🔹 MSFragger/FragPipe continues to evolve rapidly and will continue to be an extraordinarily important tool for MS-based chemical proteomic research (msfragger.nesvilab.org).
(7/11)
(7/11)
MSFragger
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
msfragger.nesvilab.org
November 5, 2026 at 2:49 PM
🔹 MSFragger/FragPipe continues to evolve rapidly and will continue to be an extraordinarily important tool for MS-based chemical proteomic research (msfragger.nesvilab.org).
(7/11)
(7/11)
"Single-cell proteomics with Tesorai Search:
29% more unique peptides in NanoPOTS*
37% higher MS2 ID rate in DISCO
Vs. FragPipe, one-cell conditions, 1% FDR, MBR off.
*Pooled across 10 runs.
Our new application note covers the benchmarks and browser workflow.
www.tesorai.com/resources/si...
29% more unique peptides in NanoPOTS*
37% higher MS2 ID rate in DISCO
Vs. FragPipe, one-cell conditions, 1% FDR, MBR off.
*Pooled across 10 runs.
Our new application note covers the benchmarks and browser workflow.
www.tesorai.com/resources/si...
October 27, 2026 at 4:10 PM
"Single-cell proteomics with Tesorai Search:
29% more unique peptides in NanoPOTS*
37% higher MS2 ID rate in DISCO
Vs. FragPipe, one-cell conditions, 1% FDR, MBR off.
*Pooled across 10 runs.
Our new application note covers the benchmarks and browser workflow.
www.tesorai.com/resources/si...
29% more unique peptides in NanoPOTS*
37% higher MS2 ID rate in DISCO
Vs. FragPipe, one-cell conditions, 1% FDR, MBR off.
*Pooled across 10 runs.
Our new application note covers the benchmarks and browser workflow.
www.tesorai.com/resources/si...
I had a great time visiting the University of Michigan yesterday and giving a talk with a very good discussion afterwards.
It was amazing to re-connect with Alexey Nesvizhskii and Fengchao Yu and discuss all the cool new applications that are possible in MS-based proteomics using FragPipe.
It was amazing to re-connect with Alexey Nesvizhskii and Fengchao Yu and discuss all the cool new applications that are possible in MS-based proteomics using FragPipe.
October 20, 2026 at 3:36 PM
I had a great time visiting the University of Michigan yesterday and giving a talk with a very good discussion afterwards.
It was amazing to re-connect with Alexey Nesvizhskii and Fengchao Yu and discuss all the cool new applications that are possible in MS-based proteomics using FragPipe.
It was amazing to re-connect with Alexey Nesvizhskii and Fengchao Yu and discuss all the cool new applications that are possible in MS-based proteomics using FragPipe.
Authors published a paper in Biorxiv, they used Fragpipe in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
www.biorxiv.org
October 6, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used Fragpipe in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #OpenScience
Expectations in de novo search field:
1. Cascadia working;
2. Casanovo reporting RT and making non-tryptic ckpt compatible with the last release;
3. InstaNovo with winnow integrated;
4. GUI for InstaNovo;
5. Fragnovo release in FragPipe;
6. this is one interesting: langtaosha.org.cn/lts/en/prepr...
1. Cascadia working;
2. Casanovo reporting RT and making non-tryptic ckpt compatible with the last release;
3. InstaNovo with winnow integrated;
4. GUI for InstaNovo;
5. Fragnovo release in FragPipe;
6. this is one interesting: langtaosha.org.cn/lts/en/prepr...
Accurate and ultra-fast de novo HLA-I immunopeptide sequencing with FoxNovo
We present FoxNovo, a hybrid deep learning-combinatorial framework for de novo sequencing of immunopeptides trained on a large-scale HLA-I immunopeptidomics dataset assembled and reprocessed from publ
langtaosha.org.cn
August 6, 2026 at 12:58 PM
Expectations in de novo search field:
1. Cascadia working;
2. Casanovo reporting RT and making non-tryptic ckpt compatible with the last release;
3. InstaNovo with winnow integrated;
4. GUI for InstaNovo;
5. Fragnovo release in FragPipe;
6. this is one interesting: langtaosha.org.cn/lts/en/prepr...
