《蛋白质组研究杂志》出版内容涵盖全球蛋白质分析和功能的各个方面，包括基因组学、时空蛋白质组学、代谢组学和代谢组学、临床和农业蛋白质组学的动态方面，以及包括生物信息学在内的方法学进展。主题和重点是通过不同类型的“组学”之间的协同作用，对生命科学采取多学科方法。

The Journal of Proteome Research covers various aspects of global protein analysis and functionality, including genomics, spatiotemporal proteomics, metabolomics, and dynamic studies in clinical and agricultural proteomics, as well as methodological advancements including bioinformatics. The journal focuses on a multidisciplinary approach to life sciences through the synergy of different types of 'omics'.

《Journal of Proteome Research》涵盖全球蛋白质分析和功能的各个方面，包括基因组学、时空蛋白质组学、代谢组学、临床和农业蛋白质组学的动态研究，以及生物信息学等方法学的进展。该期刊的主题和重点是通过不同类型的“组学”之间的协同作用，采用多学科的方法来研究生命科学。

Journal of Proteome Research

Efficient and reproducible sample preparation is a prerequisite for any robust and sensitive quantitative bottom-up proteomics workflow. Here, we performed an independent comparison between single-pot solid-phase-enhanced sample preparation (SP3), filter-aided sample preparation (FASP), and a commercial kit based on the in-StageTip (iST) method. We assessed their performance for the processing of proteomic samples in the low μg range using varying amounts of HeLa cell lysate (1–20 μg of total protein). All three workflows showed similar performances for 20 μg of starting material. When handling sample sizes below 10 μg, the number of identified proteins and peptides as well as the quantitative reproducibility and precision drastically dropped in case of FASP. In contrast, SP3 and iST provided high proteome coverage even in the low μg range. Even when digesting 1 μg of starting material, both methods still enabled the identification of over 3000 proteins and between 25 000 and 30 000 peptides. On average, the quantitative reproducibility between experimental replicates was slightly higher in case of SP3 (R2 = 0.97 (SP3); R2 = 0.93 (iST)). Applying SP3 toward the characterization of the proteome of FACS-sorted tumor-associated macrophages in the B16 tumor model enabled the quantification of 2965 proteins and revealed a "mixed" M1/M2 phenotype.

Malte Sielaff

Jörg Kuharev

Toszka Bohn

Jennifer Hahlbrock

Tobias Bopp

Stefan Tenzer

Ute Distler

Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

Post-translational modifications are crucial in regulating biological functions across both prokaryotes and eukaryotes. In

Guibin Wang

Linxin Chen

Juanqi Lian

Lanqing Gong

Feng Tian

Yuqian Wang

Xiangmin Lin

Yanling Liu

Proteomic Insights into the Regulatory Role of CobQ Deacetylase in Aeromonas hydrophila

蛋白质组学揭示CobQ脱乙酰酶在嗜水气单胞菌中的调控作用

Epidemiological data from patients undergoing radiotherapy for thoracic tumors clearly show the damaging effect of ionizing radiation on cardiovascular system. The long-term impairment of heart function and structure after local high-dose irradiation is associated with systemic inflammatory response, contraction impairment, microvascular damage, and cardiac fibrosis. The goal of the present study was to investigate molecular mechanisms involved in this process. C57BL/6J mice received a single X-ray dose of 16 Gy given locally to the heart at the age of 8 weeks. Radiation-induced changes in the heart transcriptome and proteome were investigated 40 weeks after the exposure. The omics data were analyzed by bioinformatics tools and validated by immunoblotting. Integrated network analysis of transcriptomics and proteomics data elucidated the signaling pathways that were similarly affected at gene and protein level. Analysis showed induction of transforming growth factor (TGF) beta signaling but inactivation of peroxisome proliferator-activated receptor (PPAR) alpha signaling in irradiated heart. The putative mediator role of mitogen-activated protein kinase cascade linking PPAR alpha and TGF beta signaling was supported by data from immunoblotting and ELISA. This study indicates that both signaling pathways are involved in radiation-induced heart fibrosis, metabolic disordering, and impaired contractility, a pathophysiological condition that is often observed in patients that received high radiation doses in thorax.

