BN_Chymo_Velos
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Velos
ORGANISM(S): Rattus Norvegicus
SUBMITTER: Henk van den Toorn
PROVIDER: PAe004321 | PeptideAtlas | 2013-12-31
REPOSITORIES: PeptideAtlas
Similar Datasets
Project description:BN-Lx_liver, LysC, LTQ Orbi Velos
2013-12-31 | PAe004326 | PeptideAtlas
Project description:BN-Lx_liver, Trypsin, LTQ Orbi Velos
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Project description:BN-Lx_liver, GluC, LTQ Orbi Velos
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Project description:BN-Lx_liver, AspN, LTQ Orbi Velos
2013-12-31 | PAe004324 | PeptideAtlas
Project description:The product ion scans were acquired with a 2.0-unit isolation width and a normalized collision energy of 35 in an LTQ-Orbitrap Velos Pro MS spectrometer (Orbitrap Velos Pro, Thermo Fisher Scientific, US).
2023-06-05 | PXD042745 |
Project description:In this project, we aim to pair-wise analyze the genomes, transcriptomes and proteomes of in-bred rats originating from two different genetic backgrounds. These two strains are Brown Norway (BN-Lx) and Spontaneously Hypertensive Rats (SHR). First, we re-sequenced the genomes for both BN and SHR rats, followed by RNA-seq and proteomics of their liver tissues. We then append novel predicted gene models, non-synonymous SNPs and INDELs (derived from genome re-sequencing), as well as transcript variants such as RNA-editing and alternative splicing (derived from RNA-seq) that can diversify existing protein sequences onto the ENSEMBL rat FASTA (Build 68) to build an enhanced database. For proteomics studies, equal amount of liver lysates were digested with trypsin, LysC, GluC, AspN and chymotrypsin and were individually fractionated with strong cationic exchange chromatography. Doubly- and triply-charged fractions were analyzed with an Triple-TOF 5600 with collision-activated dissociation (CAD); while electron-transfer dissociation (ETD) was applied for fractions containing triple charges and above with a LTQ-Orbitrap Velos. Data analysis: Peak List generation: For Wiff files generated from TripleTOF 5600, tandem MS spectra were de-isotoped, charge- deconvoluted and peak lists converted to Mascot generic format (MGF) files using AB Sciex Data Converter (version 1.1). For data generated from the LTQ-Orbitrap Velos, Raw files were converted to MGF files using Proteome Discoverer (version 1.3). The non-fragment filter was used to simplify ETD spectra and the Top N filter for the HCD spectra. Three MGF files were generated (one for HCD, one for ETD IT and one for ETD FT). The files with an orbitrap readout were deisotoped and charge de-convoluted. Database Searching: All MGF files were queried with Mascot search engine (version 2.3) via Proteome Discoverer version 1.3 (PD 1.3, Thermo Fisher) for submission. The spectra were searched against in-house database (NGS_COMBINED). One of the five different enzymes used (Trypsin/P, LysC/P, Chymotrypsin, GluC-DE and AspN_ambic) were selected for each file and up to 9 missed cleavages were allowed. Cysteine carbamidomethylation was set as fixed modification, and oxidation of methionine and acetylation of the N-term as variable modifications. Peptide tolerance was initially set to 50 ppm and the MS/MS tolerance was set to 0.1 Da (for TOF readout), 0.02 Da (orbitrap readout) and 0.5 Da (ion trap readout). All peptide-spectrum matches (PSMs) were evaluated with Percolator for validation. We classified each PSM based on their q value. For proteins identification, we used set a high stringency filter of q = 0 (0% FDR). For peaks lists that do not yield any peptide matches, we exported them with PD 1.3 for further analysis. De novo search with PEAKS: Unassigned peak lists that are exported were re-analyzed with another software suite i.e. PEAKS Studio (version 6.0). The identification workflows is as follows. Peak lists were first filtered with a quality value of 0.65 as suggested by the manufacturer followed by de novo spectra interpretation. In this step, both peptide tolerance and MS/MS tolerance were set according to MASCOT search. To broaden the search space for these unassigned spectra, we additionally set de-amidation of asparagine and glutamine, and pyro-glu from glutamic acid and glutamine as variable modifications, on top of the other modifications indicated above. Maximum allowed variable PTM per peptide was set to 3. Finally de novo interpreted PSMs were submitted to PEAKS DB database matching, this time allowing semi-enzymatic specificity and a maximum cleavages per peptide of 2. Database used was set to NGS_COMBINED. FDR was estimated using decoy-fusion. The genomics and transcriptomics data are already deposited in the respective EBI repositories. Some of these data are derived from an already published manuscript. For the genomics data (from: Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel by Simonis et al PMID:22541052) DNA data in Sequence Read Archive (SRA): BN-Lx genome: ERP001355 http://www.ebi.ac.uk/ena/data/view/ERP001355, SHR genome: ERP001371, BN reference genome: ERP000510, http://www.ebi.ac.uk/ena/data/view/ERP000510. RNA data in ArrayExpress: BN-Lx and SHR fragment RNA-seq data: E-MTAB-1029 http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1029, BN-Lx and SHR paired-end RNA-seq data: to be submitted.
2013-11-29 | PXD000131 | Pride
Project description:Endogenous peptides are extracted and seperated with nLC with HCD fragmentation on a LTQ Orbitrap Velos. Data analysis was done with Mascot and MaxQuant
2016-05-03 | PXD002431 | Pride
Project description:Leiomyoma with bizarre nuclei (LM-BN) is a rare variant of leiomyoma with a benign clinical course. In contrast, leiomyosarcoma (LMS) is a high-grade, malignant neoplasm characterized by high recurrence rates and poor survival. While LM-BN and LMS show distinct morphologies, they share similar immunoprofile and molecular alterations, with both considered “DNA unstable”. Rare cases of LM-BN associated with LMS have been reported, however the histogenesis and molecular relationship between these two tumors remains unclear. In this study, we assessed 11 cases of LMS arising in conjunction with LM-BN and further analyzed the clinical, histologic, and molecular characteristics of these lesions. Tumor slides were examined by histology and immunohistochemistry to confirm the presence of both LMS and LM-BN components. LM-BN and LMS had similar p16 and p53 IHC patterns, but LMS had a higher Ki-67 index and lower ER/PR expression. Digital image analysis based on nuclear and cytologic features revealed spatial relationships between LMS and LM-BN. Genomic copy number alteration (CNA) demonstrated the same clonal origin of LMS from existing LM-BN through conserved copy number alterations. LMS harbored higher CNAs and frequent loss of the TP53, Rb, PTEN, and/or CDKN2A genomic region than LM-BN, indicative of tumor progression. Spatial transcriptome analysis defined uniquely expressed gene signatures in a geographical distribution, demonstrating molecular evidence of regional cell specific differences of LM-BN and LMS. Mutation analysis of large oncogenic panel revealed many shared functional gene alterations in both LM-BN and LMS, but more highly enriched in LMS. Our findings for the first time suggest that a subset of LMS arise from an existing LM-BN.
2024-11-05 | GSE270865 | GEO
Project description:Integrin adhesion complexes were isolated from mouse fibroblasts treated with or without blebbistatin. Adhesion complexes were resolved by SDS-PAGE, digested with trpysin and analysed by LC-MS/MS using an LTQ Velos mass spectrometer
2015-10-19 | PXD000018 | Pride
Project description:SHR_liver, GluC, LTQ Orbi Velos
2013-12-31 | PAe004337 | PeptideAtlas