1. Cascadia working;
2. Casanovo reporting RT and making non-tryptic ckpt compatible with the last release;
3. InstaNovo with winnow integrated;
4. GUI for InstaNovo;
5. Fragnovo release in FragPipe;
6. this is one interesting: langtaosha.org.cn/lts/en/prepr...
The following fragment of code if from fragpipe de novo. Does that mean that de novo in fragpipe will run DIA?
private static final String[] MODEL_OPTIONS = {
"DDA_MassIVE",
"ddaPASEF",
"DIA_Orbitrap",
"diaPASEF",
"nonspecific"
}
private static final String[] MODEL_OPTIONS = {
"DDA_MassIVE",
"ddaPASEF",
"DIA_Orbitrap",
"diaPASEF",
"nonspecific"
}
June 16, 2026 at 8:03 PM
The following fragment of code if from fragpipe de novo. Does that mean that de novo in fragpipe will run DIA?
private static final String[] MODEL_OPTIONS = {
"DDA_MassIVE",
"ddaPASEF",
"DIA_Orbitrap",
"diaPASEF",
"nonspecific"
}
private static final String[] MODEL_OPTIONS = {
"DDA_MassIVE",
"ddaPASEF",
"DIA_Orbitrap",
"diaPASEF",
"nonspecific"
}
I have used a BL21 proteome and tried the "recomended" fasta header. The names in fragpipe were messed.
April 24, 2026 at 11:09 PM
I have used a BL21 proteome and tried the "recomended" fasta header. The names in fragpipe were messed.
Is there a file generated by FragPipe that stores information similar to the msms.txt file from MaxQuant? That is, matches (b and y ions), intensities, and m/z values. If not, adding this information would be invaluable.
#FragPipe
#FragPipe
March 29, 2026 at 9:36 PM
Is there a file generated by FragPipe that stores information similar to the msms.txt file from MaxQuant? That is, matches (b and y ions), intensities, and m/z values. If not, adding this information would be invaluable.
#FragPipe
#FragPipe
BTW: You may have noticed how much I like DIANN and FragPipe :)
March 14, 2026 at 3:30 PM
BTW: You may have noticed how much I like DIANN and FragPipe :)
FragPipe users: I've updated PSManalyst shiny app. Check it out and enjoy the easiest way to evaluate the quality of your runs. Now you can map peptides to protein coverage counting PSMs.
github.com/41ison/PSMan...
github.com/41ison/PSMan...
March 13, 2026 at 11:54 PM
FragPipe users: I've updated PSManalyst shiny app. Check it out and enjoy the easiest way to evaluate the quality of your runs. Now you can map peptides to protein coverage counting PSMs.
github.com/41ison/PSMan...
github.com/41ison/PSMan...
I've updated the PSManalyst app for individual psm files. Now you can check how some modifications affect the RT of peptides. Give it a try ;)
github.com/41ison/PSMan...
github.com/41ison/PSMan...
GitHub - 41ison/PSManalyst: Dashboard for PSM and protein information visualization from FragPipe search
Dashboard for PSM and protein information visualization from FragPipe search - GitHub - 41ison/PSManalyst: Dashboard for PSM and protein information visualization from FragPipe search
github.com
December 17, 2025 at 9:18 PM
I've updated the PSManalyst app for individual psm files. Now you can check how some modifications affect the RT of peptides. Give it a try ;)
github.com/41ison/PSMan...
github.com/41ison/PSMan...
It would be amazing if the report.parquet could report the adjacent sequence. Let's say 4 AA before and after the peptide Stripped.Sequence. I do it with left_join from UniProt
id_mapping. This would make the graphical output more complete (as in PSManalyst for FragPipe, github.com/41ison/PSMan...)
id_mapping. This would make the graphical output more complete (as in PSManalyst for FragPipe, github.com/41ison/PSMan...)
October 7, 2025 at 1:14 PM
It would be amazing if the report.parquet could report the adjacent sequence. Let's say 4 AA before and after the peptide Stripped.Sequence. I do it with left_join from UniProt
id_mapping. This would make the graphical output more complete (as in PSManalyst for FragPipe, github.com/41ison/PSMan...)
id_mapping. This would make the graphical output more complete (as in PSManalyst for FragPipe, github.com/41ison/PSMan...)
It's now properly published. If you want to easily check important characteristics of your data before diving into complicated statistics, check out PSManalyst.
