Maz
@taghioskoui.bsky.social
Exploring Mass Spectrometry & the Origins of Life: Is Life a Common Cosmic Phenomenon?
These days, you can almost always guess which technique is reported to outperform the rest just by reading the conflict of interest (COI) statement.
August 4, 2025 at 12:13 AM
These days, you can almost always guess which technique is reported to outperform the rest just by reading the conflict of interest (COI) statement.
Deep Blood Proteomics Identifies over 12,000 Proteins Providing Valuable Information about the State of the Human Body. www.biorxiv.org/content/10.1...
August 4, 2025 at 12:11 AM
Deep Blood Proteomics Identifies over 12,000 Proteins Providing Valuable Information about the State of the Human Body. www.biorxiv.org/content/10.1...
And the same statement on the ASMS poster.
August 2, 2025 at 5:09 PM
And the same statement on the ASMS poster.
The cited grant (3R35GM118110) is not even relevant. The grant is for CryoEM+MS work & specifically defines the scope as "In particular we propose the addition of surface-induced dissociation (SID) and activated-ion ETD (AI-ETD) to the mass spectrometer used for grid preparation."
August 2, 2025 at 4:55 PM
The cited grant (3R35GM118110) is not even relevant. The grant is for CryoEM+MS work & specifically defines the scope as "In particular we propose the addition of surface-induced dissociation (SID) and activated-ion ETD (AI-ETD) to the mass spectrometer used for grid preparation."
@slavov-n.bsky.social l @coonlab.bsky.social: I disclosed this concept in the Super Mass Spec patent published on September 21, 2023 (see Figures 15D–E): patents.google.com/patent/US202...
Happy to collaborate if you're open to coming together and putting science first to push the field forward.
Happy to collaborate if you're open to coming together and putting science first to push the field forward.
July 31, 2025 at 3:30 PM
@slavov-n.bsky.social l @coonlab.bsky.social: I disclosed this concept in the Super Mass Spec patent published on September 21, 2023 (see Figures 15D–E): patents.google.com/patent/US202...
Happy to collaborate if you're open to coming together and putting science first to push the field forward.
Happy to collaborate if you're open to coming together and putting science first to push the field forward.
@vadim-demichev.bsky.social Your name is not on the ASMS poster presentation but it appears on the paper. Did anything change from the ASMS poster? Why you are not listed on the poster?
July 31, 2025 at 2:03 PM
@vadim-demichev.bsky.social Your name is not on the ASMS poster presentation but it appears on the paper. Did anything change from the ASMS poster? Why you are not listed on the poster?
Speaking of measurement theory, what do you think about this fancy “alpha value”?
"Alpha values greater than 1.0 suggest an overestimation of ion counts (i.e., reported intensity is higher than true ion current), while values less than 1.0 suggest underestimation"
"Alpha values greater than 1.0 suggest an overestimation of ion counts (i.e., reported intensity is higher than true ion current), while values less than 1.0 suggest underestimation"
July 27, 2025 at 4:53 AM
Speaking of measurement theory, what do you think about this fancy “alpha value”?
"Alpha values greater than 1.0 suggest an overestimation of ion counts (i.e., reported intensity is higher than true ion current), while values less than 1.0 suggest underestimation"
"Alpha values greater than 1.0 suggest an overestimation of ion counts (i.e., reported intensity is higher than true ion current), while values less than 1.0 suggest underestimation"
Roger that. I have not been able to locate any. There is a reproducibility crisis and some people do not want to talk about it at all.
July 25, 2025 at 3:07 PM
Roger that. I have not been able to locate any. There is a reproducibility crisis and some people do not want to talk about it at all.
Elon Musk slashed 6,000 jobs at Twitter and thinks a similar approach could “reshape” the federal government, which has 2.25 million employees (375X). But scaling laws don’t work like that. He knows(?) Falcon 9 → Starship or toy car → Tesla weren’t just “make it bigger.”
January 29, 2025 at 4:14 AM
Elon Musk slashed 6,000 jobs at Twitter and thinks a similar approach could “reshape” the federal government, which has 2.25 million employees (375X). But scaling laws don’t work like that. He knows(?) Falcon 9 → Starship or toy car → Tesla weren’t just “make it bigger.”
