Tuesday, January 28, 2020

Publicly available (unpublished?) proteomic, metabolomic and lipidomic (MERS-CoV) coronavirus data!

Wow. Do I ever love ProteomeXchange!

Skip my reading and go to MASSIVE and get proteomic data from cancer cells infected with a coronavirus and -- if you're into that sort of thing -- you can get metabolomic data here and lipidomic data here! 

The RAW files currently heating my apartment may not have been published yet, but they are publicly available and I just contacted the uploader, but I'm moving fast because this data is 1) awesome and 2) pertinent

The Wuhan Coronavirus (2019-CoV) has a very close neighbor (possibly the closest according to my rough pBLAST of the entire translated sequence, but that may just be a consequence that it emerged more recently, as sequencing technology has gotten cheaper and more common -- leading to more data) -- that is called the MERS-CoV (here is the entry from UniProt) or Middle East respiratory syndrome-related coronavirus.

The experiment is 9 files from infected Calu cells (appears to be an immortalized and/or human cancer cell line) infected with the virus and 3 files from "Mock" (presumably uninfected).

The files were acquired on an Orbitrap Velos in "high/low" mode (120k resolution MS1 and CID ion trap fragmentation). The files appear to originate from PNNL, where it is rumored they know a thing or two about running mass spectrometers.

MetaMorpheus recalibration shows the MS1 is spot on, something like -1ppm off actual when compared against human and -- get this -- I can get >70% coverage of the main capsule protein from the virus in the virus infected proteomes. This is really cool because that protein is well conserved betweent the 2 (by pBLAST score, anyway).

Update: More fast moving science!! Just because the pBLAST scores line up, it doesn't mean that the peptides do -- check this out!

Again -- big disclaimer -- this is a mass spectrometrist's blog. I know very little about viruses and is just interested in this topic!

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