The intrinsic and regulated proteomes of barley seeds in response to fungal infection

Kerr, Edward D.; Phung, Toan K.; Caboche, Christopher H.; Fox, Glen; Platz, G. J.; Schulz, Benjamin L.

doi:10.1016/j.ab.2019.06.004

Cited by 49 publications

(40 citation statements)

References 33 publications

(35 reference statements)

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“…2 and Supplementary Table S1) [23][24][26][27][28][29][30][31] . The organic solvent used here was a 1:1 mixture of methanol and acetone [44][45] . All methods have been previously shown to eliminate detergents from diverse samples [24][25][46][47][48] , and organic solvent precipitation [61][62][63][64] and FASP 56-60 have been previously used to prepare bioreactor supernatant samples for LC-MS/MS proteomics.…”

Section: Resultsmentioning

confidence: 99%

S-Trap eliminates cell culture media polymeric surfactants for effective proteomic analysis of mammalian cell bioreactor supernatants

Zacchi

Recinos

Otte

et al. 2020

Preprint

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AbstractProteomic analysis of bioreactor supernatants can inform on cellular metabolic status, viability, and productivity, as well as product quality, which can in turn help optimize bioreactor operation. Incubating mammalian cells in bioreactors requires the addition of polymeric surfactants such as Pluronic F68, which reduce the sheer stress caused by agitation. However, these surfactants are incompatible with mass spectrometry proteomics and must be eliminated during sample preparation. Here, we compared four different sample preparation methods to eliminate polymeric surfactants from filtered bioreactor supernatant samples: organic solvent precipitation; filter-assisted sample preparation (FASP); S-Trap; and single-pot, solid-phase, sample preparation (SP3). We found that SP3 and S-Trap substantially reduced or eliminated the polymer(s), but S-Trap provided the most robust clean-up and highest quality data. Additionally, we observed that SP3 sample preparation of our samples and in other published datasets was associated with partial alkylation of cysteines, which could impact the confidence and robustness of protein identification and quantification. Finally, we observed that several commercial mammalian cell culture media and media supplements also contained polymers with similar mass spectrometry profiles, and we suggest that proteomic analyses in these media will also benefit from the use of S-Trap sample preparation.

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Section: Resultsmentioning

confidence: 99%

S-Trap eliminates cell culture media polymeric surfactants for effective proteomic analysis of mammalian cell bioreactor supernatants

Zacchi

Recinos

Otte

et al. 2020

Preprint

Self Cite

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“…For analysis of peptide modifications, the abundance of each form within a peptide family was normalised to the summed abundance for all detected forms within the peptide family. For determining time- and temperature-dependent changes, statistical analysis was done by reformatting the PeakView output using python script (https://github.com/bschulzlab/reformatMS) 17 , and significant differences in protein and peptide abundances between stages were determined using MSstats (2.4) in R (21), with a significance threshold of p = 0.05 as previously implemented 1 .…”

Section: Methodsmentioning

confidence: 99%

Benchtop micro-mashing: high-throughput, robust, experimental beer brewing

Kerr

Caboche

Josh

et al. 2020

Preprint

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Brewing science is undergoing a renaissance with the use of modern analytical chemistry and microbiology techniques. However, these modern analytical tools and techniques are not necessarily aligned with the scale and scope of brewing science. In particular, brewing processes can be time consuming, ingredient intensive, and require specialised technical equipment. These drawbacks compound with the need for appropriate numbers of replicates for adequately powered experimental design. Here, we describe a micro-scale mash method that can be performed using a common laboratory benchtop shaker/incubator, allowing for high throughput mashing and easy sample replication for statistical analysis. Proteomic profiles at both the protein and peptide levels were consistent between the 1 mL micro-mash and a 23 L Braumeister mash. The experimental flexibility offered by our micro-mash method allowed us to investigate the effects of altered mash parameters on the beer brewing proteome.

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“…Sequential window acquisition of all theoretical mass spectra (SWATH)-MS relative quantitative proteomics [34] data was analyzed with PeakView v2.1 (SCIEX). Statistical analyses were performed using MSstats in R as previously described [35,36] to identify differentially abundant (DA) proteins with a p value lower than 0.05 adjusted for multiple testing [37].…”

Section: Methodsmentioning

confidence: 99%

Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)

Tahir

Nguyen

Schulz

et al. 2019

Genes

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High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus–pituitary–ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.

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The intrinsic and regulated proteomes of barley seeds in response to fungal infection

Cited by 49 publications

References 33 publications

S-Trap eliminates cell culture media polymeric surfactants for effective proteomic analysis of mammalian cell bioreactor supernatants

S-Trap eliminates cell culture media polymeric surfactants for effective proteomic analysis of mammalian cell bioreactor supernatants

Benchtop micro-mashing: high-throughput, robust, experimental beer brewing

Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)

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