# \#proteomics **URL:** https://help.galaxyproject.org/tag/proteomics/228.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [SAINTexpress data](https://help.galaxyproject.org/t/saintexpress-data/16394)
**Author:** [@Bernard](https://help.galaxyproject.org/u/Bernard)\ **Replies:** 7\ **Last updated:** [April 8, 2026, 2:22am UTC](https://help.galaxyproject.org/t/saintexpress-data/16394 "2026-04-08T02:22:26Z")
How does one specify if input data submitted to SAINTexpress are spectral counts or MS1 intensities? Also, should MS1 intensities be Log transformed? Thank you --- ## [GrowthPred troubleshooting](https://help.galaxyproject.org/t/growthpred-troubleshooting/16559)
**Author:** [@Darshan\_Singh](https://help.galaxyproject.org/u/Darshan_Singh)\ **Replies:** 3\ **Last updated:** [December 15, 2025, 7:12pm UTC](https://help.galaxyproject.org/t/growthpred-troubleshooting/16559 "2025-12-15T19:12:13Z")
Hi, were you able to solve this using the aforementioned solution. When I had done so it did not work. --- ## [Issues running GrowthPred with genomes](https://help.galaxyproject.org/t/issues-running-growthpred-with-genomes/8268)
**Author:** [@Rosave](https://help.galaxyproject.org/u/Rosave)\ **Replies:** 3\ **Last updated:** [September 23, 2022, 6:46pm UTC](https://help.galaxyproject.org/t/issues-running-growthpred-with-genomes/8268 "2022-09-23T18:46:46Z")
Hi I have high-quality draft genomes and I’m having issues running them on GrowthPred to calculate predicted ideal growth temperature. I’ve uploaded the following files (see below) and in all instances I’ve received the… --- ## [Generating MD Topology (ACPYPE)](https://help.galaxyproject.org/t/generating-md-topology-acpype/15017)
**Author:** [@XavierB](https://help.galaxyproject.org/u/XavierB)\ **Replies:** 6\ **Last updated:** [September 26, 2025, 1:07am UTC](https://help.galaxyproject.org/t/generating-md-topology-acpype/15017 "2025-09-26T01:07:46Z")
Hi I desperately try (for months) to generate GROMACS topology for a ligand using Galaxy.EU server ACPYPE tool. Trying to use PDB or mol2 input file, trying to calculate the charges (bcc) or not, each times the job fai… --- ## [Peptide Shaker Job Failure](https://help.galaxyproject.org/t/peptide-shaker-job-failure/15881)
**Author:** [@Lincoln\_Liburd](https://help.galaxyproject.org/u/Lincoln_Liburd)\ **Replies:** 2\ **Last updated:** [July 16, 2025, 4:22pm UTC](https://help.galaxyproject.org/t/peptide-shaker-job-failure/15881 "2025-07-16T16:22:39Z")
Galaxy Tool Error Report from https://usegalaxy.org/ Error Localization Dataset 128537196 (f9cad7b01a47213591554cf62bef75f3) History 11033459 (bbd44e69cb8906b5610647652733cf85) Failed Job 104: Peptide Shaker o… --- ## [Galaxy's Maxquant problem](https://help.galaxyproject.org/t/galaxys-maxquant-problem/15347)
**Author:** [@Christos-Kotsopoulos](https://help.galaxyproject.org/u/Christos-Kotsopoulos)\ **Replies:** 2\ **Last updated:** [April 30, 2025, 11:10pm UTC](https://help.galaxyproject.org/t/galaxys-maxquant-problem/15347 "2025-04-30T23:10:37Z")
Hello everyone, I am facing a problem with i am trying to do a mass spec analysis with galaxys Maxquant. I initially used the .raw files from this experiment (PRIDE id:PXD027714) and imported them on galaxy and followed… --- ## [Check Format for running the statistical analysis of Mass spectrometry intensity data](https://help.galaxyproject.org/t/check-format-for-running-the-statistical-analysis-of-mass-spectrometry-intensity-data/14637)