Vikram Subramanian

Ingar Seemann

Juliane Merl-Pham

Stefanie M. Hauck

Fiona A. Stewart

Michael J. Atkinson

Soile Tapio

Omid Azimzadeh

Role of TGF Beta and PPAR Alpha Signaling Pathways in Radiation Response of Locally Exposed Heart: Integrated Global Transcriptomics and Proteomics Analysis

局部暴露心脏辐射反应中TGF Beta和PPAR Alpha信号通路的作用：综合全局转录组学和蛋白质组学分析

Although tuberculosis (TB) has been the greatest killer due to a single infectious disease, pediatric TB is still hard to diagnose because of the lack of sensitive biomarkers. Metabolomics is increasingly being applied in infectious diseases. But little is known regarding metabolic biomarkers in children with TB. A combination of a NMR-based plasma metabolic method and classification and regression tree (CART) analysis was used to provide a broader range of applications in TB diagnosis in our study. Plasma samples obtained from 28 active TB children and 37 non-TB controls (including 21 RTIs and 16 healthy children) were analyzed by an orthogonal partial least-squares discriminant analysis (OPLS-DA) model, and 17 metabolites were identified that can separate children with TB from non-TB controls. CART analysis was then used to choose 3 of the markers, l-valine, pyruvic acid, and betaine, with the least error. The sensitivity, specificity, and area under the curve (AUC) of the 3 metabolites is 85.7% (24/28, 95% CI, 66.4%, 95.3%), 94.6% (35/37, 95% CI, 80.5%, 99.1%), and 0.984(95% CI, 0.917, 1.000), respectively. The 3 metabolites demonstrated sensitivity of 82.4% (14/17, 95% CI, 55.8%, 95.3%) and specificity of 83.9% (26/31, 95% CI, 65.5%, 93.9%), respectively, in 48 blinded subjects in an independent cohort. Taken together, the novel plasma metabolites are potentially useful for diagnosis of pediatric TB and would provide insights into the disease mechanism.

Lin Sun

Jie-qiong Li

Na Ren

Hui Qi

Fang Dong

Jing Xiao

Fang Xu

Wei-wei Jiao

Chen Shen

Wen-qi Song

A-dong Shen

Utility of Novel Plasma Metabolic Markers in the Diagnosis of Pediatric Tuberculosis: A Classification and Regression Tree Analysis Approach

新型血浆代谢标志物在儿童结核病诊断中的应用：分类与回归树分析方法

N-glycosylation of proteins is well known to occur at asparagine residues that fall within the canonical consensus sequence N-X-S/T but has also been identified at a small number of asparagine residues within N-X-C motifs, including the N491 residue of human serotransferrin. Here we report novel glycosylation sites within noncanonical consensus motifs, in the conformation N-X-C, based on mass spectrometry analysis of partially deglycosylated glycopeptide targets. Alpha-1-acid glycoprotein (A1AG) and serotransferrin (Tf) were observed for the first time to be N-glycosylated on asparagine residues within a total of six unique noncanonical motifs. N-glycosylation was initially predicted in silico based on the evolutionary conservation of the N-X-C motif among related mammalian species and demonstrated experimentally in A1AG from porcine, canine, and feline sources and in human serotransferrin. High-resolution liquid chromatography-tandem mass spectrometry was employed to collect fragmentation data of predicted GlcNAcylated peptides and to assign modification sites within N-X-C motifs. A combination of targeted analytical techniques that includes complementary mass spectrometry platforms, enzymatic digestions, and partial-deglycosylation procedures was developed to confirm the novel observations. Additionally, we found that A1AG in porcine and canine sources is highly N-glycosylated at a noncanonical motif (N-Q-C) based on semiquantitative multiple reaction monitoring analysis-the first report of an N-X-C motif exhibiting substantial N-glycosylation. Although reports of N-X-C motif N-glycosylation are relatively uncommon in the literature, this work adds to a growing list of glycoproteins reported with glycosylation at various forms of noncanonical motifs.

