Peptides from archeological chicken eggshell
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Galliformes (ncbitaxon:8976) Gallus Gallus (ncbitaxon:9031)
SUBMITTER: 
Carli Peters Robert Sprengler Kristine Korzow Richter
PROVIDER: MSV000088794 | MassIVE | Mon Feb 07 11:32:00 GMT 2022
SECONDARY ACCESSION(S): PXD031493
REPOSITORIES: MassIVE
Similar Datasets
Project description:Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching. Jurkat T-cell mRNA was analyzed on an Illumina HiSeq2000. ~80 million paired end reads (2x200bp, ~350bp lengths) were collected.
2013-05-17 | E-GEOD-45428 | biostudies-arrayexpress
Project description:Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching.
2013-05-17 | GSE45428 | GEO
Project description:MS/MS spectra of archaeological (Oncorhynchus) and modern (Salmo salar) bone collagen.
2019-04-15 | MSV000083687 | MassIVE
Project description:We performed a retrospective study on CSF from 20 DMT-naïve MS patients to investigate the correlation between intrathecal immune proteins and clinical MS phenotype.
2024-09-25 | GSE256426 | GEO
Project description:Lipopolysaccharides (LPS) are cell wall components of gram-negative bacteria and endotoxins that cause inflammation and sickness in vertebrate animals. Our objective to identify the plasma proteomic changes in an avian model of inflammation. Chickens were treated with either saline or LPS and the blood was collected 24 hours after injection. The pooled plasma samples were depleted of high abundant proteins, analyzed by Matrix assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography–tandem mass spectrometry (LC-MS/MS). MALDI-TOF analyses showed an increase in fibrinogen beta derived peptide and decrease in apolipoprotein AII- isoform X1 derived peptide in LPS samples. Label free quantitation of LC-MS/MS spectra revealed an increase in alpha-1 acid glycoprotein, chemokine-CCLI10, and cathelicidin-2 and decrease in interferon stimulated gene-12-2 in the LPS group. These differentially expressed proteins are associated with inflammation, cytokines, immunomodulation, and defense which are useful as candidate biomarkers of infection and inflammation.
2016-08-09 | PXD003335 | Pride
Project description:Accurate postmortem estimation of breastfeeding status for archaeological or forensic neonatal remains is difficult. Confident identification of milk-specific proteins associated with these remains, would provide direct evidence of breastmilk consumption. We used liquid chromatography coupled to tandem mass spectrometry (MS) to confidently identify beta-lactoglobulin-1 (LGB1) and whey acidic protein (WAP), major whey proteins associated with a neonatal dog (Canis lupus familiaris) skeleton (430–960 cal AD), from an archaeological site in Hokkaido, Japan. The age at death of the individual was estimated to be approximately two weeks after birth. Protein residues extracted from rib and vertebra fragments were analyzed and identified by matching tandem MS spectra against the dog reference proteome. A total of 200 dog protein groups were detected and at least 1 peptide from canine LGB1 and two peptides from canine WAP were confidently identified. These milk proteins most probably originated from the mother’s breastmilk, ingested by the neonate just before it died. We suggest the milk diffused outside the digestive apparatus during decomposition, and by being absorbed into the bones, it partially preserved. The result of this study suggests that proteomic analysis can be used for postmortem reconstruction of the breastfeeding status at the time of death of neonatal mammalian, by analyzing their skeletal archaeological remains. This method is also applicable to forensic and wildlife studies.
