Michael Steidel
@michaelsteidel.bsky.social
#Cellzome #TeamMassSpec #Proteomics opinions are my own
“Very interesting! Do you know whether ProteomeSciences is already testing the new DXT tags with selected customers or collaborators, or is it still entirely in-house at this stage?”
November 20, 2025 at 11:54 AM
“Very interesting! Do you know whether ProteomeSciences is already testing the new DXT tags with selected customers or collaborators, or is it still entirely in-house at this stage?”
Reposted by Michael Steidel
Bonus, info about DIA multiplex tags, up to 30-plex:
"trademark DXT for our DIA multiplex tags...advances have been made in DXT multiplexing since ASMS with the number of tags increased from 6 to 11 and with the potential to
increase these to beyond 30"
"trademark DXT for our DIA multiplex tags...advances have been made in DXT multiplexing since ASMS with the number of tags increased from 6 to 11 and with the potential to
increase these to beyond 30"
November 18, 2025 at 10:09 AM
Bonus, info about DIA multiplex tags, up to 30-plex:
"trademark DXT for our DIA multiplex tags...advances have been made in DXT multiplexing since ASMS with the number of tags increased from 6 to 11 and with the potential to
increase these to beyond 30"
"trademark DXT for our DIA multiplex tags...advances have been made in DXT multiplexing since ASMS with the number of tags increased from 6 to 11 and with the potential to
increase these to beyond 30"
Which LC & Flow?
October 7, 2025 at 4:38 PM
Which LC & Flow?
Surprised that u go so low. With EvoSep 24 min method we can load lots more on our Ultra2 until reaching saturation especially with ICC2.0
October 7, 2025 at 2:56 PM
Surprised that u go so low. With EvoSep 24 min method we can load lots more on our Ultra2 until reaching saturation especially with ICC2.0
How much are you loading per injection? Is ICC 2.0 enabled on the Ultra2? And which library are you using?
October 7, 2025 at 6:01 AM
How much are you loading per injection? Is ICC 2.0 enabled on the Ultra2? And which library are you using?
True — but the odd part is that the Human Reference Proteome is not really ‘canonical only’. Non-canonical entries from TrEMBL are included, yet the curated SwissProt isoforms are missing default. That’s what undermines the idea of a high-quality reference set.
October 2, 2025 at 6:34 AM
True — but the odd part is that the Human Reference Proteome is not really ‘canonical only’. Non-canonical entries from TrEMBL are included, yet the curated SwissProt isoforms are missing default. That’s what undermines the idea of a high-quality reference set.
On a separate note: I was surprised to find that none of the non-canonical SwissProt isoforms are included in the official human reference proteome (UP000005640).
Anyone know what’s going on here? 🤔
#proteomics #bioinformatics @pwilmarth.bsky.social il
Anyone know what’s going on here? 🤔
#proteomics #bioinformatics @pwilmarth.bsky.social il
October 1, 2025 at 3:13 PM
On a separate note: I was surprised to find that none of the non-canonical SwissProt isoforms are included in the official human reference proteome (UP000005640).
Anyone know what’s going on here? 🤔
#proteomics #bioinformatics @pwilmarth.bsky.social il
Anyone know what’s going on here? 🤔
#proteomics #bioinformatics @pwilmarth.bsky.social il
By the way.. 43% of current TREMBL entries will be dropped soon anyway insideuniprot.blogspot.com/2025/06/capt...
Capturing the Diversity of Life - Reorganizing the Protein Space in UniProtKB
Advances in genome sequencing technology means that large-scale efforts such as the Earth Biogenome project and the Darwin Tree of Life ...
insideuniprot.blogspot.com
September 30, 2025 at 2:22 PM
By the way.. 43% of current TREMBL entries will be dropped soon anyway insideuniprot.blogspot.com/2025/06/capt...
Reposted by Michael Steidel
Without #2, a lower ion count is needed just to be sure that the full MS range is scanned, but with more accurate ion counts, you can go to the max S/N without losing ions on the edges.
This could also work for the Orbitrap Astral.
Bonus: DIAPASEF on Thermo - patentscope.wipo.int/search/en/de...
This could also work for the Orbitrap Astral.
Bonus: DIAPASEF on Thermo - patentscope.wipo.int/search/en/de...
September 28, 2025 at 1:25 PM
Without #2, a lower ion count is needed just to be sure that the full MS range is scanned, but with more accurate ion counts, you can go to the max S/N without losing ions on the edges.
This could also work for the Orbitrap Astral.
Bonus: DIAPASEF on Thermo - patentscope.wipo.int/search/en/de...
This could also work for the Orbitrap Astral.
Bonus: DIAPASEF on Thermo - patentscope.wipo.int/search/en/de...
Thanks @pwilmarth.bsky.social - also included the less-redundant "one protein per gene" db here ...Has anybody assessed potential benefits of the reduced search space on sensitivity?
September 25, 2025 at 9:21 PM
Thanks @pwilmarth.bsky.social - also included the less-redundant "one protein per gene" db here ...Has anybody assessed potential benefits of the reduced search space on sensitivity?
aaah guess its "hidden" there :)
September 25, 2025 at 1:39 PM
aaah guess its "hidden" there :)
Great thanks! Where can I find the one protein per gene option?
September 25, 2025 at 1:34 PM
Great thanks! Where can I find the one protein per gene option?
Is that narrow windowed thin-PASEF?
July 9, 2025 at 9:49 PM
Is that narrow windowed thin-PASEF?
Using 32-Core Threadripper for DIA-NN. Gamechanger for large studies as multithreading is efficiently used. Also in case if several user need to process different jobs at same time.
June 25, 2025 at 1:38 PM
Using 32-Core Threadripper for DIA-NN. Gamechanger for large studies as multithreading is efficiently used. Also in case if several user need to process different jobs at same time.
If I got that correctly its not „truly“ open, as only predefined offset masses can be selected.
Have tried Fragpipe22? You can do ion mining from DIA data …
Have tried Fragpipe22? You can do ion mining from DIA data …
June 24, 2025 at 3:55 PM
If I got that correctly its not „truly“ open, as only predefined offset masses can be selected.
Have tried Fragpipe22? You can do ion mining from DIA data …
Have tried Fragpipe22? You can do ion mining from DIA data …
..diaPASEF down to 1 ng Hela looks ok (using E.Coli entrapment)
June 24, 2025 at 2:27 PM
..diaPASEF down to 1 ng Hela looks ok (using E.Coli entrapment)