IIT Bombay Proteomics - COVID_PLASMA

Validation of host proteins differentially expressed between COVID severe and non-severe plasma samples
Data License: CC BY 4.0 | ProteomeXchange: PXD022475
  • Organism: Homo sapiens
  • Instrument: TSQ Altis
  • SpikeIn: Yes
  • Keywords: COVID, Plasma, MRM, SARS-COV-2, host proteome
  • Lab head: Sanjeeva Srivastava Submitter: Sanjeeva Srivastava
It is well known now that a COVID-19 causes several changes in the proteome of the affected individuals. This data is part of our study where we explore the host proteome dysregulation in COVID-19 patient's plasma samples. The MRM experiment primarily focuses on proteins that are over-expressed in severe vs non severe patient samples.
Created on 11/11/20, 9:21 AM
Clustergrammer Heatmap
COVID_Plasma_sevVSnonsevere_2020-11-10_18-46-04.sky.zip2020-11-11 09:21:091029291832429

In this experiment we monitored 34 peptides, belonging to 12 proteins that were found to be over-expressed in COVID severe vs non severe from the lab's LFQ data. We ran 12 (6 severe and 6 non severe) COVID plasma samples in replicates on a triple quadrupole mass spectrometer against this list of 35 peptides (including one spiked in heavy labelled synthetic peptide to monitor run to run response). Only peptides that showed differential regulation in the MRM data were retained in the final Skyline files. We also created a library using the shotgun data and further refined the transition list. The submitted Skyline file has this refined list of 29 peptides and 183 transitions. The two bio-replicates of the same sample ID were run on two different days to check reproducibility.

A subset of the raw data files and search results used to build the Bibliospec spectrum library used in this analysis are available in the PRIDE repository with the accession PXD020580.