#massSOS

Does anyone know how to extract how many MS2s contain particular contaminate fragments? (i.e. the percentage of MS2 with 136.061 m/z Adenine accounting for ppm error) Either with R, python, MSfragger, MaxQuant or Skyline is preferred. #massSOS #proteomics

#MassSos anyone have contact closure issues on the neo/eclipse? I have had this before but can't remember the exact fix. It will pick up sample but stuck in loading.

Has anyone got a reference MSMS spectrum for semaglutide? Someone wants me to measure it. Looking at the structure, it is an "interesting" peptide.

#massSOS

#massSOS

#MassSOS

Nanoviper fitting broke inside the trap column. Is any familiar with this part number or demensions? The nano viper tubing, not the cartridge. #TeamMassSpec #MassSOS

A very basic Q.. if a peptide is identified in two charge states, in order to get the peptide quan, would you average the XIC area of both charges or add the respective XIC area?? Shouldn't it be the latter as the total peptide is separated into two different m/z here?? #TeamMassSpec #MassSOS

Anyone with experience of converting Waters .raw files into mzML (or something) that can be searched with Fragpipe and other software? MS Convert settings that work would be very helpful. #MassSOS

Seeing really high polysiloxane background with IonOpticks TS and low flow/Whisper methods. Nanospray flex source. Any similar experience? #MassSOS

#MassSOS #TeamMassSpec #Proteomics

Any solid advice on dilution factors of 2% SDS cell lysates for BCA? I am getting some wonky results on a current pilot.

I have tried 2,5,10 fold dilutions and sampled 10,5,2,1 of that dilution respectively. Vastly different estimations of true concentration.

#massSOS

#massSOS

#massSOS anyone out there consider themselves an expert on Spectronaut, in particular version differences? Maybe it's the sleep deprivation talking but I have questions the user manual can't answer...

Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of ... High abundant protein depletion is a common strategy applied to increase analytical depth in global plasma proteomics experiment setups. The standard strategies for depletion of the highest abundant p...

#massSOS proteomics

I likewise don’t know the current state of the state (Seer?), but we have the IgY-14 from Sigma in the lab (c2018), and I feel like there was a super mix depletion add on that did 50 more mid abundance proteins.

👇This paper looks to discuss more modern things.

#MassSOS #teammassspec anyone have experience with resolving spray current issues. I have tried everything in my book. I am able to get it for a short period of time but is randomly lost or is lost when a sample is injected. Newish ion opticks column on neo Eclipse combo.

TwinScape TwinScape™ processes instrument parameters and quality control data of your LC-MS system.

Mass spec skeople: I assume the new Bruker twinScape thing costs money, right? As opposed to Biognosys QuiC, which is still free. #massSOS #proteomics

#massSOS are beads still the best way to do phosphopeptide enrichment for low input samples? They seem so messy but I know resins have downsides and don't seem to be available most places anymore. Anyone willing to share?

Were you on the radio hour yesterday? Weirdly enough this was a topic.
👀 @ucdproteomics.bsky.social @leannewg.bsky.social et al. #POTRH #massSOS

The limit fold change model: A practical approach for selecting differentially expressed genes from ... Background The biomedical community is developing new methods of data analysis to more efficiently process the massive data sets produced by microarray experiments. Systematic and global mathematical ...

#MassSOS

I have never bought the idea of a single cutoff value being “significant”, but know that variance changes with abundance, and smaller variance at higher abundance can be very biologically important and vice versa. I don’t cite it or use it, but this paper is my foundation.

#massSOS

Though you figured it out.

Lazy question: what proteomics software generates IBAQ values? I can get them in Spectronaut, but surely there are more DDA options for this, or maybe I just calculate on my own? Yasset @ypriverol.bsky.social has me wanting more IBAQ.

#MassSOS

I need to add #msSOS (to go with #massSOS).

For sure feasible. Check out @garcialabms.bsky.social work. My impression is because of all the lysine’s middle down works better than traditional bottoms up for quant but i have not read up latest developments. Antibodies for histone PTMs are problematic. #proteomics #massSOS

#MassSOS

#massSOS
What are the rules for searching DDA data with a limited database?

I have always been of the mind that the database should minimally contain all proteins that are in the sample.

But teamDIA are a bunch of cheetahBois that only use a couple peptides.

So can DDA do the same?

I’m not a computer, but ping the hivemind. #massSOS

MAM Consortium – A forum for Muti-Attribute Method and other LC/MS applications in the pharmaceuti...

The MAM consortium might be a good place to start, but is all I know.

#massSOS

#massSOS

So @pastelbio.bsky.social, I took some of the extra mass spec-y terms from @asms.org MassSpecSky and combined those with help or SOS or hivemind or consult. Or just use #massSOS (rec by @cportgrrl.bsky.social and @drawheatcraft.bsky.social).

@cportgrrl.bsky.social and @drawheatcraft.bsky.social, I think this works. It 100% collects #massSOS (your idea is great!), but also any other combo of mass spec-y terms and asking for help|SOS|hivemind|consult.

bsky.app/profile/did:...