E104v2 Tryptase Antibody Epitope Mapping
Ontology highlight
ABSTRACT:
INSTRUMENT(S): MZXML (Originally collected with a thermo orbitrap)
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Bob Lazarus Henry Maun Benjamin Walters JT Koerber
PROVIDER: MSV000086370 | MassIVE | Mon Oct 26 17:12:00 GMT 2020
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. 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.
2022-12-14 | MSV000090905 | 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. 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 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: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 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.
2013-07-31 | GSE34003 | 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.
2013-07-31 | GSE16764 | GEO
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:Leishmania are protists (class: Kinetoplastida) with a single multifunctional flagellum, which forms a canonical motile 9+2 microtubule axoneme in the promastigote forms. Deletion of gene CFAP44 (LmxM.14.1430) caused a reduction in promastigote motility (Beneke et al., PLoS Pathogens, 2019; accepted). To study the changes in protein composition in CFAP44 deficient axonemes, flagellar skeletons were isolated from CFAP44 knockout mutants and the parental cell line L. mex Cas9 T7 (Beneke et al., R Soc Open Sci. 2017; 4(5):170095) using a modified version of the method by Robinson et al., (Methods Enzymol. 1991; 196:285-99). Liquid chromatography tandem mass spectrometry and a label-free quantitation method (SINQ; Trudgian et al., 2011, Proteomics 10.1002) were used to identify proteins enriched in each fraction. This PRIDE upload contains .RAW and .XML files, as well as the SINQ quantification output file “SINQ_raw_data”. XML files are named SUB9810; MSS11680. .RAW files are structured as follows: “CFAP44 mutants: Qex01_SVH_180422_TomBeneke_B29_F_001”; “Cas9 T7 parentals: Qex01_SVH_180422_TomBeneke_Cas9_F_005”.
2020-01-20 | PXD014077 | Pride
Project description:This study explores the profiles of genes expressed during conditional differentiation of inner ear hair cell precursors in vitro. The cell line UB/OC-1 was derived from mouse embryonic organs of Corti (Rivolta et al, Proc. R. Soc. Lond. B 265: 1595-1603, 1998) and it can be induced to differentiate upon a temperature shift. The study has been replicated in two separate populations of cells, named Exp A and Exp B. Exp A includes daily time points from 0 to 9 days, then 11 and 14 days. Exp B includes days 0, 2, 4, and 9. The manuscript associated to this work is Rivolta et al., Genome Research 12(7):1091-1099, 2002. Keywords: time-course
2002-07-08 | GSE36 | GEO