**Author:** [@Nan\_khan\_Cho](https://help.galaxyproject.org/u/Nan_khan_Cho)\ **Replies:** 1\ **Last updated:** [February 3, 2025, 8:06pm UTC](https://help.galaxyproject.org/t/check-format-for-running-the-statistical-analysis-of-mass-spectrometry-intensity-data/14637 "2025-02-03T20:06:18Z")
I could not run tool after put the data of Mass Spectrometry intensity data.May I get the idea to solve the problems. Thank you. --- ## [MSMetaEnhancer can't reach services if running on usegalaxy.eu](https://help.galaxyproject.org/t/msmetaenhancer-cant-reach-services-if-running-on-usegalaxy-eu/11821)
**Author:** [@hechth](https://help.galaxyproject.org/u/hechth)\ **Replies:** 5\ **Last updated:** [January 9, 2025, 6:38pm UTC](https://help.galaxyproject.org/t/msmetaenhancer-cant-reach-services-if-running-on-usegalaxy-eu/11821 "2025-01-09T18:38:00Z")
The MSMetaEnhancer tool can’t reach webservices like PubChem and IDSM when running on usegalaxy.eu. An example history is available here: Galaxy The tool passes but the logfile - dataset 3 - contains the information tha… --- ## [PDB format versus PQR format](https://help.galaxyproject.org/t/pdb-format-versus-pqr-format/14041)
**Author:** [@doughfanb](https://help.galaxyproject.org/u/doughfanb)\ **Replies:** 2\ **Last updated:** [December 14, 2024, 10:12am UTC](https://help.galaxyproject.org/t/pdb-format-versus-pqr-format/14041 "2024-12-14T10:12:44Z")
Hi. I uploaded my protein in pdb but galaxy is identifying the format as pqr. What can I do about this? --- ## [Troubleshooting protein-ligand docking tutorial](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011)
**Author:** [@FOZIAH\_ALSHUBAILY](https://help.galaxyproject.org/u/FOZIAH_ALSHUBAILY)\ **Replies:** 2\ **Last updated:** [November 28, 2024, 6:12am UTC](https://help.galaxyproject.org/t/troubleshooting-protein-ligand-docking-tutorial/14011 "2024-11-28T06:12:24Z")
I have same problem, please help --- ## [Persistent problems with RMSD analysis relate to the Guide "High Throughput Molecular Dynamics and Analysis"](https://help.galaxyproject.org/t/persistent-problems-with-rmsd-analysis-relate-to-the-guide-high-throughput-molecular-dynamics-and-analysis/13971)
**Author:** [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Replies:** 1\ **Last updated:** [November 26, 2024, 2:03am UTC](https://help.galaxyproject.org/t/persistent-problems-with-rmsd-analysis-relate-to-the-guide-high-throughput-molecular-dynamics-and-analysis/13971 "2024-11-26T02:03:38Z")
Dear Jennai, Thank you very much for your time and the clear explanations you provided. I also noticed that you’re one of the authors of the Guide—it’s great to be working with someone so knowledgeable! I’ve attempted … --- ## [Problems with RMSD analysis relate to the Guide "High Throughput Molecular Dynamics and Analysis"](https://help.galaxyproject.org/t/problems-with-rmsd-analysis-relate-to-the-guide-high-throughput-molecular-dynamics-and-analysis/13919)
**Author:** [@henrrik\_prendushi](https://help.galaxyproject.org/u/henrrik_prendushi)\ **Replies:** 2\ **Last updated:** [November 20, 2024, 8:40am UTC](https://help.galaxyproject.org/t/problems-with-rmsd-analysis-relate-to-the-guide-high-throughput-molecular-dynamics-and-analysis/13919 "2024-11-20T08:40:09Z")
Dear Friends I’m going, a little slowly, through the Guide—questions of time. I have a problem and I will try to describe it. I arrived at the RMSD analysis, seemingly, without problems. When I ran the RMSD analysis … --- ## [can i perform docking for a protein without ligand](https://help.galaxyproject.org/t/can-i-perform-docking-for-a-protein-without-ligand/13822)
