Twitter | Search | |
Claire McWhite
Grad student at UT Austin. Prev Rice. Proteomics, Systems Bio, comparing things to each other. Status: Cilia, plants.
1,872
Tweets
704
Following
484
Followers
Tweets
Claire McWhite retweeted
Alberta Claw Jun 18
Replying to @albertonykus
Oreoicids are a small group of orioloids. The best known is the crested bellbird, which has the unusual habit of paralyzing hairy caterpillars and incorporating them into its nest. (📷Peter Jacobs)
Reply Retweet Like
Claire McWhite Jun 12
Replying to @FoxandtheFlu
Funny, I just last week loaded all those graphing packages and thunderdomed them for my needs. Maybe you need a dendrogram object idk?
Reply Retweet Like
Claire McWhite retweeted
Pastel BioScience Jun 12
Protein Extraction Methods Shape Much of the Extracted Proteomes |
Reply Retweet Like
Claire McWhite retweeted
Claus Wilke Jun 10
New book chapter: Optimize the data–ink ratio.
Reply Retweet Like
Claire McWhite Jun 7
Cool new stuff from the Ellington lab: Recoded, stable selenocysteine-dependent bacterial strain for all your selenoprotein brewing needs. blogpost: free link to paper: paper:
Reply Retweet Like
Claire McWhite Jun 1
Replying to @thomas_mock @rstudio
Definitely!
Reply Retweet Like
Claire McWhite Jun 1
Replying to @thomas_mock @rstudio
Congrats Thomas!
Reply Retweet Like
Claire McWhite May 29
Really great news! The .RAW files are the main important thing for reproducing. Also, feel free to email me or post here if you have any questions about the technicalities of our complaint with the protein quantification methods.
Reply Retweet Like
Claire McWhite retweeted
Aashiq H Kachroo May 28
Do you want to engineer complex human biological processes in yeast. Join and be a part of an exciting young team
Reply Retweet Like
Claire McWhite May 27
Probably, assuming the output files were kept, and the .raw files are there, someone could do a partial PRIDE submission. It's not an extremely fun process - I can see someone putting it off
Reply Retweet Like
Claire McWhite May 27
I wouldn't publicly call out something like this frivolously. It's not as Antoniou says just 'isoforms and PTMs' or me needing to read an Intro to Mass Spec textbook. The papers' statistics are wrong. What's the course to take? 5/5
Reply Retweet Like
Claire McWhite May 27
There's a small excel of peptide measurement output that the journal was supposed to post, and that I have locally. But it's already a highly processed form of the data. Thermo .Raw files are massive. Analysis scripts would be nice to see...
Reply Retweet Like
Claire McWhite May 27
My proteomics colleague at UT and I sent a Letter to the Editor of Scientific Reports. I've described the quantification methods in Mesnage 2016 & 2017 to every TMT expert I've met, and they encourage me that: No, it's not OK, keep going, keep following up w/ the journal. 4/5
Reply Retweet Like
Claire McWhite May 27
Peptide-level quantification just isn't equivalent to a protein-level quantification. Using a single peptide species to make conclusions about a protein's level while ignoring measurements of all its other peptides will definitely lead to high numbers of false-positives. 3/5
Reply Retweet Like
Claire McWhite May 27
I found that while the papers claimed to find protein-level changes, they actually quantified peptides. If any peptide measured differently between samples the entire protein was called perturbed - Even if all other peptides mapping to that protein had no/conflicting changes 2/5
Reply Retweet Like
Claire McWhite May 27
It is a frustrating situation. To give context to others I track plant proteomics. When I read Mesnage 2016 something felt off. In the suppl data, protein masses were way too small, and there were protein IDs listed multiple times w/ both increasing & decreasing fold changes 1/5
Reply Retweet Like
Claire McWhite May 26
Replying to @Robin_Mesnage
On that note... I've been independently trying to get the TMT10Plex raw data for Mesnage 2016 (& 2017) for like half a year through a Scientific Reports editor. It's been months since you guys said you'd deposit the data. I'd just like to know, what's going on :/ ?
Reply Retweet Like
Claire McWhite May 21
Replying to @riddhimankg @DunhamLab
Reply Retweet Like
Claire McWhite May 21
Replying to @DunhamLab @riddhimankg
Ooh, call it "Funktional genomics of weird yeasts" For their um, unique flavors.
Reply Retweet Like
Claire McWhite May 21
Replying to @DunhamLab @riddhimankg
You definitely got us into talking about all things yeast with brewers 😊
Reply Retweet Like