Journal of proteins and proteomics最新文献

Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system. 在先天性免疫系统研究中分析蛋白质-蛋白质相互作用的质谱方法的进展。

Journal of proteins and proteomics Pub Date : 2024-09-01 Epub Date: 2024-06-28 DOI: 10.1007/s42485-024-00156-6

Doeun Kim, Aleksandra Nita-Lazar

{"title":"Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system.","authors":"Doeun Kim, Aleksandra Nita-Lazar","doi":"10.1007/s42485-024-00156-6","DOIUrl":"10.1007/s42485-024-00156-6","url":null,"abstract":"Understanding protein-protein interactions (PPIs) is pivotal for deciphering the intricacies of biological processes. Dysregulation of PPIs underlies a spectrum of diseases, including cancer, neurodegenerative disorders, and autoimmune conditions, highlighting the imperative of investigating these interactions for therapeutic advancements. This review delves into the realm of mass spectrometry-based techniques for elucidating PPIs and their profound implications in biological research. Mass spectrometry in the PPI research field not only facilitates the evaluation of protein-protein interaction modulators but also discovers unclear molecular mechanisms and sheds light on both on- and off-target effects, thus aiding in drug development. Our discussion navigates through six pivotal techniques: affinity purification mass spectrometry (AP-MS), proximity labeling mass spectrometry (PL-MS), cross-linking mass spectrometry (XL-MS), size exclusion chromatography coupled with mass spectrometry (SEC-MS), limited proteolysis-coupled mass spectrometry (LiP-MS), and thermal proteome profiling (TPP).","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"15 3","pages":"545-559"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11460538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigating the ATP-binding pocket of CX3CL1-binding protein 2 using in silico approach 利用硅学方法研究 CX3CL1 结合蛋白 2 的 ATP 结合袋

Journal of proteins and proteomics Pub Date : 2024-03-26 DOI: 10.1007/s42485-024-00133-z

Rimjhim Kumari, Satinder Kaur, Rachna Hora, P. Mishra

引用次数: 0

Prediction of B cell epitopes in envelope protein of dengue virus using immunoinformatics approach 利用免疫信息学方法预测登革热病毒包膜蛋白中的 B 细胞表位

Journal of proteins and proteomics Pub Date : 2024-03-25 DOI: 10.1007/s42485-024-00134-y

Ajay Kumar, Siddharth Gupta, Hari Sharan, Fariya Khan

引用次数: 0

Identification of potential inhibitors of shikimate kinase from Mycobacterium tuberculosis using in silico approach 利用硅学方法鉴定结核分枝杆菌莽草酸激酶的潜在抑制剂

Journal of proteins and proteomics Pub Date : 2024-03-21 DOI: 10.1007/s42485-024-00132-0

M. A. Isa, Mohammed Mustapha Mohammed, Muhammad Musa Ibrahim, F. Gubio, Fatimah Buba, Somia Shehzadi

引用次数: 0

Tree based models for classification of membrane and secreted proteins in heart 基于树状模型的心脏膜蛋白和分泌蛋白分类法

Journal of proteins and proteomics Pub Date : 2024-03-21 DOI: 10.1007/s42485-024-00131-1

Sona Charles, A. Subeesh, Jeyakumar Natarajan

引用次数: 0

Histone protein profiling in rice reveals a correlation between canonical and noncanonical function and evolution 水稻组蛋白图谱揭示了规范功能和非规范功能与进化之间的相关性

Journal of proteins and proteomics Pub Date : 2024-03-01 DOI: 10.1007/s42485-024-00129-9

Atreyee Sengupta, Kanika Narula, Archana Sharma, N. Chakraborty, S. Chakraborty

引用次数: 0

An immunoinformatics study to explore HTL epitopes for fungal pathogen Aspergillus lentulus 探索真菌病原体曲霉（Aspergillus lentulus）HTL 表位的免疫信息学研究

Journal of proteins and proteomics Pub Date : 2024-01-23 DOI: 10.1007/s42485-023-00125-5

Shreesh Kumar Dubey, Manoj Kumar Mishra, Fariya Khan, N. Akhtar, Ajay Kumar

引用次数: 0

Interrogating data-independent acquisition LC-MS/MS for affinity proteomics. 探究用于亲和蛋白质组学的独立于数据采集的 LC-MS/MS。

Journal of proteins and proteomics Pub Date : 2024-01-01 Epub Date: 2024-09-17 DOI: 10.1007/s42485-024-00166-4

David L Tabb, Mohammed Hanzala Kaniyar, Omar G Rosas Bringas, Heaji Shin, Luciano Di Stefano, Martin S Taylor, Shaoshuai Xie, Omer H Yilmaz, John LaCava

{"title":"Interrogating data-independent acquisition LC-MS/MS for affinity proteomics.","authors":"David L Tabb, Mohammed Hanzala Kaniyar, Omar G Rosas Bringas, Heaji Shin, Luciano Di Stefano, Martin S Taylor, Shaoshuai Xie, Omer H Yilmaz, John LaCava","doi":"10.1007/s42485-024-00166-4","DOIUrl":"10.1007/s42485-024-00166-4","url":null,"abstract":"Data-Independent Acquisition (DIA) LC-MS/MS is an attractive partner for co-immunoprecipitation (co-IP) and affinity proteomics in general. Reducing the variability of quantitation by DIA could increase the statistical contrast for detecting specific interactors versus what has been achieved in Data-Dependent Acquisition (DDA). By interrogating affinity proteomes featuring both DDA and DIA experiments, we sought to evaluate the spectral libraries, the missingness of protein quantity tables, and the CV of protein quantities in six studies representing three different instrument manufacturers. We examined four contemporary bioinformatics workflows for DIA: FragPipe, DIA-NN, Spectronaut, and MaxQuant. We determined that (1) identifying spectral libraries directly from DIA experiments works well enough that separate DDA experiments do not produce larger spectral libraries when given equivalent instrument time; (2) experiments involving mock pull-downs or IgG controls may feature such indistinct signals that contemporary software will struggle to quantify them; (3) measured CV values were well controlled by Spectronaut and DIA-NN (and FragPipe, which implements DIA-NN for the quantitation step); and (4) when FragPipe builds spectral libraries and quantifies proteins from DIA experiments rather than performing both operations in DDA experiments, the DIA route results in a larger number of proteins quantified without missing values as well as lower CV for measured protein quantities.Supplementary information: The online version contains supplementary material available at 10.1007/s42485-024-00166-4.","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"15 3","pages":"281-298"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular docking and molecular dynamics studies of anti-allergic medicines as inhibitors against COVID-19 抗过敏药物作为 COVID-19 抑制剂的分子对接和分子动力学研究

Journal of proteins and proteomics Pub Date : 2023-12-14 DOI: 10.1007/s42485-023-00122-8

Mrinal Kanti Si, M. R. Patle, Shraddha Pandey

引用次数: 0

A journey to unravel the pathophysiology of stable and exacerbated Chronic Obstructive Pulmonary Disease through erythrocyte proteomics: a combined mass spectrometry/bioinformatics approach 通过红细胞蛋白质组学揭示稳定型和加重型慢性阻塞性肺病病理生理学的旅程：质谱/生物信息学联合方法

Journal of proteins and proteomics Pub Date : 2023-12-13 DOI: 10.1007/s42485-023-00120-w

Sonu Das, Mathew John, E. Maria, Vanditha Mohan, Supriya Adiody, Jinsu Varghese

引用次数: 0