**Author:** [@FOZIAH\_ALSHUBAILY](https://help.galaxyproject.org/u/FOZIAH_ALSHUBAILY)\ **Replies:** 1\ **Last updated:** [November 5, 2024, 7:44pm UTC](https://help.galaxyproject.org/t/can-i-perform-docking-for-a-protein-without-ligand/13822 "2024-11-05T19:44:47Z")
Docking of a protein with no ligand --- ## [FragPipe - Academic Research and Education User License (Non-Commercial)](https://help.galaxyproject.org/t/fragpipe-academic-research-and-education-user-license-non-commercial/13782)
**Author:** [@Lizex](https://help.galaxyproject.org/u/Lizex)\ **Replies:** 1\ **Last updated:** [October 29, 2024, 5:23pm UTC](https://help.galaxyproject.org/t/fragpipe-academic-research-and-education-user-license-non-commercial/13782 "2024-10-29T17:23:23Z")
Hi I tried running Fragpipe tool but I get an error message saying there is a new version of MSFragger. How can I update this tool or any of the other tools like Fragpipe. --- ## [Questions about uploading PDB file to 'Prepare receptor'](https://help.galaxyproject.org/t/questions-about-uploading-pdb-file-to-prepare-receptor/13438)
**Author:** [@jjh1998](https://help.galaxyproject.org/u/jjh1998)\ **Replies:** 1\ **Last updated:** [September 13, 2024, 6:19pm UTC](https://help.galaxyproject.org/t/questions-about-uploading-pdb-file-to-prepare-receptor/13438 "2024-09-13T18:19:01Z")
Hi, I’m trying to convert pdb file into pdbqt file for VINA docking. But even if I upload my pdb file to ‘Prepare receptor’, the program recognizes the file as pqr format. Is there a way to solve this? I generated pdb… --- ## [MSstats tool error](https://help.galaxyproject.org/t/msstats-tool-error/13125)
**Author:** [@esinsahin](https://help.galaxyproject.org/u/esinsahin)\ **Replies:** 2\ **Last updated:** [August 5, 2024, 5:35pm UTC](https://help.galaxyproject.org/t/msstats-tool-error/13125 "2024-08-05T17:35:01Z")
Hello, I have been trying to use MSStat tool in Galaxy, where I uploaded SRM data in MSstat format however, I got an error: cant assign 4 names to a 0 column data table. How can I solve this? I also tried uploading sky… --- ## [GROMACs troubleshooting](https://help.galaxyproject.org/t/gromacs-troubleshooting/13005)
**Author:** [@aczoo\_rs\_University](https://help.galaxyproject.org/u/aczoo_rs_University)\ **Replies:** 20\ **Last updated:** [July 29, 2024, 10:43pm UTC](https://help.galaxyproject.org/t/gromacs-troubleshooting/13005 "2024-07-29T22:43:57Z")
I am also having trouble with the Gromacs initial setup. Galaxy… this is my history, please help me with this. --- ## [GROMACS simulation](https://help.galaxyproject.org/t/gromacs-simulation/13000)
**Author:** [@Prasanna\_s\_BIOLOGY](https://help.galaxyproject.org/u/Prasanna_s_BIOLOGY)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 8:29pm UTC](https://help.galaxyproject.org/t/gromacs-simulation/13000 "2024-07-17T20:29:16Z")
For how long MD simulation can be performed in Galaxy platform? --- ## [GROMACS MD Simulation](https://help.galaxyproject.org/t/gromacs-md-simulation/11287)
