Michael Steidel
@michaelsteidel.bsky.social
#Cellzome #TeamMassSpec #Proteomics opinions are my own
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
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
Hey #TeamMassSpec,
Many non-human proteomics studies still search against taxon-filtered FASTAs.
❌ Redundant sequences
❌ Inflated search space
✅ Reference proteomes cut redundancy, improve annotation, and make results comparable.
👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot
Many non-human proteomics studies still search against taxon-filtered FASTAs.
❌ Redundant sequences
❌ Inflated search space
✅ Reference proteomes cut redundancy, improve annotation, and make results comparable.
👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot
September 30, 2025 at 2:21 PM
Hey #TeamMassSpec,
Many non-human proteomics studies still search against taxon-filtered FASTAs.
❌ Redundant sequences
❌ Inflated search space
✅ Reference proteomes cut redundancy, improve annotation, and make results comparable.
👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot
Many non-human proteomics studies still search against taxon-filtered FASTAs.
❌ Redundant sequences
❌ Inflated search space
✅ Reference proteomes cut redundancy, improve annotation, and make results comparable.
👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot
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 :)
Hey #TeamMassSpec,
When you run proteomics on non-human species (mouse, rat, macaque, etc.) — which protein FASTA do you prefer?
Taxonomy-filtered UniProt (all entries)
Reference proteome (SwissProt+TrEMBL)
Ensembl/GENCODE
Something else?
When you run proteomics on non-human species (mouse, rat, macaque, etc.) — which protein FASTA do you prefer?
Taxonomy-filtered UniProt (all entries)
Reference proteome (SwissProt+TrEMBL)
Ensembl/GENCODE
Something else?
September 25, 2025 at 12:41 PM
Hey #TeamMassSpec,
When you run proteomics on non-human species (mouse, rat, macaque, etc.) — which protein FASTA do you prefer?
Taxonomy-filtered UniProt (all entries)
Reference proteome (SwissProt+TrEMBL)
Ensembl/GENCODE
Something else?
When you run proteomics on non-human species (mouse, rat, macaque, etc.) — which protein FASTA do you prefer?
Taxonomy-filtered UniProt (all entries)
Reference proteome (SwissProt+TrEMBL)
Ensembl/GENCODE
Something else?
Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
July 19, 2025 at 9:01 AM
Astral Zoom hits >7,000 protein groups & 67,000 precursors — on a 500 SPD EvoSep ENO run.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
June 27, 2025 at 10:13 AM
..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)
April 8, 2025 at 10:51 AM
Slice-PASEF: Almost as beautiful as gazing into the starry sky at night
March 18, 2025 at 9:07 PM
Slice-PASEF: Almost as beautiful as gazing into the starry sky at night
Ion mobility stability over time is a helpful metric which we always generate to control for weather-related, or ITI-contamination driven drift effects..
March 11, 2025 at 7:58 PM
Ion mobility stability over time is a helpful metric which we always generate to control for weather-related, or ITI-contamination driven drift effects..
For those interested: Have found the segmentation feature in timsControl. Simply right click in the 'chromatogram' pannel, and select 'Insert New Segment'.
March 5, 2025 at 12:09 PM
For those interested: Have found the segmentation feature in timsControl. Simply right click in the 'chromatogram' pannel, and select 'Insert New Segment'.
That would be the "official" publication
February 18, 2025 at 8:11 PM
That would be the "official" publication
Based on full text search:
February 14, 2025 at 10:25 AM
Based on full text search:
Popularity of current DIA data analysis tools (vendor-independent, based on citations of initial publication) Updated for 2024:
February 14, 2025 at 10:24 AM
Popularity of current DIA data analysis tools (vendor-independent, based on citations of initial publication) Updated for 2024:
Inerestingly, this picture changes when using fulltext search where algorithms based on Sequest (as implemented in ProteomeDiscover) dominate...
January 30, 2024 at 5:09 PM
Inerestingly, this picture changes when using fulltext search where algorithms based on Sequest (as implemented in ProteomeDiscover) dominate...
Trying to estimate popularity of search engines. (Something widespread I missed out?)
Based on citations/year of initial publication it seems as MSFragger would take over soon...
Based on citations/year of initial publication it seems as MSFragger would take over soon...
January 30, 2024 at 5:08 PM
Trying to estimate popularity of search engines. (Something widespread I missed out?)
Based on citations/year of initial publication it seems as MSFragger would take over soon...
Based on citations/year of initial publication it seems as MSFragger would take over soon...