Relative signal intensities of NUP peptides in pre-labeling KARMA assay samples

Supplementary analyzed data from Manuscript:
TITLE: Maturation kinetics of a multiprotein complex revealed by metabolic labeling.
JOURNAL: CELL.
Article Type: Research Article
Authors: Evgeny Onischenko*, Elad Noor*, Jonas S. Fischer*, Ludovic Gillet, Matthias Wojtynek, Pascal Vallotton, Karsten Weis
*Equally Contributing Authors
Corresponding Authors: Evgeny Onischenko and Karsten Weis

Related to Figure S2; Table S4

Relative signal intensities of NUP peptides in pre-labeling KARMA assay samples.
The target protein complex is isolated from cell lysates by affinity pulldowns, tryptically digested and analyzed with LC-MS on an Orbitrap mass-spectrometer. The MS2 fragmentation spectra are acquired in a DIA mode for all samples. Peptide intensities are extracted from the DIA datasets with Spectronaut software (Biognosis) using complementary assay spectral libraries.

Individual plots: The fraction of protein's signal intensity in each sample (red track) is given by the median of the signal fraction across all high quality precursor ions (green tracks). Low quality precursor ions (grey tracks) are excluded from quantification. x-axis: individual samples, y-axis: fraction of precursor ion signal in a sample (precursor signal intensity in a sample normalised for the total across all 34 samples). Individual precursor ion values across samples are connected, forming a track.