Journal Name:Journal of Proteome Research

Issue:2019 March

Shared by: Weining Zhao

1.     Acetylome:

Zhuo Zhou et al from Zhejiang University profiled the lysine acetylome as protein acetylation which is believed to play a key role in autophagy. Employing a SILIC method in human cell culture, they found 421 acetylation sites significantly altered on 296 proteins. 80.8% of sites were downregulated while only 19.2% upregulated suggesting a deacetylation-preponderant profile during autophagy.1 Lysine acetylation occurs not only in eukaryotic cells but also prokaryotic ones. Lysine succinylome and acetylome of the extracellular compartment of clinically important pathogen P. aeruginosa was reported for the first time. The key virulence factors LasB and CbpD from Pseudomonas aeruginosa were found to be multi-modified on lysine residues. Moreover, Charlotte et al demonstrate lysine is prone to be modified and various modifications (9 kinds of modifications were tested) can take place in vitro. However, these modification patterns still need further in vivo verification.2

2.      

a) Milk Protein-Derived Peptides:

One piece of milk related work was published in JPR 2019 March issue which may raise our interest and aid our in-house milk formula project. This work focuses on preterm infants and provides a comprehensive profile of milk peptides released during gastric digestion over time.3

b) Cystic Fibrosis Newborns:

Cystic fibrosis (CF) is one of the most common fatal genetic diseases and the patients can benefit from early therapeutic interventions. The current CF screening method for newborns suffer from low positive predictive value although it is sensitive. Nontargeted metabolite profiling experiments with highthroughput capillary electrophoresis-mass spectrometry (MS) platform reveal 32 metabolites are differentially expressed in CF newborns and normal ones (q < 0.05) while 6 CF-specific biomarker candidates satisfying a Bonferroni adjustment (p < 7.25 × 10–5).4 Nevertheless, the application of this discovery into clinical labs still needs more efforts and unlikely to replace the current screening methods due to its current sensitivity.

3.     Method Development:

a) Immunogen Structure Generation:

One crosslinking mass spectrometry (XL-MS) based approach was developed for structure generation and delineation of immunogens. This approach is demonstrated by case study of host transferrin (Tf) and bacterial vaccine target transferrin binding protein B (TbpB). Nonetheless, since this approach is based on crosslinking mass spectrometry data, the cross-linkers are vital for successful modeling. As suggested by Daniel et al, photoactivatable diazirine containing cross-linker allows fast snapshot of the protein interactions while the commonly used N-hydroxysuccinimide ester traps dynamic states in the ensemble.5 This work actually highlights the proper selection of cross-linkers in XL-MS research as well as the importance of developing new methodologies.

b) Proteoform Identifications:

TopMCMC method was developed for accurately estimating the statistical significance of proteoform identifications with modifications in Top-down mass spec data. This is a good complement since most current top-down data analysis softwares employ estimation methods designed for proteoform identifications without modifications. With TopMCMC, more spectra were identified and the data is shown by Xiaowen Liu et al.6

c) DIA Tutorial:

Data-Independent Acquisition (DIA) is one important mass-spec technique and a number of scientific groups perform DIA experiments with orbitrap analyzer. Léon et al proposed one DIA method development strategy for Orbitrap Q Exactive HF in their tutorial. In this tutorial, the authors do not provide optimal settings but show the steps in construction and optimization of the DIA method. The method discussion inside further points out possible tailoring.7 This method is quite beneficial for fresh DIA researchers.

