Pub Date : 2024-09-01Epub Date: 2024-06-28DOI: 10.1007/s42485-024-00156-6
Doeun Kim, Aleksandra Nita-Lazar
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).
了解蛋白质与蛋白质之间的相互作用（PPIs）对于破解错综复杂的生物过程至关重要。PPIs 失调是一系列疾病（包括癌症、神经退行性疾病和自身免疫性疾病）的基础，这凸显了研究这些相互作用以促进治疗的必要性。本综述将深入探讨基于质谱的 PPIs 阐释技术及其在生物研究中的深远影响。质谱技术在 PPI 研究领域的应用不仅有助于评估蛋白质-蛋白质相互作用调节剂，还能发现不明确的分子机制，揭示靶标内外效应，从而帮助药物开发。我们的讨论将通过六种关键技术展开：亲和纯化质谱法（AP-MS）、邻近标记质谱法（PL-MS）、交联质谱法（XL-MS）、尺寸排阻色谱耦合质谱法（SEC-MS）、有限蛋白水解耦合质谱法（LiP-MS）和热蛋白质组分析法（TPP）。
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Pub Date : 2024-03-26DOI: 10.1007/s42485-024-00133-z
Rimjhim Kumari, Satinder Kaur, Rachna Hora, P. Mishra
{"title":"Investigating the ATP-binding pocket of CX3CL1-binding protein 2 using in silico approach","authors":"Rimjhim Kumari, Satinder Kaur, Rachna Hora, P. Mishra","doi":"10.1007/s42485-024-00133-z","DOIUrl":"https://doi.org/10.1007/s42485-024-00133-z","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"108 45","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140380405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-25DOI: 10.1007/s42485-024-00134-y
Ajay Kumar, Siddharth Gupta, Hari Sharan, Fariya Khan
{"title":"Prediction of B cell epitopes in envelope protein of dengue virus using immunoinformatics approach","authors":"Ajay Kumar, Siddharth Gupta, Hari Sharan, Fariya Khan","doi":"10.1007/s42485-024-00134-y","DOIUrl":"https://doi.org/10.1007/s42485-024-00134-y","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":" 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140381861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-21DOI: 10.1007/s42485-024-00132-0
M. A. Isa, Mohammed Mustapha Mohammed, Muhammad Musa Ibrahim, F. Gubio, Fatimah Buba, Somia Shehzadi
{"title":"Identification of potential inhibitors of shikimate kinase from Mycobacterium tuberculosis using in silico approach","authors":"M. A. Isa, Mohammed Mustapha Mohammed, Muhammad Musa Ibrahim, F. Gubio, Fatimah Buba, Somia Shehzadi","doi":"10.1007/s42485-024-00132-0","DOIUrl":"https://doi.org/10.1007/s42485-024-00132-0","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":" 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140221909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-21DOI: 10.1007/s42485-024-00131-1
Sona Charles, A. Subeesh, Jeyakumar Natarajan
{"title":"Tree based models for classification of membrane and secreted proteins in heart","authors":"Sona Charles, A. Subeesh, Jeyakumar Natarajan","doi":"10.1007/s42485-024-00131-1","DOIUrl":"https://doi.org/10.1007/s42485-024-00131-1","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":" 49","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140221227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-01DOI: 10.1007/s42485-024-00129-9
Atreyee Sengupta, Kanika Narula, Archana Sharma, N. Chakraborty, S. Chakraborty
{"title":"Histone protein profiling in rice reveals a correlation between canonical and noncanonical function and evolution","authors":"Atreyee Sengupta, Kanika Narula, Archana Sharma, N. Chakraborty, S. Chakraborty","doi":"10.1007/s42485-024-00129-9","DOIUrl":"https://doi.org/10.1007/s42485-024-00129-9","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"34 8","pages":"1-14"},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140084567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-23DOI: 10.1007/s42485-023-00125-5
Shreesh Kumar Dubey, Manoj Kumar Mishra, Fariya Khan, N. Akhtar, Ajay Kumar
{"title":"An immunoinformatics study to explore HTL epitopes for fungal pathogen Aspergillus lentulus","authors":"Shreesh Kumar Dubey, Manoj Kumar Mishra, Fariya Khan, N. Akhtar, Ajay Kumar","doi":"10.1007/s42485-023-00125-5","DOIUrl":"https://doi.org/10.1007/s42485-023-00125-5","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"43 18","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139603532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-01Epub Date: 2024-09-17DOI: 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
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.
独立数据采集（DIA）LC-MS/MS 是免疫共沉淀（co-IP）和亲和蛋白质组学的理想合作伙伴。与数据独立获取（DDA）相比，通过 DIA 减少定量的可变性可以提高检测特定相互作用者的统计对比度。通过分析亲和蛋白质组中的 DDA 和 DIA 实验，我们试图评估代表三个不同仪器制造商的六项研究中的光谱库、蛋白质数量表的缺失以及蛋白质数量的 CV。我们考察了四种当代 DIA 生物信息学工作流程：FragPipe、DIA-NN、Spectronaut 和 MaxQuant。我们发现：(1) 直接从 DIA 实验中识别谱库的效果很好，在仪器时间相当的情况下，单独的 DDA 实验不会产生更大的谱库；(2) 涉及模拟拉低或 IgG 对照的实验可能会出现信号不清晰的情况，当代软件很难对其进行量化；(3) Spectronaut 和 DIA-NN（以及 FragPipe，它在定量步骤中实现了 DIA-NN）能很好地控制测量的 CV 值；(4) 当 FragPipe 从 DIA 实验中建立光谱库并定量蛋白质，而不是在 DDA 实验中执行这两项操作时，DIA 途径会导致更多蛋白质被定量，而不会出现缺失值，同时也会降低蛋白质测量量的 CV 值。补充信息：在线版本包含补充材料，可查阅 10.1007/s42485-024-00166-4。
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Pub Date : 2023-12-14DOI: 10.1007/s42485-023-00122-8
Mrinal Kanti Si, M. R. Patle, Shraddha Pandey
{"title":"Molecular docking and molecular dynamics studies of anti-allergic medicines as inhibitors against COVID-19","authors":"Mrinal Kanti Si, M. R. Patle, Shraddha Pandey","doi":"10.1007/s42485-023-00122-8","DOIUrl":"https://doi.org/10.1007/s42485-023-00122-8","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"13 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138972673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-13DOI: 10.1007/s42485-023-00120-w
Sonu Das, Mathew John, E. Maria, Vanditha Mohan, Supriya Adiody, Jinsu Varghese
{"title":"A journey to unravel the pathophysiology of stable and exacerbated Chronic Obstructive Pulmonary Disease through erythrocyte proteomics: a combined mass spectrometry/bioinformatics approach","authors":"Sonu Das, Mathew John, E. Maria, Vanditha Mohan, Supriya Adiody, Jinsu Varghese","doi":"10.1007/s42485-023-00120-w","DOIUrl":"https://doi.org/10.1007/s42485-023-00120-w","url":null,"abstract":"","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"136 29","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139003994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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