Non-cytotoxic xibalbin ICK variants from remipede crustaceans
Ontology highlight
ABSTRACT:
INSTRUMENT(S): ultrafleXtreme
ORGANISM(S): Xibalbanus Tulumensis
SUBMITTER: 
Benjamin-Florian Hempel
PROVIDER: MSV000091677 | MassIVE | Tue Apr 11 04:59:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:COVID-19 vaccines are continuing to become more widely available, but accurate and rapid testing remains a crucial tool for slowing the spread of the SARS-CoV-2 virus. Although quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains the most prevalent testing methodology, numerous tests have been developed that are predicated on detection of the SARS-CoV-2 nucleocapsid protein, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immunoassay based approaches. The continuing emergence of SARS-CoV-2 variants has complicated these approaches, as both qRT-PCR and antigen detection methods can be prone to missing viral variants. In this study, we describe a number of cases with COVID-19 where we were unable to detect the expected peptide targets from clinical nasopharyngeal swab samples that are typically identifiable in a targeted mass spectrometric assay. Whole genome sequencing revealed that single nucleotide polymorphisms in the gene encoding the viral nucleocapsid protein led to sequence variants that were not monitored in the targeted assay. Small modifications to the LC-MS/MS method ensured detection of the variants of the target peptide. Additional nucleocapsid variants were detected by performing bottom-up proteomic analysis of whole viral genome sequenced samples. This study demonstrates the importance of considering variants of SARS-CoV-2 in the assay design and highlights the flexibility of mass spectrometry-based approaches to detect variants as they evolve.
2022-02-17 | PXD026795 | Pride
Project description:CUD samples: TMT-proteomics using Orbitrap FusionTM LumosTM TribridTM Mass Spectrometer, TMT10plex (N=8 sample batch) or TMT16plex (2x N=16 sample batches) Isobaric Label Reagent (Thermo Fisher Scientific, Waltham, MA, USA), experiment type: bottom-up proteomics; data-dependent acquisition.
| EGAD00010002703 | EGA
Project description:Ctrl samples: TMT-proteomics using Orbitrap FusionTM LumosTM TribridTM Mass Spectrometer, TMT10plex (N=8 sample batch) or TMT16plex (2x N=16 sample batches) Isobaric Label Reagent (Thermo Fisher Scientific, Waltham, MA, USA), experiment type: bottom-up proteomics; data-dependent acquisition.
| EGAD00010002702 | EGA
Project description:Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technological face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry (MS)-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph™ Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, MS-based proteomics approach. We identify 184 protein-altering variants (PAVs) in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.
2023-12-19 | PXD042852 | Pride
Project description:We report the use of hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) to profile intact glycoform distributions of high mannose-type N-glycosylated proteins, using an industrially produced fungal lipase for the food industry as an example. We compared these results with conventional reversed phase LC-MS (RPLC-MS) and sodium dodecyl sulfate–polyacrylamide gel-electrophoresis (SDS-PAGE). HILIC appeared superior in resolving lipase heterogeneity, facilitating mass assignment of N-glycoforms and sequence variants. Fractions representing the four main HILIC elution bands for lipase were subjected to SDS-PAGE confirming that HILIC retention increased with the number of glycosylation sites (0-3) occupied. Additional bottom-up proteomic analysis of the fractions enabled the identification of the most abundant glycosylation sites. Compared to RPLC-MS, HILIC-MS provided a stronger reduction of the sample complexity delivered to the mass spectrometer, facilitating the assignment of the masses of glycoforms and sequence variants as well as increasing the number of glycoforms detected (69 more proteoforms, 177% increase). The HILIC-MS method required relatively short analysis time (< 30 min), in which over 100 glycoforms were distinguished. We suggest that HILIC-MS can be used to characterize bioengineering processes aimed at steering protein glycoform expression as well as to check the consistency of product batches.
2020-05-04 | PXD016215 | Pride
Project description:Postcopulatory sexual selection is recognized as a key driver of reproductive trait evolution, including the machinery required to produce endogenous nuptial gifts. Despite the importance of such gifts, the molecular composition of the non-gametic components of male ejaculates and their interactions with female reproductive tracts remain poorly understood. During mating, male Photinus fireflies transfer to females a spermatophore gift manufactured by multiple reproductive glands. Here we combined transcriptomics of both male and female reproductive glands with proteomics and metabolomics to better understand the synthesis, composition and fate of the spermatophore in the common Eastern firefly, Photinus pyralis. Our transcriptome of male glands revealed up-regulation of proteases that may enhance male fertilization success and activate female immune response. Using bottom-up proteomics we identified 208 functionally annotated proteins that males transfer to the female in their spermatophore. Targeted metabolomic analysis also provided the first evidence that Photinus nuptial gifts contain lucibufagin, a firefly defensive toxin. The reproductive tracts of female fireflies showed increased gene expression for several proteases that may be involved in egg production. This study offers new insights into the molecular composition of male spermatophores, and extends our understanding of how nuptial gifts may mediate postcopulatory interactions between the sexes.
2016-12-22 | MTBLS362 | MetaboLights
Project description:The degree to which alternative RNA splicing influences the function and structure of voltage gated calcium channel (VGCC) splice variants is poorly understood. Here we used long-read RNA-sequencing to catalog rat Cacna1e (Cav2.3) splice variants, and computationally prioritize which are likely to impact channel function. We sequenced Cacna1e transcripts from rat thalamus using Oxford Nanopore sequencing yielding the structure of 2,110 Cacna1e splice variants. Of these, up to 154 had the potential encode for a functional channel based on predicted amino acid sequences. Our analysis revealed a total of 31 cassette splicing events (in various combinations) potentially affecting channel function, with three cassette exons appreciably expressed and conserved.
2025-07-03 | GSE295903 | GEO
Project description:Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technological face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry (MS)-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph™ Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, MS-based proteomics approach. We identify 184 protein-altering variants (PAVs) in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.
2024-10-31 | MSV000096270 | MassIVE
Project description:Lon protease is a global regulator in bacteria, affecting biofilm formation, antibiotic resistance, toxin-antitoxin complexes and proteolysis of damaged proteins. This study uses bottom-up proteomics to identify Klebsiella pneumoniae proteins with altered secretion patterns in the absence of lon and provide insight into Lon mediation of the extracellular environment.
2024-11-01 | PXD057415 | Pride