HX mapping of the binding interface between a DCP and murine LRRC-15
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF-X
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
Benjamin Walters
PROVIDER: MSV000100920 | MassIVE | Fri Feb 20 07:07:00 GMT 2026
REPOSITORIES: MassIVE
Similar Datasets
Project description:Filetypes:
DATE_PeptideReference_MSMS.csv - contains the identity of peptides and expected retention times to be tracked over the experiment.
These are determined from an MSMS experiment, see *MSMS* in the filename. Use file dates for file associations.
Files are included for experiments involving APO FBXO22 +/- BRM or BRM+Ligand. All data uses the FBXO22.fasta sequence file.
Raw Mass Spectrum Files:
There are three types, all have been converted to MZXML from Thermo .RAW format.
-One MSMS file (producing the identifications to be tracked through the experiment)
-Pool files - ms-only files of unlabeled peptides run on the day of the experiment.
-Timeseries Files - ms-only files containing deuterated timepoints.
*Note, there may be two sets of apo files as experiments may be collected at different dates and a new apo dataset is often collected.
Search Engine Files:
ExMS 2 software used to produce "finaltables" result files: PMID: 31082210, DOI: 10.1021/acs.analchem.9b01682
A unique identifier is included in each type of result file, provided below.
*MSMS* - file contains the identity of peptides and expected retention times to be tracked over the experiment.
These are determined from an MSMS experiment, see *MSMS* in the filename. Use file dates for file associations.
*Pool* - Output from ExMS2 on reference ms-only unlabeled data
*sec* - Timepoint from the experiment.
Other information is provided in the filename of each result file, note that the name of the raw mass spectrum file used to produce the result file is included in the result file name.
2025-02-18 | MSV000097140 | MassIVE
Project description:HDX data is included in this partial submission.
Raw Mass Spectrum Files:
There are three types, all have been converted to MZXML from Thermo .RAW format.
-Pool files - ms-only files of unlabeled peptides run on the day of the experiment.
-Timeseries Files - ms-only files containing deuterated timepoints.
*Note, there may be two sets of apo files as experiments may be collected at different dates and a new apo dataset is often collected.
Search Engine Files:
ExMS 2 software used to produce "finaltables" result files: PMID: 31082210, DOI: 10.1021/acs.analchem.9b01682
A unique identifier is included in each type of result file, provided below.
*Pool* - Output from ExMS2 on reference ms-only unlabeled data
*sec* - Timepoint from the experiment.
Other information is provided in the filename of each result file, note that the name of the raw mass spectrum file used to produce the result file is included in the result file name.
2025-06-12 | MSV000098179 | MassIVE
Project description:Some triple-negative breast cancer (TNBC) patients evaluated as Miller-Payne 4 with ypN0 after neoadjuvant chemotherapy (NACT) who have better prognosis should avoid escalation of therapy. We aim to identify these patients through evaluating pretherapeutic spatial distributions of immunophenotypes. Our retrospective study in patients with TNBC assessed as Miller-Payne grade 4/5 with ypN0 showed that Miller-Payne 4 with ypN0 group had poorer 5-year disease-free survival (DFS, 63.8% vs 83.0%, p=0.003) and the 5-year overall survival (OS, 71.0% vs 85.5%, p=0.007) than Miller-Payne 5 with ypN0 group. High TILs were significantly associated with better DFS and OS in patients with Miller-Payne 4 and ypN0 (both p=0.016). Spatially, detected by multiplexed ion beam imaging by time of flight combined with proteomics, tumors assessed as Miller-Payne 4 and ypN0 with good prognosis exhibited an inflamed phenotype, with dominant CD8+ T cells on tumor center, few scattered CD68+ myeloid-derived cells far away from T cells, and deposit of increased activated molecules of lymphocyte. While those with poor prognosis presented excluded phenotype, with few CD8+ T cells restricted to invasive margin and a high density of CD14+CD68+CD11c+ myeloid cells. A good classifier model based on 29 spatial immunophenotypes was established by the random forest algorithm (AUC=0.975), for identifying patients with Miller-Payne 4 and ypN0 who had favorable prognosis. We also observed similar signatures in patients with Miller-Payne 5 and ypN0. Taken together, spatial immunophenotypes may assess the prognosis in TNBC patients with Miller-Payne 4 and ypN0 after NACT.
2023-07-08 | PXD029186 | Pride
Project description:Two high throughput transcript sequencing methods, Digital Gene Expression (DGE) Tag Profiling and RNA-Seq, were used to compare the transcriptional profiles in wild-type (cv. Clark standard, CS) and a mutant (cv. Clark glabrous, i.e., trichomeless or hairless, CG) soybean isoline that carries the dominant P1 allele. DGE data and RNA-Seq data were mapped to the cDNAs (Glyma models) predicted from the reference soybean genome, Williams 82. Extending the model length by 250 bp at both ends resulted in significantly more matches of authentic DGE tags indicating that many of the predicted gene models are prematurely truncated at the 5’ and 3’ UTRs. The genome-wide comparative study of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. One highly-expressed gene, Glyma04g35130, in wild-type soybean was of interest as it has high homology to the cotton gene GhRDL1 gene that has been identified as being involved in cotton fiber initiation and is a member of the BURP protein family. Sequence comparison of Glyma04g35130 among Williams 82 with our sequences derived from CS and CG isolines revealed various SNPs and indels including addition of one nucleotide C in the CG and insertion of ~60 bp in the third exon of CS that causes a frameshift mutation and premature truncation of peptides in both lines as compared to Williams 82. 2 samples examined: Clark standard (wild type) and Clark glabrous (soybean hairless mutant)
2011-10-25 | E-GEOD-33155 | biostudies-arrayexpress
Project description:Two high throughput transcript sequencing methods, Digital Gene Expression (DGE) Tag Profiling and RNA-Seq, were used to compare the transcriptional profiles in wild-type (cv. Clark standard, CS) and a mutant (cv. Clark glabrous, i.e., trichomeless or hairless, CG) soybean isoline that carries the dominant P1 allele. DGE data and RNA-Seq data were mapped to the cDNAs (Glyma models) predicted from the reference soybean genome, Williams 82. Extending the model length by 250 bp at both ends resulted in significantly more matches of authentic DGE tags indicating that many of the predicted gene models are prematurely truncated at the 5’ and 3’ UTRs. The genome-wide comparative study of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. One highly-expressed gene, Glyma04g35130, in wild-type soybean was of interest as it has high homology to the cotton gene GhRDL1 gene that has been identified as being involved in cotton fiber initiation and is a member of the BURP protein family. Sequence comparison of Glyma04g35130 among Williams 82 with our sequences derived from CS and CG isolines revealed various SNPs and indels including addition of one nucleotide C in the CG and insertion of ~60 bp in the third exon of CS that causes a frameshift mutation and premature truncation of peptides in both lines as compared to Williams 82.