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results
FragPipe is recognized as one of the fastest computational platforms in proteomics, making it a practical solution for the rapid quality control of high-throughput sample analyses. Starting with version 23.0, FragPipe introduced the “Generate Summary Report” feature, offering .pdf reports with essential quality control metrics to address the challenge of intuitively assessing large-scale proteomics data. While traditional spreadsheet formats (e.g., tsv files) are accessible, the complexity of the data often limits user-friendly interpretation. To further enhance accessibility, PSManalyst, a Shiny-based R application, was developed to process FragPipe output files (psm.tsv, protein.tsv, and combined_protein.tsv) and provide interactive, code-free data visualization. Users can filter peptide-spectrum matches (PSMs) by quality scores, visualize protease cleavage fingerprints as heatmaps and SeqLogos, and access a range of quality control metrics and representations such as peptide length distributions, ion densities, mass errors, and wordclouds for overrepresented peptides. The tool facilitates seamless switching between PSM and protein data visualization, offering insights into protein abundance discrepancies, samplewise similarity metrics, protein coverage, and contaminants evaluation. PSManalyst leverages several R libraries (lsa, vegan, ggfortify, ggseqlogo, wordcloud2, tidyverse, ggpointdensity, and plotly) and runs on Windows, MacOS, and Linux, requiring only a local R setup and an IDE. The app is available at (https://github.com/41ison/PSManalyst.
pubs.acs.org
August 15, 2025 at 7:45 PM
It's now properly published. If you want to easily check important characteristics of your data before diving into complicated statistics, check out PSManalyst.
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...
And you still can use the PSManalyst for a nice view of the FragPipe search results github.com/41ison/PSMan...
GitHub - 41ison/PSManalyst: Dashboard for PSM and protein information visualization from FragPipe search
Dashboard for PSM and protein information visualization from FragPipe search - GitHub - 41ison/PSManalyst: Dashboard for PSM and protein information visualization from FragPipe search
github.com
July 15, 2025 at 10:55 PM
And you still can use the PSManalyst for a nice view of the FragPipe search results github.com/41ison/PSMan...
They really invested in graphics. Nice. I'm still thinking of building some sort of GUI for this exploratory analysis. Already did it for FragPipe and DIANN. Thinking on next steps, just for fun.
July 4, 2025 at 12:40 AM
They really invested in graphics. Nice. I'm still thinking of building some sort of GUI for this exploratory analysis. Already did it for FragPipe and DIANN. Thinking on next steps, just for fun.
I think it might be useful for some people using FragPipe. You can take advantage of the search speed in FragPipe to quickly check for calibration loss in your mass spectrometry instrument.
You will find an R script and the explanation on how to use it.
Enjoy the code!
github.com/41ison/mass-...
You will find an R script and the explanation on how to use it.
Enjoy the code!
github.com/41ison/mass-...
March 12, 2025 at 12:21 AM
I think it might be useful for some people using FragPipe. You can take advantage of the search speed in FragPipe to quickly check for calibration loss in your mass spectrometry instrument.
You will find an R script and the explanation on how to use it.
Enjoy the code!
github.com/41ison/mass-...
You will find an R script and the explanation on how to use it.
Enjoy the code!
github.com/41ison/mass-...
It's the worst comparison I've ever seen. Right should be: both search engines without rescore or both search engines with the same rescore tool.
www.matrixscience.com/blog/mascot-...
www.matrixscience.com/blog/mascot-...
Mascot vs FragPipe: Uncovering endogenous proteolytic processing
www.matrixscience.com
February 15, 2025 at 12:31 PM
It's the worst comparison I've ever seen. Right should be: both search engines without rescore or both search engines with the same rescore tool.
www.matrixscience.com/blog/mascot-...
www.matrixscience.com/blog/mascot-...
Hi Luke, so it nicely outperforms FragPipe on DDA? Cool :) if something is not working (single charge peptides?), please do post on github, I can take a look at logs and data, maybe config that can be adjusted.
June 21, 2026 at 8:56 AM
Hi Luke, so it nicely outperforms FragPipe on DDA? Cool :) if something is not working (single charge peptides?), please do post on github, I can take a look at logs and data, maybe config that can be adjusted.
