Has someone benchmarked different summarization approaches for proteomics identification features (i.e., stripped peptide) from precursor quants?
Mean/median?
Max?
Sum?
I'm leaning towards sum but I see variation in approaches.
@pwilmarth @DemichevLab@nesvilab
@MattWFoster @nesvilab That's a good point. Not only in-source fragments, but also certain experimental conditions can lead to spontaneous cleavage. We are not able to classify semi-specific peptides as such, but we use the differential abundance to define something as biologically relevant.
Thank you very much for the shout out Alexey @nesvilab!
I am happy that our work is receiving good attention.
Digging deeper into MS-#proteomics data not only requires powerful tools such as FragPipe, but also data analysis frameworks to contextualize their results.
Are you using mass spec based proteomics to study endogenous proteolytic activity? This work describes an R package TermineR for downstream processing (annotation, visualization, differential analysis etc.) of semi-specific search results from #FragPipe. https://t.co/2yZ6MzAFp4
“I am going to create two maximum security prisons for all of the young people protesting and they will have no chance for parole or ever be pardoned….and we will have them to work, have them produce for the state !” Bro thinks he invented the concentration camp
Hi all,
Is there a current recommendation for submission to .d files to the Massive repo?
I just noticed that trying to convert them to mzML would blow the size to extremes (from 2.5 to 75GB).
Email I sent in response to @NatureComms´s request for me to act as a reviewer today (part 1 of 2).
#OpenAccess isn´t open if those of us in developing countries are economically excluded from publishing equitably.
Have you considered applying to our current open call for PhD positions but are unsure if it is for you? Learn more about our training concept and research by three short films: https://t.co/biowD2qXIb
P.S.: one week left to apply!
@FrauPelusa Yo siento igual, en museos y con la lectura. Me parece que leo muy lento y que por eso me he perdido de leer muchas cosas que aún me interesan. Últimamente con los museos, asumo que no puedo apreciar todo, y me enfoco en algunas piezas... Y trato de evitar juzgarme por eso.