Also, export control on proteomics studies involving more than 1,000 persons…
January 16, 2025 at 6:09 AM
Also, export control on proteomics studies involving more than 1,000 persons…
January 15, 2025 at 3:43 PM
Note that for all TIC profiles, the report states 300ng peptide being loaded on the same LCMS. That means aside from sample prep, LC and ESI (ion suppression, etc) are variables. That is, integrating the area under each TIC profile corresponds to the total ion current from the 300ng of peptides.
January 14, 2025 at 4:17 PM
Note that for all TIC profiles, the report states 300ng peptide being loaded on the same LCMS. That means aside from sample prep, LC and ESI (ion suppression, etc) are variables. That is, integrating the area under each TIC profile corresponds to the total ion current from the 300ng of peptides.
Also, the paper states "We found that only about 12 to 16% of the PreOmics, Seer, and Acid prepared peptides resulted from
missed tryptic cleavages while that number increased to 23 and 25% with the Mag-Net and Neat methods..." So, major different TIC profiles did not result from missed cleavages.
missed tryptic cleavages while that number increased to 23 and 25% with the Mag-Net and Neat methods..." So, major different TIC profiles did not result from missed cleavages.
January 14, 2025 at 3:58 PM
Also, the paper states "We found that only about 12 to 16% of the PreOmics, Seer, and Acid prepared peptides resulted from
missed tryptic cleavages while that number increased to 23 and 25% with the Mag-Net and Neat methods..." So, major different TIC profiles did not result from missed cleavages.
missed tryptic cleavages while that number increased to 23 and 25% with the Mag-Net and Neat methods..." So, major different TIC profiles did not result from missed cleavages.
Can you help me understand this?
January 14, 2025 at 3:03 AM
Can you help me understand this?
I was hoping Mike would address my question, but he stopped responding abruptly. Can anyone clarify what’s happening with the TICs of the same sample? There should be at least a few common peaks. What are these different sample preparations doing to the sample?
January 14, 2025 at 12:49 AM
I was hoping Mike would address my question, but he stopped responding abruptly. Can anyone clarify what’s happening with the TICs of the same sample? There should be at least a few common peaks. What are these different sample preparations doing to the sample?
For those following the conversation, Mike MacCoss suddenly blocked me, and I’m not sure why. Perhaps he was having a bad day. I hope he reconsiders and returns so we can resume our challenging science discussions. Without these discussions, the empty race for protein IDs will continue.
January 14, 2025 at 12:17 AM
For those following the conversation, Mike MacCoss suddenly blocked me, and I’m not sure why. Perhaps he was having a bad day. I hope he reconsiders and returns so we can resume our challenging science discussions. Without these discussions, the empty race for protein IDs will continue.
But the above is at least better the below for the same sample.
January 13, 2025 at 7:12 PM
But the above is at least better the below for the same sample.
"To compare the six plasma proteomic methods – Neat, Acid, PreOmics, Mag-Net, Seer, and Olink – we used the same starting plasma sample split into aliquots. ... Representative chromatograms from the various MS-based plasma reparation
technologies are shown in Supplemental Figure 1."
technologies are shown in Supplemental Figure 1."
January 13, 2025 at 5:38 PM
"To compare the six plasma proteomic methods – Neat, Acid, PreOmics, Mag-Net, Seer, and Olink – we used the same starting plasma sample split into aliquots. ... Representative chromatograms from the various MS-based plasma reparation
technologies are shown in Supplemental Figure 1."
technologies are shown in Supplemental Figure 1."
Again, the conflict of interest statement appears to correlate with the study findings.
January 13, 2025 at 5:22 PM
Again, the conflict of interest statement appears to correlate with the study findings.
This is helpful and not looking good.
January 13, 2025 at 3:43 AM
This is helpful and not looking good.
True, it’s not their money, but a project of this scale isn’t awarded arbitrarily. Proper due diligence was conducted, involving a contracting process with over a dozen entities. For a $300M project, they could easily build a facility and purchase MS systems. Sapient already has plenty of timsTOFs.
January 12, 2025 at 3:41 PM
True, it’s not their money, but a project of this scale isn’t awarded arbitrarily. Proper due diligence was conducted, involving a contracting process with over a dozen entities. For a $300M project, they could easily build a facility and purchase MS systems. Sapient already has plenty of timsTOFs.