HDX-MS data for VHL Apo/Drug/Ternary states
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF-X
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Benjamin Walters
PROVIDER: MSV000090905 | MassIVE | Wed Dec 14 21:03:00 GMT 2022
REPOSITORIES: MassIVE
Similar Datasets
Project description:These open source (.mzxml files) are processed using ExMS (a matlab program, ref 1) and are directly readable. ExMS produces these outfiles (.txt) which are then parsed and fitted using binomial decomposition to determine the number of carried deuterium at a given time point as indicated in the filenames. The all H file is used to define appropriate retention times as described in the original manuscript for the ExMS v1 program (ref 1). The general methodology used is described in ref 2, below.
REF 1
Kan, Z. Y., et al. (2011). "ExMS: data analysis for HX-MS experiments." J Am Soc Mass Spectrom 22(11): 1906-1915.
REF 2
Mayne, L., et al. (2011). "Many Overlapping Peptides for Protein Hydrogen Exchange Experiments by the Fragment Separation-Mass Spectrometry Method." J Am Soc Mass Spectrom 22(11): 1898-1905.
2020-10-26 | MSV000086368 | MassIVE
Project description:These open source (.mzxml files) are processed using ExMS (a matlab program, ref 1) and are directly readable. ExMS produces these outfiles (.txt) which are then parsed and fitted using binomial decomposition to determine the number of carried deuterium at a given time point as indicated in the filenames. The all H file is used to define appropriate retention times as described in the original manuscript for the ExMS v1 program (ref 1). The general methodology used is described in ref 2, below.
Note - a hard drive failure caused us to lose a subset of the raw files for the unbound time points. The outfiles produced by ExMS are available for inspection for all of the time points as these were not lost (they include XICs) as are all of the raw files that we were able to recover.
REF 1
Kan, Z. Y., et al. (2011). "ExMS: data analysis for HX-MS experiments." J Am Soc Mass Spectrom 22(11): 1906-1915.
REF 2
Mayne, L., et al. (2011). "Many Overlapping Peptides for Protein Hydrogen Exchange Experiments by the Fragment Separation-Mass Spectrometry Method." J Am Soc Mass Spectrom 22(11): 1898-1905.
2020-10-26 | MSV000086370 | MassIVE
Project description:To investigate the participation of deafness genes in the genetic program of the superior olivary complex (SOC), a prominent auditory brainstem center, we performed a comparative genome-wide microarray based gene expression analysis of the rat SOC and the rat brain at postnatal days (P) P4 and P25. Data were validated by qRT-PCR. Statistical analyses revealed 912 oligos up-regulated in the SOC at P4 and 1609 at P25. A total of 453 oligos were up-regulated in the SOC at both developmental stages. Subsequently, a list of 138 transcripts associated with hearing-impairment was extracted from publically available databases and literature. 26 of these transcripts were present in SOC-related gene signature lists, whereas only 11 were present in brain-related gene signature lists. Furthermore, in all 3 SOC-related gene signature lists, transcripts associated with hearing impairment were significantly enriched. Finally, there was a tendency of the SOC-related genes to map to human deafness loci with unknown etiology. Altogether, our study identified a tight genetic link between the SOC-related genetic program and deafness genes.
2013-07-31 | GSE16764 | GEO
Project description:To investigate the participation of deafness genes in the genetic program of the superior olivary complex (SOC), a prominent auditory brainstem center, we performed a comparative genome-wide microarray based gene expression analysis of the rat SOC and the rat brain at postnatal days (P) P4 and P25. Data were validated by qRT-PCR. Statistical analyses revealed 912 oligos up-regulated in the SOC at P4 and 1609 at P25. A total of 453 oligos were up-regulated in the SOC at both developmental stages. Subsequently, a list of 138 transcripts associated with hearing-impairment was extracted from publically available databases and literature. 26 of these transcripts were present in SOC-related gene signature lists, whereas only 11 were present in brain-related gene signature lists. Furthermore, in all 3 SOC-related gene signature lists, transcripts associated with hearing impairment were significantly enriched. Finally, there was a tendency of the SOC-related genes to map to human deafness loci with unknown etiology. Altogether, our study identified a tight genetic link between the SOC-related genetic program and deafness genes. The genome wide expression during the postnatal development of the SOC and the brain was investigated at two different time points: at postnatal (P) day 4 (before hearing onset) and at P25 (after hearing onset). Samples were hybridized onto two color platforms. At least 6 up to nine biological replicates per sample were performed.