2019-09-09 | PXD014657 | Pride
Project description:We retrospectively investigated sera, obtained from 47 patients after the complete cure of liver cancer, using follow-up proteome analysis for 8 years, and found a protein, whose expression increased over time, peaked at the definitive diagnosis of bone metastases by bone scintigraphy, and tapered after the start of subsequent treatment. Fractions obtained by the reverse-phase HPLC of this protein were digested with trypsin and examined by LC-MS/MS analysis. The data were analyzed with a Mascot database search. As a result, the mass of fragment 576-628 of the C-terminal region of alpha-fibrinogen precursor was 5,805, which corresponded to that of the target peak. On the other hand, the mass of region 576-629 (with Val at the C-terminal) was 5,904, a mass value 99 higher than the target peak. This corresponds to a peak detected in the serum sample at a mass value 100 higher than the target peak. This peak with a mass value 100 higher was the same as the target peak in terms of chromatographic behavior, indicating that this peak had a protein sequence similar to that of the target peak. The isoelectric point (pI) of the fragment of region 576-628 was 8.07. This is consistent with the fact that the target peak indicates the behavior of a basic material in ion exchange. Thus, we concluded that the target peak 5,813 was a fragment of C-terminal region 576-628 of the alpha-fibrinogen precursor.
2017-12-16 | GSE43105 | GEO
Project description:Host Defence Peptides and derived peptides are promising classes of antimicrobial and immunomodulatory lead compounds. For this purpose we examined whether chicken cathelicidin-2 (CATH-2)-derived peptides modulate the function and inflammatory response of avian immune cells. Using a chicken macrophage cell line (HD11) we found that full-length CATH-2 dose-dependently induced transcription of chemokines CXCLi2/IL-8, MCP-3 and CCLi4/RANTES, but not of pro-inflammatory cytokine IL-1?. In addition, CATH-2 efficiently inhibited IL-1? and nitric oxide production by HD11 cells induced by different sources of lipopolysaccharides (LPS). N-terminal truncated CATH-2 derived peptides maintained the capacity to selectively induce chemokine transcription, but despite their high LPS affinity several analogs lacked LPS-neutralizing capacity. Substitution of phenylalanine residues by tryptophan introduced endotoxin neutralization capacity in inactive truncated CATH-2 derived peptides. In contrast, amino acid substitution of phenylalanine by tyrosine abrogated endotoxin neutralization activity of CATH-2 analogs. These findings support a pivotal role for aromatic residues in peptide-mediated endotoxin neutralization by CATH-2 analogs and were shown to be independent of LPS affinity. The capacity to modulate chemokine production and dampen endotoxin-induced pro-inflammatory responses in chicken immune cells implicates that small CATH-2 based peptides could serve as leads for the design of CATH-2 based immunomodulatory anti-infectives.
| S-EPMC4743981 | biostudies-literature
Project description:The KRAS peptide library is a part of our larger effort to understand peptide variants in shotgun proteomics. Herein, the interest is in discrimination of homologous peptides---a problem related to detection of peptide variants. The dataset contains MS/MS spectra of 400 synthetic peptides of form LVVVGA-XX-VGK. Each peptide is measured in separate LC-MS/MS run, thus the actual peptide for each dataset is known. In summary, the dataset contains annotated spectra of homologous peptides and can be used for development and optimization of peptide detection methods.
2021-11-25 | PXD013421 | Pride
Project description:Currently, evaluation of quality semen is based on traditional in vitro sperm tests as measures of motility, viability and acrosomic reaction. However, the results are not always well correlated with real male fertility. In the present study, we evaluated Intact Cell MALDI-TOF Mass Spectrometry (ICM-MS) method as diagnostic molecular tool to substitute in vitro tests in order to phenotype semen with more robustness. For that, we investigated a large male population of known fertility that included two highly different genetic lines (meat and egg laying lines). Our optimized ICM-MS-based method through automation and the construction of fertility-predictive mathematical models was able to discriminate individuals on their reproductive capacity in the two lines studied. Furthermore, we showed a better diagnostic accuracy than traditional in vitro sperm quality tests and demonstrated that differential markers presenting a high discriminating power between fertile and subfertile sperm cells in sperm were implicated in fertility processes. To characterize m/z peaks observed in ICM-MS spectra, we performed high-throughput top-down protein identification of sperm cell extracts. Therefore, we identified more than 75% of the m/z peaks, revealing that these comprises mostly degradation products of testis-specific proteins implicated in the most important functional pathways in sperm cells such as energy metabolism and structure/movement.
2016-04-11 | PXD002768 | Pride