Miguel Cosenza-Contreras

Biologist. Proteomics Data Science. #R4DS enthusiast. Expect tweets about science, #rstats, politics, video games and random stuff EN/ES/PT

[Miguel Cosenza-Contreras @MiguelCos]

@AndreFornerino ¿Ya estás planchando blusas?... ¿O planchas también las pantaletas 😱?

[Miguel Cosenza-Contreras @MiguelCos]

I keep saying that I need to go away from R and learn new tools...

But R just seems to keep wanting to solve all my problems...

[Aedin Culhane (@[email protected]) @AedinCulhane]

Native workflow manager in R. Works like nf ot snakemake.

[Miguel Cosenza-Contreras @MiguelCos]

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

[Miguel Cosenza-Contreras @MiguelCos]

@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.

[Miguel Cosenza-Contreras @MiguelCos]

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.

[Alexey Nesvizhskii @nesvilab]

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

[Joanna Hausmann Jatar @Joannahausmann]

“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

[Miguel Cosenza-Contreras @MiguelCos]

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).

[Alicia Kowaltowski @AJKowaltowski]

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.

[Miguel Cosenza-Contreras @MiguelCos]

@Jquintanalcala ¡Felicitaciones Juan!

[PhD Research Training Group MeInBio @RTG_MeInBio]

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!

[Miguel Cosenza-Contreras @MiguelCos]

@yosoy_mari ¿Tú como que viviste el mismo 2022 que yo? ¡Feliz año!

[Miguel Cosenza-Contreras @MiguelCos]

@Lord3mil Feliz año lord 😘

[Miguel Cosenza-Contreras @MiguelCos]

@AndreFornerino @elalexgoncalves Ácida

[Miguel Cosenza-Contreras @MiguelCos]

A definitive hallmark of adulthood in millennials is getting excited about leftover food.

[Miguel Cosenza-Contreras @MiguelCos]

@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.

[Miguel Cosenza-Contreras @MiguelCos]

#NewProfilePic

[Miguel Cosenza-Contreras @MiguelCos]

Thank goodness for that...

[Sayantani Chatterjee @csayantani9]

What a fun #HUPO2022 gala night! Making new friends, experiencing the culture and lots of dancing! 🥳