4.  Simple Ideas:

a) Hybrid Insulin Peptides:

Hybrid insulin peptides (HIPs) were discovered as a novel class of post-translationally modified peptides in murine-derived beta cell tumors, and Aaron et al identified the presence of these peptide in mouse and human islets with mass-spec.8

b) Exosome and macrophage:

The proteome of THP-1-derived macrophages and their exosomes secreted with or without IFN-α treatment were analyzed via label-free liquid chromatography–tandem mass spectrometry quantitation technologies. The analysis of the proteomic data indicates the exosomes can act as cargos of IFN-α-induced antiviral molecules.9

c) Protein Function and Interaction Network:

The pathogen resistance phenotype of Arabidopsis to Pseudomonas syringae pv tomato (Pst) DC3000 is verified with the biological assays when MAP kinase 4 (MPK4) is overexpressed. Further systems level analysis of how MPK4 regulates plant immunity is achieved via immunoprecipitation coupled with mass spectrometry (IP-MS) by comparing the interaction network in the presence and absence of MPK4 activator flg22.10

1.     Zhou, Z.; Chen, Y.; Jin, M.; He, J.; Guli, A.; Yan, C.; Ding, S., Comprehensive Analysis of Lysine Acetylome Reveals a Site-Specific Pattern in Rapamycin-Induced Autophagy. J Proteome Res 2019, 18 (3), 865-877.

2.     Gaviard, C.; Cosette, P.; Jouenne, T.; Hardouin, J., LasB and CbpD Virulence Factors of Pseudomonas aeruginosa Carry Multiple Post-Translational Modifications on Their Lysine Residues. J Proteome Res 2019, 18 (3), 923-933.

3.     Beverly, R. L.; Underwood, M. A.; Dallas, D. C., Peptidomics Analysis of Milk Protein-Derived Peptides Released over Time in the Preterm Infant Stomach. J Proteome Res 2019, 18 (3), 912-922.

4.     DiBattista, A.; McIntosh, N.; Lamoureux, M.; Al-Dirbashi, O. Y.; Chakraborty, P.; Britz-McKibbin, P., Metabolic Signatures of Cystic Fibrosis Identified in Dried Blood Spots For Newborn Screening Without Carrier Identification. J Proteome Res 2019, 18 (3), 841-854.

5.     Ziemianowicz, D. S.; Ng, D.; Schryvers, A. B.; Schriemer, D. C., Photo-Cross-Linking Mass Spectrometry and Integrative Modeling Enables Rapid Screening of Antigen Interactions Involving Bacterial Transferrin Receptors. J Proteome Res 2019, 18 (3), 934-946.

6.     Kou, Q.; Wang, Z.; Lubeckyj, R. A.; Wu, S.; Sun, L.; Liu, X., A Markov Chain Monte Carlo Method for Estimating the Statistical Significance of Proteoform Identifications by Top-Down Mass Spectrometry. J Proteome Res 2019, 18 (3), 878-889.

7.     Reubsaet, L.; Sweredoski, M. J.; Moradian, A., Data-Independent Acquisition for the Orbitrap Q Exactive HF: A Tutorial. J Proteome Res 2019, 18 (3), 803-813.

8.     Aaron Wiles, T.; Powell, R.; Michel, C. R.; Scott Beard, K.; Hohenstein, A.; Bradley, B.; Reisdorph, N.; Haskins, K.; Delong, T., Identification of Hybrid Insulin Peptides (HIPs) in Mouse and Human Islets by Mass Spectrometry. J Proteome Res 2019, 18 (3), 814-825.

9.     Yao, Z.; Jia, X.; Megger, D. A.; Chen, J.; Liu, Y.; Li, J.; Sitek, B.; Yuan, Z., Label-Free Proteomic Analysis of Exosomes Secreted from THP-1-Derived Macrophages Treated with IFN-alpha Identifies Antiviral Proteins Enriched in Exosomes. J Proteome Res 2019, 18 (3), 855-864.

10.   Zhang, T.; Schneider, J. D.; Lin, C.; Geng, S.; Ma, T.; Lawrence, S. R.; Dufresne, C. P.; Harmon, A. C.; Chen, S., MPK4 Phosphorylation Dynamics and Interacting Proteins in Plant Immunity. J Proteome Res 2019, 18 (3), 826-840.

Some JPR highlights (JPR 2019 March)的更多相关文章

  1. Go package(1) time 用法

    golang使用的版本: go version go1.10.3 一:功能介绍 time的一些功能,比如时区,像linux中的定时器,时间计算等 格式化时间 时区(Location) 时间计算 Tic ...

