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ProteomicsExopeptidase assisted N- and C-terminal proteome sequencing
Due to mechanisms such as alternative translation starts or proteolytic processing, in-vivo proteoforms do not necessarily correspond to those encoded in the genome. Therefore, knowledge of protein termini is an indispensable prerequisite to understand protein function. Sequencing of protein N- and ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-10-15 | PXD015612 | Pride
Protein sequencing Proteomics Terminomics 
TranscriptomicsThe mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteom...
ORGANISM(S): Homo sapiens 
2012-06-01 | E-GEOD-38356 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by high throughput sequencing of HeLa human cancer cell line
Illumina single-end sequencing of Hela_2 (HeLa cell line). While the number and identity of proteins expressed in a single human cell type is currently unknown, this fundamental question can be addressed by advanced mass spectrometry (MS)-based proteomics. On-line liquid chromatography coupled to hi...
ORGANISM(S): Homo sapiens 
2011-11-12 | E-MTAB-823 | biostudies-arrayexpress
TranscriptomicsThe mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [protein occupancy profiling]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteom...
ORGANISM(S): Homo sapiens 
2012-06-01 | E-GEOD-38355 | biostudies-arrayexpress
ProteomicsIntegrated with Proteome-sequencing, bulk RNA-sequencing and Single cell RNA-sequencing to identify potential biomarkers in different grades of intervertebral disc degeneration
We selected humann intervertebral disc samples to perform proteomics analysis. There were 1 case of grade I , 1 case of grade II, 3 cases of grade Ⅲ and 3 cases of grade Ⅳ according to Pfirrmann classfication. RNA seqencing analysis and single-cell RNA sequencing were integrated with proteomics data...
ORGANISM(S): Homo sapiens (Human) 
2023-05-10 | PXD040593 | Pride
Intervertebral disc degeneration Proteome-sequencing 
TranscriptomicsThe mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [PAR-CLIP]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteom...
ORGANISM(S): Homo sapiens 
2012-06-01 | E-GEOD-38201 | biostudies-arrayexpress
TranscriptomicsTowards a reference human platelet transcriptome: evaluation of inter-individual correlations and of its relationship with a platelet proteome
For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes’ relationship is with the platelet proteome. We generated RNA-seq pro-files of the long R...
ORGANISM(S): Homo sapiens 
2015-01-20 | E-GEOD-50858 | biostudies-arrayexpress
ProteomicsApplication of de novo sequencing to large-scale complex proteomics datasets
Dependent on concise, pre-defined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference datab...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2016-01-12 | PXD003317 | Pride
De novo peptide sequencing Ms/ms Large-scale computational analysis Yeast Bos Mass spectrometry Proteomics 
TranscriptomicsRNAseq and Lariat sequencing of different S. pombe growth conditions
We performed lariat sequencing to profile the diversity of spliced RNA lariats in S. pombe identify annotated and alternate introns. Three different growth conditions were used to grow S. pombe wt and S. pombe Δdbr1. Lariat sequencing of the Δdbr1 strains and RNAseq of the wt and Δdbr1 strains were ...
ORGANISM(S): Schizosaccharomyces pombe 
2015-09-03 | E-GEOD-68345 | biostudies-arrayexpress
ProteomicsMS-based sequencing of the anti-FLAG-M2 antibody
We demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by LC-MS/MS in a bottom-up fashion. Furthermore, we apply a dual fragmentation...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-01-11 | PXD023419 | Pride
Antibody Stepped hcd Ethcd De novo sequencing 
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