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ProteomicsSequence coverage by multiple reads in shotgun proteomics to validate single amino acid variants
Mass spectrometry-based shotgun proteomics is currently based on assigning matches between mass-spectra of protein fragments resulting from protease digestion and amino acid sequences predicted from nucleic acid sequences. At the same time, the method lacks reliability in identification of every sin...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-12-07 | MSV000088536 | MassIVE
MetabolomicsSex differences modulate blood metabolome profiles in Parkinson’s disease patients harbouring rare genetic variants

Background: Recent findings from our group indicate that sex differences in Parkinson's disease (PD) patients with idiopathic conditions or carrying pathogenic mutations significantly influence the blood occurrence of D and L-amino acids, lipids, antioxidants, and energy-related metabolites when ...

2026-06-26 | MTBLS12746 | MetaboLights
ProteomicsMulti-Stage Native UVPD-MS to Characterize Single Amino Acid Variants of Human Mitochondrial BCAT2
We report a multi-stage approach combining collisional activation and 193 nm ultraviolet photodissociation (UVPD) to characterize single amino acid variants of the human mitochondrial enzyme branched-chain amino acid transferase 2 (BCAT2), a protein implicated in chemotherapeutic resistance in gliob...
ORGANISM(S): Homo Sapiens (human) 
2018-05-31 | PXD009447 | JPOST Repository
ProteomicsProtein sequencing with single amino acid resolution discerns peptides that discriminate tropomyosin proteoforms
Protein variants of the same gene—proteoforms—can have high molecular similarity yet exhibit different biological functions. Thus, identifying unique peptides that unambiguously map to proteoforms can provide crucial biological insights. In humans, four human tropomyosin (TPM) genes produce similar ...
ORGANISM(S): Homo Sapiens 
2025-09-03 | PXD057918 | panorama
ProteomicsTargeted Detection of SARS-CoV-2 Protein Variants by Mass Spectrometry
COVID-19 vaccines are continuing to become more widely available, but accurate and rapid testing remains a crucial tool for slowing the spread of the SARS-CoV-2 virus. Although quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains the most prevalent testing methodology, nume...
ORGANISM(S): Homo sapiens (Human) 
2022-02-17 | PXD026795 | Pride
Nucleocapsid Sars-cov-2 Single amino acid protein variants Tandem mass spectrometry 
ProteomicsQuantifying mistranslation from alanine tRNA anticodon variants in S. cerevisiae
Transfer RNAs (tRNAs) maintain translational fidelity through strict charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic code is incorporated into a protein. Since al...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-10-02 | PXD038242 | Pride
Lc-msms Mistranslation Trna variants Yeast 
ProteomicsFunctional dissection of SPOP in the amino acid level reveals comprehensive functional landscape of variants on tumorigenesis
Numerous proteins display pleiotropic functions in different clinical contexts. However, molecular mechanism underlying such effects is rarely understood. The Speckle-type POZ protein (SPOP) is a typical example, showing tumor-suppressing or promoting effects due to different amino acid changes in d...
ORGANISM(S): Staphylococcus aureus 
2026-04-20 | PXD067557 | Pride
Yeast Tmt Spop 
ProteomicsSingle Amino-acid Polymorphisms of Human Gut Ecosystem
Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in gut microbial metagenome and host genome but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from non-synonymous SNPs can cause functional changes of ...
ORGANISM(S): Homo Sapiens 
PXD062661 |
GenomicsDNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus
DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus
PRJNA981519 | ENA
ProteomicsnextPP for chromosome-based proteomic research using neXtProt and GENCODE databases
In this study, we introduce a streamlined pipeline using customized and concatenated GENCODE and neXtProt databases with controlled false discovery rate (FDR) for finding GENCODE ASVs and missing proteins while mapping onto single amino acid variants (SAAVs) from Hippocampal dataset.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-07-25 | MSV000081385 | MassIVE
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