David Peeney

Staff Scientist at NCI. Working towards an understanding of the mass changes in pathology-associated extracellular matrix

[David Peeney @DavidPeeney]

@CarolynLazaroff @FaccioLab It was a sure thing 😉

[David Peeney @DavidPeeney]

Check out our new review on the diverse roles of #TIMPs in pathophysiology. There is still plenty of science to be performed on this intriguing family of #matrisome proteins.

https://t.co/o7YO2nvzWM

#extracellularmatrix @NCIResearchCtr

[David Peeney @DavidPeeney]

These findings are helping us shed light on TIMP2's intriguing roles in health and disease

@NCIResearchCtr

[David Peeney @DavidPeeney]

Fresh news in the #matrisome world! Our team used extracellular proximity labeling to unravel the hidden interactome of TIMP2, a key homeostatic regulator in the extracellular matrix.

Check out our preprint for more info: https://t.co/soNTbvPHxI

#interactome #proteomics #ECM

[David Peeney @DavidPeeney]

Keep an eye out for future work aimed at improving the effectiveness and serum half-life of recombinant TIMP2. @NCIResearchCtr

[David Peeney @DavidPeeney]

New work from the team investigating the therapeutic potential of recombinant TIMP2 in lung carcinoma. We see systemic changes that suggest recombinant TIMP2 may prove to be a useful adjuvant in solid tumor therapy.

https://t.co/pHS0LUdnXv

[David Peeney @DavidPeeney]

@FaccioLab @CarolynLazaroff Great to see continually Carolyn growing as a scientist!!

[David Peeney @DavidPeeney]

Thanks to the excellent postbacs who put great effort into this! Sasha Coates-Park, @CarolynLazaroff, @sdchyagrng, and Josh Rich! Also to our collaborators @OverallLabNews.

@NCIResearchCtr

[David Peeney @DavidPeeney]

New work from the lab, best explained by the following meme...

[David Peeney @DavidPeeney]

https://t.co/4oQsfvLWCB

[Rama Khokha @rmkhokha]

We are hiring and looking for 2 postdoc researchers interested in cell heterogeneity and early detection of breast cancer. This is an exciting opportunity to work with us and our @tfri_research @BreastCancerCDN and @CIHR_ICR funded projects!

Please RT and reach out to us

[David Peeney @DavidPeeney]

@JustinWWalley @dormichicken Thanks! In the end I compared SDS elution and SP3 clean-up vs on-bead digestion (using trypsin resistant strep beads). Found that on-bead digestion was a little better (albeit a single experiment)

[David Peeney @DavidPeeney]

#TeamMassSpec ... Has anyone had considerable success with on-magnetic bead tryp/lysC digestion (streptavidin mag beads)?

[David Peeney @DavidPeeney]

@AJ_Brenes @byu_sam @PastelBio I will give this a whirl tomorrow

[David Peeney @DavidPeeney]

Anyone have advice on how they normalize TMT channel data when the samples are from a pulldown? Normalization methods assume that peptide abundances should be broadly equal across samples...

#TeamMassSpec #MassSpec #proteomics

[David Peeney @DavidPeeney]

@JoelisSteele I've tried 8-plex and 4-plex, I preferred the results of the 4-plex... The additive effects of non-specific hits was a bit overwhelming in the 8. I'm sure we could improve it though

[David Peeney @DavidPeeney]

@camtflower Although we do normalize by A205 before labeling, I am slightly uncomfortable doing so because the signal in the samples are assumed to be higher as they should include additional proximal interactors

[David Peeney @DavidPeeney]

@JustinWWalley @JoelisSteele In our case, the controls have lower noise than most PL methods... Largely because our reaction occurs predominantly in the extracellular space. Without that specific localization, the background signal can be overwhelming

[David Peeney @DavidPeeney]

@JohnRYatesIII The problem with this method was that the controls notoriously have less biotinylated protein, so by normalizing that expected skew we lose hits.

[David Peeney @DavidPeeney]

@dlswaney With some heavy washing and an on-bead digestion, we seem to not suffer so much with too much background! We use cytiva blocked magnetic beads and we generate a trypsin resistant version of these

[David Peeney @DavidPeeney]

@edemmott @byu_sam @PastelBio I think the latter point is a good shout, I will try that out with my current data.

[David Peeney @DavidPeeney]

@byu_sam @PastelBio Yes, that is something we will have to keep in mind when discussing the data. A pre-pulldown spike would not survive, and we normalize by A205 before labeling (which is almost contrary to my earlier comments about the expected skew in our data)... Proteomics is tough 😆