Danielle Swaney @dlswaney

Associate Professor at UCSF, visiting scientist at the Gladstone Institutes. Expertise in mass spectrometry and proteomics. Views are my own. profiles.ucsf.edu/danielle.swaney San Francisco, CA Joined July 2015

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Danielle Swaney @dlswaney

2 years ago

@J_my_sci Reviewers get a copy of your A0 summary statement, so they know. They use this to see if you addressed concerns from A0 reviewers.

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Danielle Swaney @dlswaney

2 years ago

@MelOdenkirk @FemalesInMS @asmsnews (1) Practice: As you write more you will likely find go-to structures that help you. (2) Find writing buddies: It is amazing how much you can learn just from having a skillful person edit your text. (3) Read it out loud: You'll think twice when you have to speak every word.

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Danielle Swaney @dlswaney

2 years ago

@neely615 I am not exactly sure what you are looking for, since most biochem profs I know love protein structure because it helps to guide their work. Or if you want a biology-driven proteomics person, who thinks about structure constantly, @KroganLab would fit the bill.

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Danielle Swaney @dlswaney

2 years ago

This @mjmaccoss preprint about QC is too real. Like when your turbo pump explodes and sends shrapnel into every crevice of your mass spec causing problems for half a year. This QC platform help you know when your instrument is actually all clean again :) biorxiv.org/content/10.110…

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Danielle Swaney @dlswaney

2 years ago

FYI Bay area mass spec aficionados - this symposium on mass spec in drug discovery looks great! Oct 29th @ at Stanford

Steven Artandi, MD, PhD @SCIDirector

2 years ago

Join us for the inaugural SCI Advances in #MassSpectrometry Enabled Drug Discovery symposium on October 29. Hear leading experts explore current challenges, opportunities, & recent achievements across diverse applications in #DrugDevelopment. stan.md/3X0WVUC #proteomics

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Danielle Swaney @dlswaney

2 years ago

@michaelsteidel1 @UCDProteomics I don’t think so. It depends on what is determining the difference for your true PPIs out of the data. Sometimes global normalization is appropriate to adjust for differences in lysate amount. Sometimes normalization by bait is appropriate if that is driving PPI difference.

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Arun Wiita @apwiita

2 years ago

Interested in #proteomics/related data analysis but don't know where to start❓Our 2-day hands-on workshop🙌 @UCSF is for you! July 11-12 at Mission Bay campus, open to Bay Area academic or industry scientists. Info+registration (seats are limited!) wiitalab.ucsf.edu/events/biologi…

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Joe Bondy-Denomy @joeBondyDenomy

2 years ago

Did you know that phage can inject DNA, many proteins, recruit host membrane/membrane proteins and assemble a lipid vesicle to protect the genome?@MozumdarDeepto led this effort with contributions from a large multi-disciplinary team. @cellhostmicrobe sciencedirect.com/science/articl…

Joe Bondy-Denomy @joeBondyDenomy

2 years ago

The phiKZ jumbo phages build a protein based nucleus to protect their DNA(!), but what do they do before the nucleus is built? Led by outstanding post-doc @MozumdarDeepto, here we identify host and phage proteins in an immediate early phage lipid vesicle. biorxiv.org/content/10.110…

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Danielle Swaney @dlswaney

2 years ago

@TTCooper_PhD That much downtime due to connectivity is not normal. We don’t see that with our VanquishNeos.

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Danielle Swaney @dlswaney

2 years ago

@ProteomicsNews I am intrigued! In this type of situation I always second guess myself and try to do my best to show this is not the result of some sample prep or data analysis artifact that I don’t understand/appreciate. Synthetic peptides with the PTM to show similar fragmentation are good too

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Danielle Swaney @dlswaney

2 years ago

@DoctorBou Sure there is some loss (not sure how much) but we haven't noticed it to be detrimental. It is also useful because C18 plates/columns can leak beads, so those can get removed as well so they don't block your LC lines or column.

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Danielle Swaney @dlswaney

2 years ago

Also, a big thanks to our generous sponsors! Come hear from them about their latest and greatest technology and how it could help to accelerate your research. @thermofisher @bruker @NautilusBio @seer_bio

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Danielle Swaney @dlswaney

2 years ago

Bay area proteomics friends - Having some ASMS FOMO? Or just want to pregame for ASMS? Come attend our @QBI_UCSF and @rezo_tx Mass Spectrometry Symposium at UCSF on Thursday May 30, hosted by myself and Chris Adams. We have a diverse and spectacular lineup qbi.ucsf.edu/qbi-rezo-mass-…

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Danielle Swaney @dlswaney

2 years ago

@GarciaLabMS I feel that signing my reviews has helped to hold myself more accountable to this, and have my exp requests driven by rigor and not by my personal curiosity. A side benefit is being able to establish new connections with authors through mutual respect of the review process.

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Danielle Swaney @dlswaney

2 years ago

@GarciaLabMS Yes, this is what I was trying to get a feel about from the PO heading into the next submission cycle, since I’m the past they have at least given me the “be patient” or “I’d seriously consider to resubmit” nod.

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Danielle Swaney @dlswaney

2 years ago

In eRA Commons a green "Council review completed" status means a grant still has a chance for funding? I have an NIGMS grant with a fundable (but not amazing) score and it has been in this status since October. PO doesn't respond to email or call to discuss, so I am being patient

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Danielle Swaney @dlswaney

2 years ago

@chrashwood I feel like DIA means different things to different people. It started as prioritizing sensitive and selective MS2-based quant, but there has been a steady creep towards using DIA to reduce missing values in detection, but relying heavily (if not exclusively) on MS1 for quant.

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Danielle Swaney @dlswaney

2 years ago

@JesperOlsenLab @BortelPatricia @mdval_ana @PigaIlaria @ClaireKoenig6 Thanks for preprinting this phosphorylation enrichment protocol. We tried it and it worked beautifully. The rigor of testing all the conditions and showing what things matter and what things don’t matter is really helpful.

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Danielle Swaney @dlswaney

2 years ago

@J_my_sci I agree, the leaf cutter one was really cool. I also enjoyed Ed Marcotte’s co-fraction across the tree of life talk because at the beginning I was like “oh this is a crazy & fun evolutionary biology project” but by the end was impressed with the utility towards human disease.