2013-07-31 | E-GEOD-16764 | biostudies-arrayexpress
Project description:The superior olivary complex (SOC) is an essential auditory brainstem structure involved in sound localization. In order to identify the genetic program underlying its maturation, we profiled the transcriptome of the rat SOC at postnatal days (P)0, P4, P16, and P25, using genome-wide microarrays (41,012 sequences). Differences in gene expression between two consecutive stages were highest between P4 versus P16 (3.6%), but dropped to 0.06% between P16 versus P25. To identify SOC-related genetic programs, we also profiled the brain at P4 and P25. Differentially expressed sequences between SOC and brain almost doubled from P4 (4.4%) to P25 (7.6%). These datademonstrate considerable molecular specification around hearing onset, which is rapidly finalized. Prior to hearing onset, several transcription factors associated with the peripheral auditory system were up-regulated, likely coordinating auditory system development. Additionally, serotonin-related genes and crystalline-gamma subunits were highly expressed. The molecular repertoire of mature neurons was sculpted by SOC-related up- and down-regulation of several protein categories, among which voltage-gated channels and myelination were prominent. Comparison with the brain revealed a significant enrichment of deafness-related oligos in the SOC-related genetic program (26 in the SOC, only 11 in the brain). Furthermore, 29 out of 453 SOC-related oligos mapped within 19 genetic intervals associated with hearing impairment. Together, we identified sequential genetic programs in the SOC, thereby pinpointing candidates which may guide its development and ensure proper function. The enrichment of deafness-related genes in the SOC may have implications for restoring hearing, as central auditory structures might be more severely affected than previously appreciated. This SuperSeries is composed of the SubSeries listed below. The genome wide expression during the postnatal development of the SOC was investigated at four different time points: at postnatal (P) day 0, P4, P16 and P25. Concerning the brain, P4 and P25 were used. Samples were hybridized onto two color platforms. At least 6 up to nine biological replicates per sample were performed.
2013-07-31 | E-GEOD-36470 | biostudies-arrayexpress
Project description:The superior olivary complex (SOC) is an essential auditory brainstem structure involved in sound localization. In order to identify the genetic program underlying its maturation, we profiled the transcriptome of the rat SOC at postnatal days (P)0, P4, P16, and P25, using genome-wide microarrays (41,012 sequences). Differences in gene expression between two consecutive stages were highest between P4 versus P16 (3.6%), but dropped to 0.06% between P16 versus P25. To identify SOC-related genetic programs, we also profiled the brain at P4 and P25. Differentially expressed sequences between SOC and brain almost doubled from P4 (4.4%) to P25 (7.6%). These datademonstrate considerable molecular specification around hearing onset, which is rapidly finalized. Prior to hearing onset, several transcription factors associated with the peripheral auditory system were up-regulated, likely coordinating auditory system development. Additionally, serotonin-related genes and crystalline-gamma subunits were highly expressed. The molecular repertoire of mature neurons was sculpted by SOC-related up- and down-regulation of several protein categories, among which voltage-gated channels and myelination were prominent. Comparison with the brain revealed a significant enrichment of deafness-related oligos in the SOC-related genetic program (26 in the SOC, only 11 in the brain). Furthermore, 29 out of 453 SOC-related oligos mapped within 19 genetic intervals associated with hearing impairment. Together, we identified sequential genetic programs in the SOC, thereby pinpointing candidates which may guide its development and ensure proper function. The enrichment of deafness-related genes in the SOC may have implications for restoring hearing, as central auditory structures might be more severely affected than previously appreciated. This SuperSeries is composed of the SubSeries listed below.