Mark S. Lowenthal

Kiersta S. Davis

Trina Formolo

Lisa E. Kilpatrick

Karen W. Phinney

Identification of Novel N-Glycosylation Sites at Noncanonical Protein Consensus Motifs

非经典蛋白质一致性基序中新发现的N-糖基化位点的鉴定

Metabolic rewiring is required for cancer cells to survive in harsh microenvironments and is considered to be a hallmark of cancer. Specific metabolic adaptations are required for a tumor to become invasive and metastatic. Cell division and metabolism are inherently interconnected, and several cell cycle modulators directly regulate metabolism. Here, we report that TBK1, which is a noncanonical IKK kinase with known roles in cell cycle regulation and TLR signaling, affects cellular metabolism in cancer cells. While TBK1 is reported to be overexpressed in several cancers and its enhanced protein level correlates with poor prognosis, the underlying molecular mechanism involved in the tumor-promoting role of TBK1 is not fully understood. In this study, we show a novel role of TBK1 in regulating cancer cell metabolism using combined metabolomics, transcriptomics, and pharmacological approaches. We find that TBK1 mediates the regulation of nucleotide and energy metabolism through aldo-keto reductase B10 (AKRB10) and thymidine phosphorylase (TYMP) genes, suggesting that this TBK1-mediated metabolic rewiring contributes to its oncogenic function. In addition, we find that TBK1 inhibitors can act synergistically with AKRB10 and TYMP inhibitors to reduce cell viability. These findings raise the possibility that combining these inhibitors might be beneficial in combating cancers that show elevated levels of TBK1.

Meenu Maan

Neha Jaiswal

Min Liu

Harold I. Saavedra

Srikumar P. Chellappan

Mainak Dutta

TBK1 Reprograms Metabolism in Breast Cancer: An Integrated Omics Approach

TBK1 重编程乳腺癌代谢：一种综合组学方法

Chronic dacryocystitis (CD) can result in severe complications and vision impairment due to ongoing microbial infections and persistent tearing. Tear fluid, which contains essential components vital for maintaining ocular surface health, has been investigated for its potential in the noninvasive identification of ocular biomarkers through metabolomics analysis. In this study, we employed UHPLC-MS/MS to analyze the tear metabolome of CD patients. UHPLC-MS/MS analysis of tear samples from CD patients revealed significant metabolic alterations. Compared with the control group, 298 metabolites were elevated, while 142 were decreased. KEGG pathway analysis suggested that these changes primarily affected arginine and proline metabolism, biosynthesis of amino acids, and phenylalanine biosynthesis in CD. Notably, 3-dehydroquinic acid, anthranilic acid, citric acid, and l-isoleucine emerged as potential biomarker candidates of CD with high diagnostic accuracy (AUC = 0.94). These findings suggest that tear fluid metabolism, particularly amino acid biosynthesis, plays a significant role in the pathogenesis of CD. Uncovering these metabolic products and pathways provides valuable insights into the mechanisms underlying CD and paves the way for the development of diagnostic tools and targeted therapies.

Shuai Ben

Qun Zheng

Ya Zhao

Jiao Xia

Wan Mu

Mudi Yao

Biao Yan

Qin Jiang

Tear Fluid-Based Metabolomics Profiling in Chronic Dacryocystitis Patients

慢性泪囊炎患者泪液代谢组学分析

Human plasma proteomic and glycoproteomic analyses have emerged as an alternate avenue to identify disease biomarkers and therapeutic approaches. However, the vast number of high-abundance proteins in plasma can cause mass spectrometry (MS) suppression, which makes it challenging to detect low-abundance proteins (LAP). Currently, immunoaffinity-based depletion methods and strategies involving nanomaterial protein coronas have been developed to remove high-abundance proteins (HAP) and enhance the depth of plasma protein identification. Despite these advancements, there is a lack of systematic comparison and evaluation of the qualitative and quantitative effects of different strategies on the human plasma proteome and glycoproteome. In this study, we evaluated the performance of four depletion methods including combinatorial peptide ligand libraries (CPLL), Top 2, Top 14, and the nanomaterial protein corona formed by magnetic nanoparticles (MN) in both plasma proteomics and

Huohuan Tian

Ze Tao

Wanli Zhang

Yuzhe Chen

Tao Su

Xinyuan Wang

Hao Yang

Hao Cai

Shuyun Liu

Yi Zhang

Yong Zhang

Comparative Proteomics and N-Glycoproteomics Reveal the Effects of Different Plasma Protein Enrichment Technologies

