Kinetics

Protein renewal over time. Protein half lives (t50) were calculated by fitting the data to a cumulative Weibull distribution.



TURNOVER KINETICS

DATA TABLE

Ranking

Ranking of protein turnover. Proteins are ranked according to their turnover at different time points.



TURNOVER ANALYSIS OF RESTING CELLS

DATA TABLE

Time Course

Compare protein levels at different time points. Colors indicate 'identified by MS/MS' (black) and 'by matching' (red) according to the MaxQuant output. Data points that were identified by MS/MS are more reliable than matched data points.



TIME COURSE

DATA TABLE

Differential Abundance

Compare protein abundance between two conditions. In the example resting naïve (Group1, Naïve 0h) is compared to resting memory (Group2, Mem 0h). Proteins that are more abundant in resting memory T cells are shown on the right side of the volcano plot.

Under significance you can select either the p-value or the q-value (FDR adjusted p-value, more stringent).



VOLCANO PLOT

FOLDCHANGE

ENRICHMENT

Protein degradation

Disappearance of proteins in the absence of protein synthesis. Resting naïve T cells were treated for 24h with cycloheximide (CHX, blocks protein synthesis) and or with bortezomib (PS431, abbreviated as PS, blocks proteasomal degradation).



CHX2 EXPERIMENT

Global comparison

Comparison of protein synthesis rates and mRNA levels in naïve resting and activated T cells. You can hover over the dots to see gene symbols. Ribosomal proteins are shown in blue.



MRNA VS PROTEIN

mRNA translation kinetics

Left panel: The transcript read-off rate was calculated as 'Copies newly synthetized proteins per minute' divided by 'Copies mRNA'. Middle panel: 'Copies newly synthetized proteins per minute' is shown. Right panel: 'Copies mRNA' is shown.



MRNA TRANSLATION KINETICS

DATA TABLE

Network of repressed mRNAs

Graph shows a network of mRNAs that are repressed in naive T cells and >3 times faster translated following activation.



NETWORK OF REPRESSED MRNAS

Network of mTORC-independent mRNAs

Graph shows a network of mRNAs that are repressed in naive T cells and rapidly engaged following activation independently of mTORC.



NETWORK OF MTORC-INDEPENDENT MRNAS

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