2013-07-31 | GSE36470 | GEO
Project description:The superior olivary complex (SOC) is a prominent auditory brainstem center and represents one of the prime model systems to study the development of sensory circuits. We recently performed genome-wide microarray studies to analyze the SOC-related genetic program at postnatal day (P)4 and P25. Here, we extended this analysis by including two additional time points, P0 and P16. Data sets were validated by qRT-PCR. Statistical analysis were performed for the different developmental time points as well as with for differences between the SOC and our previously analyzed brain samples. This analysis revealed that after hearing-onset (P16 and P25), 918 oligos were up-regulated and 810 oligos down-regulated in the SOC compared to the two prehearing stages (P0 and P4). Of the up-regulated oligos, 530 were significantly higher expressed compared to the brain at P25. Concerning neurotransmission, SOC-related elevation was mainly observed for K+ channels, G-proteins, and myelination-related proteins, whereas Ca2+-related proteins showed a decreased expression. In the pre-hearing period, 47 oligos were up-regulated compared to the brain. Several of them were transcription factors, previously associated with other auditory structures, and might ensure coordinated development of peripheral and central auditory structures. Stage-specific comparison identified distinct genetic programs during development: Circuit formation/refinement at P4; myelination and circuit refinement/consolidation at P16; and neuroprotection at P25. Altogether, our study defines the genetic program of postnatal SOC development and provides strong functional candidates for various developmental processes. The genome wide expression during the postnatal development of the SOC was investigated at two different time points: at postnatal (P) day 0 (before hearing onset) and P16 (after hearing onset). Samples were hybridized onto two color platforms. At least 6 up to nine biological replicates per sample were performed.
2013-07-31 | E-GEOD-34003 | biostudies-arrayexpress
Project description:To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two independent experiments were carried out.
2019-09-04 | GSE117041 | GEO
Project description:Nuclear envelopes (NEs) and microsomal membranes (MMs) were isolated from HeLa cells infected or not with HSV-1 using well-established procedures as described in:
Wilkie GS, et al. (2011) Mol Cell Proteomics 10: M110 003129.
Korfali N, et al. (2010) Mol Cell Proteomics 9: 2571-2585.
Florens L, Korfali N, Schirmer EC (2008) Methods Mol Biol 432: 117-137.
Membrane pellets were denatured, reduced, alkylated then digested with endoproteinase LysC followed by trypsin. Peptides were analyzed by Multidimensional Protein Identification Technology (MudPIT) as described in:
Florens L, Washburn MP (2006) Methods Mol Biol 328: 159-175.
RAW files were extracted into ms2 file format using RawDistiller v. 1.0 as in:
Zhang, Y.; Wen, Z.; Washburn, M. P.; Florens, L. (2011) Anal Chem, 83, (24), 9344-51.
MS/MS spectra were queried for peptide sequence information using SEQUEST v.27 (rev.9) as in:
Eng J, McCormack A, Yates Jr (1994) J Am Soc Mass Spectrom 5: 976-989.
Results from different runs were compared using DTASelect and CONTRAST as in:
Tabb DL, McDonald WH, Yates JR (2002) J Proteome Res 1: 21-26.
To estimate relative protein levels, distributed normalized spectral abundance factors (dNSAFs) were calculated for each non-redundant protein as in:
Zhang Y, Wen Z, Washburn MP, Florens L (2010) Anal Chem 82: 2272-2281.
2016-07-05 | MSV000079886 | MassIVE
Project description:These are human urine samples from 4 healthy individuals. Cys residues were carbamidomethylated, proteins were digested with trypsin. Sample preparation and some of the data interpretation was described in: Pap, A.; Klement, E.; Hunyadi-Gulyas, E.; Darula, Z.; Medzihradszky, K. F. Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures. J. Am. Soc. Mass Spectrom. 2018, doi: 10.1007/s13361-018-1945-7.
Additional structures were reported: Darula, Z; Pap, A; Medzihradszky, K. F. Extended sialylated O-glycan repertoire of human urinary glycoproteins discovered and characterized using EThcD J. Prot. Res. 2018
2018-10-25 | MSV000083070 | MassIVE