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
www.nature.com
November 11, 2025 at 8:06 PM
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Our latest paper is out! 🧬 Discover how DIA-based immunopeptidomics reveals low-abundant Listeria epitopes. Next to Spectronaut directDIA and FragPipe diaTracer, we showcase the feasibility of using DIA-NN proteome-wide predicted immunopeptide libraries!
Read it here 👉 pubs.acs.org/doi/10.1021/...
Read it here 👉 pubs.acs.org/doi/10.1021/...
Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes
Mass spectrometry-based immunopeptidomics is a powerful approach to uncover peptides presented by human leukocyte antigen (HLA) molecules that can guide vaccine design and immunotherapies. While data-...
pubs.acs.org
October 31, 2025 at 12:08 PM
Our latest paper is out! 🧬 Discover how DIA-based immunopeptidomics reveals low-abundant Listeria epitopes. Next to Spectronaut directDIA and FragPipe diaTracer, we showcase the feasibility of using DIA-NN proteome-wide predicted immunopeptide libraries!
Read it here 👉 pubs.acs.org/doi/10.1021/...
Read it here 👉 pubs.acs.org/doi/10.1021/...
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results #JProteomeRes pubs.acs.org/doi/10.1021/...
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results
FragPipe is recognized as one of the fastest computational platforms in proteomics, making it a practical solution for the rapid quality control of high-throughput sample analyses. Starting with versi...
pubs.acs.org
August 16, 2025 at 10:52 AM
PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results #JProteomeRes pubs.acs.org/doi/10.1021/...
There too many such papers around these days, but now with tools such as fragpipe for intact glycopeptides, there’s no longer an excuse …
September 11, 2025 at 8:31 PM
There too many such papers around these days, but now with tools such as fragpipe for intact glycopeptides, there’s no longer an excuse …
The ceiling is not going to be reached, but cohort size is correlated.
Also think goal of search. Fragpipe and spectrum centric searches will find PTMs easier. Peptide centric searches are much faster but have more narrow scope
Also think goal of search. Fragpipe and spectrum centric searches will find PTMs easier. Peptide centric searches are much faster but have more narrow scope
March 6, 2026 at 1:51 PM
The ceiling is not going to be reached, but cohort size is correlated.
Also think goal of search. Fragpipe and spectrum centric searches will find PTMs easier. Peptide centric searches are much faster but have more narrow scope
Also think goal of search. Fragpipe and spectrum centric searches will find PTMs easier. Peptide centric searches are much faster but have more narrow scope
Dear team mass spectrometry, I am acquiring plasma proteomics data in DIA, 60SPD with Evosep-FAIMS (CV-45)Exploris 480, and the pq500 peptides spike in. Can you help me understand what kind of workflow and settings I should use on SP18 and/or on FragPipe-DIANN?
February 25, 2024 at 5:57 PM
Dear team mass spectrometry, I am acquiring plasma proteomics data in DIA, 60SPD with Evosep-FAIMS (CV-45)Exploris 480, and the pq500 peptides spike in. Can you help me understand what kind of workflow and settings I should use on SP18 and/or on FragPipe-DIANN?
From Spectra to Glycobiology: Advances in Glycoproteomics Software with MSFragger-Glyco and FragPipe
A special seminar from Dr. Dan Polasky on advances in mass spectrometry-based glycoproteomics and data analysis.
📅 Thursday, August 20
⏰ 12:30–1:30 PM
📍 CCRC Auditorium | UGA
#biofgreat #glycotime
A special seminar from Dr. Dan Polasky on advances in mass spectrometry-based glycoproteomics and data analysis.
📅 Thursday, August 20
⏰ 12:30–1:30 PM
📍 CCRC Auditorium | UGA
#biofgreat #glycotime
August 13, 2026 at 7:11 PM
From Spectra to Glycobiology: Advances in Glycoproteomics Software with MSFragger-Glyco and FragPipe
A special seminar from Dr. Dan Polasky on advances in mass spectrometry-based glycoproteomics and data analysis.
📅 Thursday, August 20
⏰ 12:30–1:30 PM
📍 CCRC Auditorium | UGA
#biofgreat #glycotime
A special seminar from Dr. Dan Polasky on advances in mass spectrometry-based glycoproteomics and data analysis.
📅 Thursday, August 20
⏰ 12:30–1:30 PM
📍 CCRC Auditorium | UGA
#biofgreat #glycotime