比较蛋白质组学和N-糖蛋白质组学揭示不同血浆蛋白质富集技术的影响

Prokaryotes and eukaryotes secrete extracellular vesicles (EVs) into the surrounding milieu to preserve and transport elevated concentrations of biomolecules across long distances. EVs encapsulate metabolites, DNA, RNA, and proteins, whose abundance and composition fluctuate depending on environmental cues. EVs are involved in eukaryote-to-prokaryote communication owing to their ability to navigate different ecological niches and exchange molecular cargo between the two domains. Among the different bacterium-host relationships, rhizobium-legume symbiosis is one of the closest known to nature. A crucial developmental stage of symbiosis is the formation of N

Paula Ayala-García

Irene Herrero-Gómez

Irene Jiménez-Guerrero

Viktoria Otto

Natalia Moreno-de Castro

Mathias Müsken

Lothar Jänsch

Marco van Ham

José-María Vinardell

Francisco Javier López-Baena

Francisco Javier Ollero

Francisco Pérez-Montaño

José Manuel Borrero-de Acuña

Extracellular Vesicle-Driven Crosstalk between Legume Plants and Rhizobia: The Peribacteroid Space of Symbiosomes as a Protein Trafficking Interface

豆科植物与根瘤菌间的胞外囊泡驱动交叉对话：共生体周细菌空间作为蛋白质运输界面

Atherosclerotic plaque rupture is a major cause of cardiovascular events. Plaque destabilization is associated with extracellular matrix (ECM) modification involving proteases which generate protein fragments with new N-termini. We hypothesized that rupture-prone plaques would contain elevated fragment levels, and their sequences would allow identification of active proteases and target proteins. Plaques from 21 patients who underwent surgery for symptomatic carotid artery stenosis were examined in an observational/cross-sectional study. Plaques were analyzed by liquid chromatography-mass spectrometry for the presence of N-terminal fragments. 33920 peptides were identified, with 17814 being N-terminal species. 5735 distinct N-terminal peptides were quantified and subjected to multidimensional scaling analysis and consensus clustering. These analyses indicated three clusters, which correlate with gross macroscopic plaque morphology (soft/mixed/hard), ultrasound classification (echolucent/echogenic), and the presence of hemorrhage/ulceration. Differences in the fragment complements are consistent with plaque-type-dependent turnover and degradation pathways. Identified peptides include signal and pro-peptides from synthesis and those from protein fragmentation. Sequence analysis indicates that targeted proteins include ECM species and responsible proteases (meprins, cathepsins, matrix metalloproteinases, elastase, and kallikreins). This study provides a large data set of peptide fragments and proteases present in plaques of differing stability. These species may have potential as biomarkers for improved atherosclerosis risk profiling.

Lasse G. Lorentzen

Karin Yeung

Auguste Zitkeviciute

Karen C. Yang-Jensen

Nikolaj Eldrup

Jonas P. Eiberg

Michael J. Davies

N-Terminal Proteomics Reveals Distinct Protein Degradation Patterns in Different Types of Human Atherosclerotic Plaques

N端蛋白质组学揭示不同类型人类动脉粥样硬化斑块中不同的蛋白质降解模式

Abbreviation	J. Proteome Res.
Journal Impact	3.64
Quartiles(Global)	BIOCHEMICAL RESEARCH METHODS(Q1)

ISSN	1535-3893, 1535-3907
h-index	183

Publication Information	Publisher: American Chemical Society，Publishing cycle: Bimonthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 2002，Proportion of original research papers: 97.97%，Self Citation Rate:10.50%， Gold OA Rate: 19.17%
Average review cycle	网友分享经验：平均3.0个月
Average recruitment ratio	网友分享经验：较难

Journal of Proteome Research

Journal Citation Format

A journal article with 1 author

A journal article with 2 authors

A journal article with 3 authors

A journal article with 5 or more authors

Books Citation Format

Thesis Citation Format

Web sites Citation Format

Patent Citation Format

Staying up late manually editing references? ivySCI automatically matches journals and helps you generate references with a single click.

Share Submission Experience