Jeffrey Shabanowitz,Jennifer G Abelin
Jeffrey Shabanowitz
Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides [0.03%]
一种统一的模型用于利用来源于体内和合成肽段的实验质谱数据进行翻译后修饰感知的从头蛋白质序列解析任务
Daniela Klaproth-Andrade,Yanik Bruns,Wassim Gabriel et al.
Daniela Klaproth-Andrade et al.
Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides from tandem mass spectra, but is hindered ...
Improved T cell surfaceomics by depleting intracellularly labelled dead cells [0.03%]
通过去除细胞内标记的死细胞改进T细胞表面组学
Christofer Daniel Sánchez,Aswath Balakrishnan,Blake Krisko et al.
Christofer Daniel Sánchez et al.
Although the plasma membrane (PM) is among the most biologically important and therapeutically targeted cellular compartments, it is among the most challenging to faithfully capture using proteomic approaches. The quality of quantitative su...
MoSAIC: An Integrated and Modular Workflow for Confident Analysis of Protein Post-Translational Modification Landscapes [0.03%]
莫塞姆：一种集成且模块化的自信分析蛋白质翻译后修饰谱的工作流程
Yuanwei Xu,Lijun Chen,T Mamie Lih et al.
Yuanwei Xu et al.
Investigating multiple protein post-translational modifications (PTMs) is critical for unraveling the complexities of protein regulation and the dynamic interplay among PTMs, a growing focus in proteomics. However, simultaneous analysis of ...
PIPI-C: A combinatorial optimization framework for identifying post-translational modification hot-spots in mass spectrometry data [0.03%]
基于组合优化的从质谱数据中鉴定后翻译修饰热点位点的算法框架PIPICS: PIPI-CS: A combinatorial optimization framework for identifying post-translational modification hot-spots in mass spectrometry data
Shengzhi Lai,Shuaijian Dai,Peize Zhao et al.
Shengzhi Lai et al.
Post-translational modifications (PTMs) are pivotal in cellular regulations, and their crosstalk is related to various diseases such as cancer. Given the prevalence of PTM crosstalk within close amino acid ranges, identifying peptides with ...
Comparative Multi-Omics Analysis of the Iridocorneal Angle Identifies an Immune-Fibrotic Profile in the DBA/2J Glaucoma Mouse Model [0.03%]
对虹睫结合部位的比较多组学分析在DBA / 2J青光鼠模型中鉴定出免疫纤维化特征
Myoung Sup Shim,Aleks Grimsrud,Vaibhav Desikan et al.
Myoung Sup Shim et al.
We present the first integrated transcriptomic and proteomic profiling of the iridocorneal region in the spontaneous murine glaucoma model DBA/2J and DBA/2J-Gpnmb+/Sj controls to define molecular changes associated with ocular hypertension ...
Assessing the Performance of Mass Spectrometry Search Strategies in Identifying Translational Errors Using PDX Proteomics Data [0.03%]
基于PDX蛋白质组数据评估质谱搜索策略识别翻译错误的性能
Araf Mahmud,Yingnan Song,Qi Zhou et al.
Araf Mahmud et al.
Translational errors (TEs) result in a mismatch between mRNA codons and the amino acids (AAs) of the corresponding protein. Unlike DNA mutations or RNA editing, where nucleotide sequences can be used to infer AA substitutions, TEs can only ...
Comparative Evaluation of Solid-Phase and Membrane Mimetic Strategies in Membrane Proteome Coverage and Disease-State Analysis [0.03%]
固相与膜模拟策略在膜蛋白质组覆盖及疾病状态分析中的比较评价
Frank Antony,Ashim Bhattacharya,Hiroyuki Aoki et al.
Frank Antony et al.
Membrane proteins (MPs) are vital to cellular signaling, metabolism, and disease pathology, yet remain underrepresented in proteomics. To address this, several independent workflows have been developed to enable the profiling of the membran...
Post-transcriptional modifications integration for ligand-receptor cellular network inference [0.03%]
泛素化修饰整合的受体-配体相互作用网络推断
Pierre Giroux,Morgan Maillard,Jacques Colinge
Pierre Giroux
Cell-cell communications are widely explored to understand tissue homeostasis and diseases. Numerous computational tools have been developed to infer cellular interactions from transcriptomic or proteomic expression data. However, proteins ...
Yannic Chen,Annica Preikschat,Annette Arnold et al.
Yannic Chen et al.
Mass spectrometry (MS) is the method of choice for high-throughput identification of immunopeptides, which are generated by intracellular proteases, unlike proteomics peptides that are typically derived from trypsin-digested proteins. There...