Regulation of non ‐canonical proteins from diverse origins through the nonsense‐mediated mRNA decay pathway
This study investigates the impact ofUPF1-knockdown on the expression of non-canonical/mutant proteins, employing proteogenomic to exploreUPF1 role within the NMD pathway. Additionally, we conducted a comprehensive pan-cancer analysis ofUPF1 expression and evaluatedUPF1 expression in Triple-Negative Breast Cancer (TNBC) tissuein-vivo. Our findings reveal thatUPF1-knockdown leads to increased translation of non-canonical/mutant proteins, particularly those originating from retained-introns, pseudogenes, long non-coding RNAs, and unannotated transcript biotypes. Moreover, our analysis demonstrates elevatedUPF1 expression in ...
Source: Proteomics - February 14, 2024 Category: Biochemistry Authors: Parthiban Periasamy,
Craig Joseph,
Adrian Campos,
Sureka Rajandran,
Christopher Batho,
James E. Hudson,
Haran Sivakumaran,
Hitesh Kore,
Keshava Datta,
Joe Yeong,
Harsha Gowda Tags: RESEARCH ARTICLE Source Type: research
Analysis of secreted small extracellular vesicles from activated human microglial cell lines reveals distinct pro ‐ and anti‐inflammatory proteomic profiles
AbstractMicroglia are a specialized population of innate immune cells located in the central nervous system. In response to physiological and pathological changes in their microenvironment, microglia can polarize into pro-inflammatory or anti-inflammatory phenotypes. A dysregulation in the pro-/anti-inflammatory balance is associated with many pathophysiological changes in the brain and nervous system. Therefore, the balance between microglia pro-/anti-inflammatory polarization can be a potential biomarker for the various brain pathologies. A non-invasive method of detecting microglia polarization in patients would have pr...
Source: Proteomics - February 12, 2024 Category: Biochemistry Authors: Xueming Niu,
Zhen Zhang,
Quan Zhou,
Alain Wuethrich,
Richard Lobb,
Matt Trau Tags: RESEARCH ARTICLE Source Type: research
Pharmaco ‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G
This study provides a pharmaco-phosphoproteomic profile of D816V- and V560G-mutant KIT cells, which reveals novel therapeutic strategies that may be applicable to a range of cancers. (Source: Proteomics)
Source: Proteomics - February 10, 2024 Category: Biochemistry Authors: Heather C. Murray,
Kasey Miller,
Matthew D. Dun,
Nicole M. Verrills Tags: DATASET BRIEF Source Type: research
An AI ‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi
AbstractThis Dataset Brief describes the computational prediction of protein structures for the ctenophoreMnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through theMnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and th...
Source: Proteomics - February 9, 2024 Category: Biochemistry Authors: R. Travis Moreland,
Suiyuan Zhang,
Sofia N. Barreira,
Joseph F. Ryan,
Andreas D. Baxevanis Tags: DATASET BRIEF Source Type: research
Assessing the precision of a detergent ‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics
AbstractDetergent-based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent-based workflow for quantitative proteomics, we herein evaluate the precision of a bottom-up sample preparation strategy incorporating cartridge-based protein precipitation with organic solvent to deplete SDS. The variance of data-independent acquisition (SWATH-MS) data was isolated from sample preparation error by modelling...
Source: Proteomics - February 2, 2024 Category: Biochemistry Authors: Jessica L. Nickerson,
Hugo Gagnon,
Peter D. Wentzell,
Alan A. Doucette Tags: RESEARCH ARTICLE Source Type: research
Top ‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms
This study highlights the potential of top-down TIMS-MS/MS for conducting enzymatic assays at the intact protein level and, more generally, for separation and identification of intact isomeric proteoforms and precise PTM localization. (Source: Proteomics)
Source: Proteomics - January 29, 2024 Category: Biochemistry Authors: Francis Berthias,
Nurg ül Bilgin,
Jasmin Mecinović,
Ole N. Jensen Tags: RESEARCH ARTICLE Source Type: research
iDVEIP: A computer ‐aided approach for the prediction of viral entry inhibitory peptides
In this study, we introduce a groundbreaking in silico approach that leverages bioinformatics analysis and machine learning to characterize and identify novel VEIPs. Cross-validation results demonstrate the efficacy of a model combining sequence-based features in predicting VEIPs with high accuracy, validated through independent testing. Additionally, an EI type model has been developed to distinguish peptides specifically acting as Eis from AVPs with alternative activities. Notably, we present iDVEIP, a web-based tool accessible athttp://mer.hc.mmh.org.tw/iDVEIP/, designed for automatic analysis and prediction of VEIPs. E...
Source: Proteomics - January 24, 2024 Category: Biochemistry Authors: Hui ‐Ju Kao,
Tzu‐Hsiang Weng,
Chia‐Hung Chen,
Yu‐Chi Chen,
Kai‐Yao Huang,
Shun‐Long Weng Tags: RESEARCH ARTICLE Source Type: research
Analyzing domain features of small proteins using a machine ‐learning method
In this study, the InterPro tool and the maximum correlation method were utilized to analyze functional domains of SPs. The purpose was to identify important functional domains that can indicate the essential differences between small and large protein sequences. First, the small and large proteins were represented by their functional domains via a one-hot scheme. Then, the MaxRel method was adopted to evaluate the relationships between each domain and the target variable, indicating small or large protein. The top 36 domain features were selected for further investigation. Among them, 14 were deemed to be highly related t...
Source: Proteomics - January 23, 2024 Category: Biochemistry Authors: ShiJian Ding,
HuiPing Liao,
FeiMing Huang,
Lei Chen,
Wei Guo,
KaiYan Feng,
Tao Huang,
Yu ‐Dong Cai Tags: RESEARCH ARTICLE Source Type: research
