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ProteomicsEvaluating sequence alignment for metaproteomics applications
This dataset was utilized to assess the performance of a novel de novo metaproteomics pipeline, which performs sequence alignment of de novo sequences from complete metaproteomics experiments. Traditionally, metaproteomics data annotation relies on database searching that requires sample-specific da...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-10-10 | PXD050548 | Pride
Microbial proteomics Sequence alignment De novo sequencing Metaproteomics 
TranscriptomicsCollagen-binding C-type natriuretic peptide enhances chondrogenesis and osteogenesis
To enhance local drug delivery and therapeutic efficacy, we developed a novel synthetic protein by fusing a collagen-binding domain (CBD) to C-type natriuretic peptide (CNP), termed CBD-CNP. CBD-CNP localized to collagen-rich tissues and promoted bone elongation.
ORGANISM(S): Mus musculus 
2025-12-05 | E-MTAB-16154 | biostudies-arrayexpress
TranscriptomicsRNA sequencing of HEK293T cells expressing peptide 9J10, a 14-3-3 interacting peptide
We investigated the transcriptome profile of HEK293T cells transfected with a plasmid encoding 9J10, a peptide isolated in a phenotypic screen from a library of peptides derived from bacterial and archaeal genomes. The peptide was identified in a screen for FOXO3a reactivation and has been shown to...
ORGANISM(S): Homo sapiens 
2021-05-28 | E-MTAB-10161 | biostudies-arrayexpress
ProteomicsHyPep: An Open-Source Software for Identification and Discovery of Neuropeptides using Sequence Homology Searching
Neuropeptides are a class of endogenous peptides that have key regulatory roles in biochemical, physiological, and behavioral processes. Mass spectrometry analyses of neuropeptides often rely on protein informatics tools for database searching and peptide identification. As neuropeptide databases ar...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2023-02-02 | PXD037058 | Pride
Peptidomics Hypep Homology Mass spectrometry Peptide De novo sequencing Fdr Neuropeptide 
UnknownGapped sequence alignment using artificial neural networks: application to the MHC class I system.
Not available
S-EPMC6402319 | biostudies-literature
TranscriptomicsRNA-seq GLV6 overexpression during lateral root initiation in Arabidopsis thaliana
The goal of this experiment was to identify the downstream targets of the GOLVEN6 peptide signaling pathway in Arabidopsis thaliana, specifically during lateral root initiation. Using an estradiol inducible GLV6 overexpression construct in wildtype and rgi1rgi5 double mutant (mutant in receptors for...
ORGANISM(S): Arabidopsis thaliana 
2022-02-13 | E-MTAB-10891 | biostudies-arrayexpress
ProteomicsLL10000 hybridization
The screening of a previously reported fluorescein labelled 10,000 member PNA encoded peptide library allowed information on the interaction between the peptide-ligands and the cell surface receptors to be extracted, identified new peptide ligands for cell surface receptors, and gave crucial informa...
ORGANISM(S): Homo sapiens 
2011-11-08 | E-MEXP-3104 | biostudies-arrayexpress
GenomicsEffect of a KRAS peptide nucleic acid clamp on the Ion Torrent sequencing protocol
To test whether the addition of a peptide nucleic acid (PNA) clamp, which binds WT KRAS at codon 12, can increase the efficacy of mutation detection for KRASG12D within a targeted NGS setting. We tested the effect of clamping the wild-type KRAS sequence in a reference standard (Tru-Q 7, 1.3% Tier fr...
ORGANISM(S): Homo sapiens 
2017-07-29 | E-MTAB-5718 | biostudies-arrayexpress
ProteomicsLibrary-1 Hybridization
High-throughput microarray analysis of a 1296-member PNA-encoded peptide library for the identification of short homing-peptides as tools for selective delivery into specific cell types.
ORGANISM(S): Homo sapiens 
2011-08-10 | E-MEXP-3101 | biostudies-arrayexpress
UnknownGibbsCluster: unsupervised clustering and alignment of peptide sequences.
Not available
S-EPMC5570237 | biostudies-literature
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