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Label-free LC-MS/MS analysis of silky fowl egg yolk

ABSTRACT: The proteomic profiles of silky fowl egg yolk (SFEY) and Leghorn egg yolk (LEY) were analysed by bottom-up label-free liquid chromatography tandem-mass spectrometry (LC-MS/MS), aiming to provide a theoretical basis for understanding the proteomic and biological differences between the two yolks and further develop the nutritional and biomedical value of silky fowl eggs.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Gallus Gallus (chicken)

TISSUE(S): Egg

SUBMITTER: Rao Wu

LAB HEAD: Xiaoying Zhang

PROVIDER: PXD032674 | Pride | 2022-05-20

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	LEY__B1_.raw	Raw
	LEY__B2_.raw	Raw
	LEY__B3_.raw	Raw
	SFEY__A1_.raw	Raw
	SFEY__A2_.raw	Raw

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1 - 5 of 9

Publications

Label-Free LC-MS/MS Analysis Reveals Different Proteomic Profiles between Egg Yolks of Silky Fowl and Ordinary Chickens.

Wu Rao R Chen Chen C Zhang Xiaoying X

Foods (Basel, Switzerland) 20220402 7

The proteomic profiles of Silky fowl egg yolk (SFEY) and Leghorn egg yolk (LEY) were analyzed by bottom-up label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). From a total of 186 identified proteins, 26 proteins were found significantly differentially abundant between two yolks, of which, 19 were up-regulated and 7 were down-regulated in SFEY, particularly, vitelline membrane outer layer protein 1, transthyretin and ovoinhibitor were up-regulated by 26, 25, and 16 times, respec ...[more]

PMID: 35407122

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Yolk-deprived Caenorhabditis elegans secure brood size at the expense of competitive fitness

Project description:Oviparous animals support reproduction via the incorporation of yolk as a nutrient source into the eggs. In Caenorhabditis elegans, however, yolk proteins seem dispensable for fecundity, despite constituting the vast majority of the embryonic protein pool and acting as carriers for nutrient-rich lipids. Here, we used yolk protein-deprived C. elegans mutants to gain insight into the traits that may yet be influenced by yolk rationing. We show that massive yolk provisioning confers a temporal advantage during embryogenesis, while also increasing early juvenile body size and promoting competitive fitness. Opposite to species that reduce egg production under yolk deprivation, our results indicate that C. elegans relies on yolk as a fail-safe to secure offspring survival, rather than to maintain offspring numbers.

2023-04-12 | PXD041110 | Pride

Proteomic portraits of egg quality in zebrafish (Danio rerio)

Project description:Humans and animals have problems producing eggs with high embryo developmental competence, but the causes of poor egg quality are usually unknown. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading model for vertebrate development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were used to create pooled or replicated sample sets subjected to different levels of fractionation before LC-MS/MS. Obtained spectra were searched against a custom zebrafish proteome database and detected proteins were annotated, categorized and quantified based on their normalized spectral counts. Manual and automated enrichment analyses were highly confirmative, showing that good and poor quality eggs have disparate proteomes. Proteins involved in protein synthesis, energy metabolism, and lipid metabolism, and certain vitellogenin products were strikingly underrepresented in poor quality eggs. Poor quality eggs also had significantly higher representation of proteins related to immune system and endosome/lysosome functioning, oncogenes, and apoptosis, as well as lectins and egg envelope proteins. Quantitative comparisons of highly abundant proteins revealed 9 candidate egg quality markers warranting further study. In conclusion, the zebrafish egg proteome appears to be linked to embryo developmental potential, a phenomenon that begs further investigation.

2017-11-27 | PXD005137 | Pride

Proteomic portraits of egg quality in zebrafish (Danio rerio)

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Deep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database

Project description:Mass spectrometry based proteomics enables the global identification and quantification of proteins and their post-translational modifications in complex biological samples. Proteomic analysis requires a complete and accurate reference set of proteins, and is therefore largely restricted to model organisms with sequenced genomes. Here, we demonstrate the feasibility of deep genome-free proteomics using a reference proteome derived from heterogeneous mRNA data. We identify more than 11k proteins with 99% confidence from the unfertilized, X. laevis egg and estimate protein abundance with approximately two-fold precision. Our reference database outperforms the provisional gene models based on genomic DNA-sequencing and references generated by other methods. Surprisingly, we find that many proteins in the egg lack mRNA support and many of these proteins are found in blood or liver, suggesting that they are taken up from the blood plasma, together with yolk, during oocyte growth and maturation, potentially contributing to early embryogenesis. To facilitate proteomics in non-model organisms, we make our platform available as an online resource which converts heterogeneous mRNA data into a protein reference set. Thus, we demonstrate the feasibility and power of genome-free proteomics while shedding new light on embryogenesis in vertebrates.

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Cryopreservation and egg yolk medium alter the proteome of ram spermatozoa

Project description:Cryopreservation causes significant lethal and sub-lethal damage to spermatozoa. In order to improve freezing outcomes, a comprehensive understanding of sub-lethal damage is required. Cryopreservation induced changes to sperm proteins have been investigated in several species, but few have employed currently available state of the art, data independent acquisition mass spectrometry (MS) methods. We used the SWATH LC-MS method to quantitatively profile proteomic changes to ram spermatozoa following exposure to egg yolk and cryopreservation. Egg yolk contributed 15 proteins to spermatozoa, including vitellogenins, apolipoproteins and complement component C3. Cryopreservation significantly altered the abundance of 51 proteins. Overall, 27 proteins increased (e.g. SERPINB1, FER) and 24 proteins decreased (e.g. CCT subunits, CSNK1G2, TOM1L1) in frozen thawed ram spermatozoa, compared to fresh spermatozoa. Chaperones constituted 20% of the proteins lost from spermatozoa following cryopreservation. These alterations may interfere with both normal cellular functioning and the ability of frozen thawed spermatozoa to appropriately respond to stress. This is the first study to apply SWATH mass spectrometry techniques to characterise proteins contributed by egg yolk based freezing media and to profile cryopreservation induced proteomic changes to ram spermatozoa.

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Life history shapes variation in egg composition in a wild passerine

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Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells

Project description:Background: Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. The aim of this study was to identify different types of small ncRNAs particularly piRNAs, and the role of piRNA pathway genes in the protection of chicken primordial germ cells (PGCs). Results: At first, we performed next-generation sequencing to identify ncRNAs in chicken PGCs, and we performed ab initio predictive analysis to identify putative piRNAs in PGCs. Then, we examined the expression of three repetitive sequence-linked piRNAs and 14 genic-transcript-linked piRNAs along with their linked genes using real-time PCR. All piRNAs and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known piRNA pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using siRNAs. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative piRNA-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs. Conclusions: Our results increase the understanding of PGC-expressed ncRNAs and the role of piRNA pathway genes in the protection of germ cells. Small ncRNA expression profiling in SSEA-1 positive PGCs, SSEA-1 negative gonadal stromal cells (GSCs), Stage X blastoderms, and chicken embryonic fibroblast (CEFs)

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