2011-10-25 | GSE33155 | GEO
Project description:Wei et al. performed microarray analysis to explore the metabolism change in diabetes and RYGB surgery treated rats.
2023-08-01 | GSE156908 | GEO
Project description:Collagen deposition is a key process during idiopathic pulmonary fibrosis (IPF); however, little is known about the dynamics of collagen formation during disease development. Tissue samples of early stages of human disease are not readily available and it is difficult to identify changes in collagen content, since standard collagen analysis does not distinguish between 'old' and 'new' collagen. Therefore, the current study aimed to (i) investigate the dynamics of new collagen formation in mice using bleomycin-induced lung fibrosis in which newly synthesized collagen was labelled with deuterated water and (ii) use this information to identify genes and processes correlated to new collagen formation from gene expression analysis. Lung fibrosis was induced in female C57BL/6 mice by bleomycin instillation and sacrificed. Animals were sacrificed at 1 to 5 weeks after fibrosis induction. Collagen synthesized during the week before sacrifice was labelled with deuterium by providing mice with deuterated drinking water. After sacrifice, lung tissue was collected for microarray analysis, determination of new collagen formation, and histology. Deuterated water labelling showed a strong increase in new collagen formation already during the first week after fibrosis induction and a complete return to baseline at five weeks. Correlation of new collagen formation data with gene expression data revealed fibrosis specific processes, of which proliferation was an unexpected one. This was confirmed by measuring cell proliferation and collagen synthesis simultaneously using deuterated water incorporation. Furthermore, new collagen formation strongly correlated with gene expression of e.g. elastin, tenascin C, MMP-14, lysyl oxidase, and type V collagen. These data demonstrate, using a novel combination of technologies, that proliferation and extracellular matrix production are correlated to the core process of fibrosis, i.e. the formation of new collagen. In addition, it identified genes directly correlated to fibrosis, thus providing more insight into the aetiology of IPF.
2013-05-26 | GSE37635 | GEO
Project description:A previous paper considered the problems that presently limit the hydrogen exchange-mass spectrometry (HX-MS) method for studying the biophysical and functional properties of proteins. Many of these problems can be overcome by obtaining and analyzing hundreds of sequentially overlapping peptide fragments that cover the protein many times over (Mayne et al. J. Am. Soc. Mass Spectrom. 2011: 10.1007/s13361-011-0235-4). This paper describes a computer program called ExMS that furthers this advance by making it possible to efficiently process crowded mass spectra and definitively identify and characterize these many peptide fragments. ExMS automatically scans through high resolution MS data to find the individual isotopic peaks and isotopic envelopes of a list of peptides previously identified by MS/MS. It performs a number of tests to ensure correct identification in spite of peptide overlap in both chromatographic and mass spectrometric dimensions and possible multi-modal envelopes due to static or dynamic structural heterogeneity or HX EX1 behavior. The program can automatically process data from many sequential HX time points with no operator intervention at the rate of ~2 sec per peptide per HX time point using desktop computer equipment, but it also provides for rapid manual checking and decision when ambiguity exists. Additional subroutines can provide a step by step report of performance at each test along the way and parameter adjustment, deconvolute isotopic envelopes, and plot the time course of single and multi-modal H-D exchange. The program will be available on an open source basis at: http://HX2.med.upenn.edu/download.html.
| S-EPMC3398505 | biostudies-literature
Project description:Despite the widespread use of MS for hydrogen/deuterium exchange measurements, no systematic, large-scale study has been conducted to compare the observed exchange rates in unstructured peptides to the chemical exchange rates predicted from NMR-derived values. Consequently, how peptide properties and post-translational modifications influence exchange rates remain unknown. In this study, we sought to test the accuracy of predicted values by performing hydrogen exchange measurements on whole cell digests to generate an unbiased dataset of approximately 1100 peptides derived from naturally-occurring protein sequences. A remarkable 97% of observed exchange rates of peptides are within two-fold of predicted values. Using fully deuterated controls, we found that for approximately 50% of the peptides, the amino acid sequence and, consequently, the intrinsic exchange rate, are the primary contributors to back exchange. A meta-analysis of the remaining peptides physicochemical properties revealed multiple features that contribute either positively or negatively to back exchange discrepancies. Employing our workflow for comparable measurements on synthetic peptide mixtures containing post-translational modifications, and their unmodified counterparts, we show that lysine acetylation has a strong effect on the observed exchange rate, whereas serine/threonine phosphorylation does not. Our automated workflow enables high-throughput determination of exchange rates in peptide mixtures with diverse properties.
2024-04-10 | MSV000094510 | MassIVE