, compared to the CorrDIA method, our approach achieves higher efficiency in terms of time, reducing the time cost of the analysis process. These results highlight the potential advantages of the CosDIA method in DIA data analysis, providing a powerful tool and method for large-scale proteomics research.

Resveratrol compares with melatonin in improving in vitro porcine oocyte maturation under heat stress

Background： Resveratrol, an important phyto-antioxidant commonly found in grapes, mulberry, and other plants,has a variety of functions including anti-aging, anti-cancer and anti-inflammatory activities. In the current study, we investigated the beneficial effects of resveratrol on in vitro porcine oocyte maturation under heat stress（HS）. The effect of resveratrol, melatonin and their combination on alleviating HS was compared according to the maturation rate of oocytes and the development competence of embryos after parthenogenetic activation（PA）.Results： Supplementation with resveratrol（2.0 μmol/L） not only improved the nuclear maturation but also raised the blastocyst rate of porcine embryos＇ PA from oocytes that underwent HS by increasing their glutathione（GSH）level, reducing reactive oxygen species（ROS） and up-regulating the expression of Sirtuin 1（SIRT1）. It was also found that melatonin（10^-7mol/L） and the combination of resveratrol（2.0 μmol/L） plus melatonin（10^-7mol/L） exhibited more potent effects than resveratrol alone regarding their protective activities on oocyte maturation under HS.Conclusions： This study compared the efficiencies of resveratrol, melatonin and their combination for protecting porcine oocytes from heat stress. The mechanisms are attributed to the fact that each treatment may have different ability to regulate the synthesis of steroid hormones and the expression of mature related genes.

Mammography combined with breast dynamic contrast-enhanced-magnetic resonance imaging for the diagnosis of early breast cancer

Objective The aim of this study was to investigate the application of mammography combined with breast dynamic contrast-enhanced magnetic resonance imaging(DCE-MRI) for the diagnosis of early breast cancer. Methods Mammography and DCE-MRI were performed for 120 patients with breast cancer(malignant, 102; benign; 18). Results The sensitivity of mammography for early diagnosis of breast cancer was 66.67%, specificity was 77.78%, and accuracy was 68.33%. The sensitivity of MRI for early diagnosis of breast cancer was 94.12%, specificity was 88.89%, and accuracy was 93.33%. However, the sensitivity of mammography combined with DCE-MRI volume imaging with enhanced water signal(VIEWS) scanning for early diagnosis of breast cancer was 97.06%, specificity was 94.44%, and accuracy was 96.67%. Conclusion Mammography combined with DCE-MRI increased the sensitivity, specificity, and accuracy of diagnosing early breast cancer.

The application study of dual-energy CT nonlinearblending technique in pulmonary angiography

Objective This study aimed to explore the feasibility of enhancing image quality in computed tomography(CT) pulmonary angiography (CTPA) and reducing radiation dose using the nonlinear blending (NLB)technique of dual-energy CT.Methods A total of 61 patients scheduled for CTPA were enrolled, and 30 patients underwent dual-energyscanning. Nonlinear blending images (NLB group) and three groups of linear blending images (LB group,80 kV group, and 140 kV group) were reconstructed after scanning;31 patients underwent single-energyscanning (120 kV group). The CT values and standard deviations of the pulmonary trunk, left and rightpulmonary arteries, and ipsilateral back muscle at the bifurcation level of the left and right pulmonaryarteries were measured. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of the fivegroups were calculated. The subjective image quality of the five groups was assessed. The radiation dosesof the dual- and single-energy groups were recorded and calculated.Results The CNR and SNR values of blood vessels in the NLB group were significantly higher than thosein the LB, 140 kV, and 80 kV groups (CNR of pulmonary artery trunk: t = 3.50, 4.06, 7.17, all P < 0.05;SNRof pulmonary trunk: t = 3.76, 4.71, 6.92, all P < 0.05). There were no statistical differences in the CNR andSNR values between the NLB group and 120 kV group (P > 0.05). The effective radiation dose of the dualenergygroup was lower than that of the single-energy group (t = –4.52, P < 0.05). The subjective scores ofimages in the NLB group were the highest (4.28 ± 0.74).Conclusion The NLB technique of dual-energy CT can improve the image quality of CTPA and reducethe radiation dose, providing more reliable imaging data for the clinical diagnosis of pulmonary embolism.