La tabacologie

Ghaemmaghami, F.

doi:10.1051/978-2-7598-2142-6

Cited by 3 publications

(11 citation statements)

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“…The proteins with validated peptides are primarily high-quantity proteins, particularly those above 10 000 molecules/cell. As the reported quantity 18 decreases, fewer detected proteins have at least one quantitative peptide (Figure 2a,b). We compared the peptides determined to be quantitative by matrix-matched calibration curves with the peptides determined to be quantitative by a more conventional synthetic peptide approach, 19 which chose candidate peptides prior to quantitative assessment and then produced paired QConCat standards for each of the candidates.…”

Section: Resultsmentioning

confidence: 98%

“…The type of matrix-matched material used for a given reference material should be chosen based on practicality. With cell culture reference materials, culturing in heavy media to incorporate heavy isotopes is feasible; however, for biofluids where it is not feasible to incorporate the heavy isotope by culturing, 18 O digestion can be used to incorporate heavy isotopes into the matrix-matched material. Each calibration curve point in the dilution series has the same total protein concentration, composed of some ratio of the reference and matrix-matched material (Figure 1a) spanning several orders of magnitude (Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…Ghaemmaghami et al affinity-tagged the protein-coding regions in yeast and reported the protein abundances in molecules-per-cell for 4102 proteins, 3869 of which could be quantified above 50 molecules/cell. 18 Using data-independent acquisition mass spectrometry (DIA-MS), 13 we detected 24 400 peptides from 2870 of the proteins they quantified in the reference yeast proteome (Figure 2a,b). Using matrix-matched calibration curves to assess the quantitative accuracy of the detected peptides, we found that half of the detected proteins had at least one quantitative peptide (1427 proteins; 8630 peptides) (Figure S2).…”

Section: Resultsmentioning

confidence: 99%

“…For the CSF reference material, we chose a commercially available pool of healthy donor CSF (Golden West Biologicals, Inc.), which we prepared following conventional protocols. For the CSF matrix-matched material, we performed a second enzymatic digest in the presence of 18 O-enriched water. This reaction preferentially exchanges one or both oxygens at the C-terminus of the peptide with 18 O, shifting the peptides by 2 or 4 mass units via incorporation of one or two 18 O atoms.…”

Section: Resultsmentioning

confidence: 99%

“…The peptide digest was desalted with a mixedmode (MCX) method, the desalted peptides split into two aliquots, and each aliquot dried down via speedvac overnight. Twenty-four hours prior to MS acquisition, one dried aliquot was resuspended in 0.05 μg/μL trypsin in 18 O-enriched water (Cambridge Isotope Laboratories, Inc.) following a standard 18 O-labeling protocol, 10 and the other was resuspended in 0.05 μg/μL trypsin in conventional molecular-grade water. The digest incubated overnight then was quenched with 5 mM DTT, cooled to room temperature, and acidified with formic acid.…”

Section: Sample Preparation and Mass Spectrometry Data Acquisitionmentioning

confidence: 99%

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Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics

et al. 2020

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Mass spectrometry is a powerful tool for quantifying protein abundance in complex samples. Advances in sample preparation and the development of data-independent acquisition (DIA) mass spectrometry approaches have increased the number of peptides and proteins measured per sample. Here, we present a series of experiments demonstrating how to assess whether a peptide measurement is quantitative by mass spectrometry. Our results demonstrate that increasing the

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Sample Preparation and Mass Spectrometry Data Acquisitionmentioning

confidence: 99%

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Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics

et al. 2020

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Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development

et al. 2019

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The condition of the placenta is a determinant of the short-and long-term health of the mother and the fetus. However, critical processes occurring in early placental development, such as trophoblast invasion and establishment of placental metabolism, remain poorly understood. To gain a better understanding of the genes involved in regulating these processes, we utilized a multi-omics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental timepoints. We found that incorporating information from both the transcriptome and proteome identifies genes associated with timepoint-specific biological processes, unlike using the proteome alone. We further inferred genes upregulated based on the proteome data but not the transcriptome data at each timepoint, leading us to identify 27 genes that we predict to have a role in trophoblast migration or placental metabolism. Finally, using the phosphoproteome dataset, we discovered novel phosphosites that may play crucial roles in the regulation of placental transcription factors. By generating the largest proteome and phosphoproteome datasets in the developing placenta, and integrating transcriptome analysis, we uncovered novel aspects of placental gene regulation.

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OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization

Cho

Brunner

et al. 2021

Preprint

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Elucidating the wiring diagram of the human cell is one of the central goals of the post-genomic era. Here, we integrate genome engineering, confocal imaging, mass spectrometry and data science to systematically map protein localization in live cells and protein interactions under endogenous expression conditions. For this, we generated a library of 1,311 CRISPR-edited cell lines harboring fluorescent tags that also serve as handles for affinity capture, and applied a new machine learning framework to encode the interaction and localization profiles of each protein. Our approach provides a data-driven description of the molecular and spatial networks that organize the human proteome. We show that unsupervised clustering of these networks delineates functional groups and facilitates biological discovery, while hierarchical analyses uncover the core features that template cellular architecture. Furthermore, we discover that localization signatures are remarkably predictive of protein function, and often contain enough information to identify molecular interactions. Paired with a fully interactive website (opencell.czbiohub.org), OpenCell is a resource for the quantitative cartography of human cellular organization.

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La tabacologie

Cited by 3 publications

References 0 publications

Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics

Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics

Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development

OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization

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