  2. CodeChef March Challenge 2019题解

    传送门 \(CHNUM\) 显然正数一组,负数一组 for(int T=read();T;--T){ n=read(),c=d=0; fp(i,1,n)x=read(),x>0?++c:++d; ...

  3. 2019中山纪念中学夏令营-Day12[JZOJ]

    Begin (题目的排序方式:题号) 每期新姿势:(今天推荐一位巨佬)Cefola-Kiroxs 推荐知识:namespace的用法(本赛我的代码中将用到) 2019.08.12[NOIP普及组]模拟 ...

  4. F#周报2019年第14期

    新闻 发布F# 4.6 SAFE Stack v1.0 发布fable编译器2.2,Fable.Core 3及其它 发布ML.NET 1.0 RC Saturn:增加路由诊断页面 Visual Stu ...

  5. POJ 2019 Cornfields [二维RMQ]

    题目传送门 Cornfields Time Limit: 1000MS   Memory Limit: 30000K Total Submissions: 7963   Accepted: 3822 ...

  6. SysML——AI-Sys Spring 2019

    AI-Sys Syllabus Projects Grading AI-Sys Spring 2019 When: Mondays and Wednesdays from 9:30 to 11:00 ...

  7. Visual Studio 2019 for Mac 离线更新方法

    当你打开Visual Studio 2019 for Mac检查更新时,如果下载更新包很慢,可以尝试如下操作: 打开Finder(访达),找到~/Library/Caches/VisualStudio ...

  8. [更新] Jetbrains IntelliJ IDEA 2019 的许可证密钥

    亲测有效.转载目的:提供一种方法,当然可以看一下原网站的更新及其他方法.转载:[更新] Jetbrains IntelliJ IDEA 2019 的许可证密钥(100%工作),By Gideon    ...

  9. Deep learning_CNN_Review:A Survey of the Recent Architectures of Deep Convolutional Neural Networks——2019

    CNN综述文章 的翻译 [2019 CVPR] A Survey of the Recent Architectures of Deep Convolutional Neural Networks 翻 ...

随机推荐

  1. A Short Introduction to Boosting

    http://www.site.uottawa.ca/~stan/csi5387/boost-tut-ppr.pdf Boosting is a general method for improvin ...

  2. Delphi的RTTI(许多参考链接)

    RTTI(RunTime Type Information): 运行时类型信息, 就是在程序运行后也能得到类型(譬如 TButton 类)的信息. 这在早期主要用于 IDE 设计时, 譬如把一个 Bu ...

  3. mongodb学习之:文档操作

    在上一章中有讲到文档的插入操作是用insert的方法.如果该集合不在该数据库中,mongodb会自动创建该集合并插入文档 用find的方法可以查找所有的集合数据 > db.maple.find( ...

  4. MongoDB 倾向于将数据都放在一个 Collection 下吗?

    不是这样的. Collection 的单个 doc 有大小上限,现在是 16MB,这就使得你不可能把所有东西都揉到一个 collection 里.而且如果 collection 结构过于复杂,既会影响 ...

  5. .PHP生成静态html文件的方法

    1. [代码][PHP]代码     1,下面使用模版的一个方法!   <?php $fp = fopen ("templets.html","a");  ...

  6. jquery之extend

    jquery的extend方法的用法1. [代码][JavaScript]代码     01<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01// ...

  7. 简单封装微信小程序

    一.不同环境配置封装 新建config文件夹,根据自己有不同环境设置不同的js文件 具体js文件内容: exports.config = { requestHost: 'https://******. ...

  8. spring mvc提交日期类型参数

    如题,spring mvc直接提交Date类型参数会报错,400 bad request的错误.在controller里加上 @InitBinder protected void initBinder ...

  9. python3 安装 opencv3 (win10,64bit)

    python3只能安装opencv3  (python2安装opencv应该比python3安装的要简单,可参阅网上其他教程)   步骤参考http://stackoverflow.com/quest ...

  10. python装饰器精髓代码

    #!/usr/bin/env python #-*- coding:utf-8 -*- import time def foo(func): def inner(): print('fs...') f ...