**Author:** [@Vibha\_Rao](https://help.galaxyproject.org/u/Vibha_Rao)\ **Replies:** 1\ **Last updated:** [December 7, 2023, 9:27pm UTC](https://help.galaxyproject.org/t/gromacs-md-simulation/11287 "2023-12-07T21:27:14Z")
I received this error when using the GROMACS initial setup tool WARNING: No ICDs were found. Either, Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or Make y… --- ## [Adding new proteomics tool on usegalaxy.eu](https://help.galaxyproject.org/t/adding-new-proteomics-tool-on-usegalaxy-eu/12233)
**Author:** [@sciordia](https://help.galaxyproject.org/u/sciordia)\ **Replies:** 2\ **Last updated:** [April 20, 2024, 10:22am UTC](https://help.galaxyproject.org/t/adding-new-proteomics-tool-on-usegalaxy-eu/12233 "2024-04-20T10:22:03Z")
Hi. I was wondering if it would be possible to add a new proteomics tool (link below) to the public usegalaxy.eu server that is associated with the protein identification using a FASTA Database?. SageAdapter Sage: Th… --- ## [msconvert problems](https://help.galaxyproject.org/t/msconvert-problems/11573)
**Author:** [@droslj](https://help.galaxyproject.org/u/droslj)\ **Replies:** 2\ **Last updated:** [January 25, 2024, 6:55am UTC](https://help.galaxyproject.org/t/msconvert-problems/11573 "2024-01-25T06:55:52Z")
To date I have tried running msconvert in Galaxy EU for AB Sciex raw data format, uploaded as composite data set, with no success, I don’t know what else to try, I keep getting the following error: msconvert\] no files f… --- ## [SGPS works on galaxy EU but not on main.](https://help.galaxyproject.org/t/sgps-works-on-galaxy-eu-but-not-on-main/11241)
**Author:** [@Edwin\_Huang](https://help.galaxyproject.org/u/Edwin_Huang)\ **Replies:** 7\ **Last updated:** [December 11, 2023, 3:19pm UTC](https://help.galaxyproject.org/t/sgps-works-on-galaxy-eu-but-not-on-main/11241 "2023-12-11T15:19:35Z")
Hi, I’m working trying to run SearchGUI & PeptideShaker on Galaxy main and I’m getting this error on PeptideShaker: Archive: searchgui\_input.zip inflating: IdentificationParametersOutput.par An error occurred when sav… --- ## [Protein-ligand docking error](https://help.galaxyproject.org/t/protein-ligand-docking-error/11229)
**Author:** [@Vibha\_Rao](https://help.galaxyproject.org/u/Vibha_Rao)\ **Replies:** 3\ **Last updated:** [November 29, 2023, 6:09pm UTC](https://help.galaxyproject.org/t/protein-ligand-docking-error/11229 "2023-11-29T18:09:04Z")
Hey, I have been trying to following this tutorial for protein-ligand docking(Protein-ligand docking). I used 200 coumarin derivatives as my ligand library which I got in pdf format from MolPort. However, the vina docki… --- ## [Hello everyone, i have problem when i do gromacs simulation for protein-ligand complex](https://help.galaxyproject.org/t/hello-everyone-i-have-problem-when-i-do-gromacs-simulation-for-protein-ligand-complex/11144)
**Author:** [@Howida\_Nail](https://help.galaxyproject.org/u/Howida_Nail)\ **Replies:** 2\ **Last updated:** [November 16, 2023, 1:55am UTC](https://help.galaxyproject.org/t/hello-everyone-i-have-problem-when-i-do-gromacs-simulation-for-protein-ligand-complex/11144 "2023-11-16T01:55:23Z")
Tool Standard Error /data/jwd05e/main/064/671/64671535/tool\_script.sh: line 26: 3429218 Segmentation fault (core dumped) gmx mdrun -nt “${GALAXY\_SLOTS:-4}” -deffnm outp &\>\> verbose.txt { “code\_desc”: “”, “desc”:… --- ## [Issue with "ConvertPrositCSVToLibrary" - completes successfully but produces 0 bytes of data](https://help.galaxyproject.org/t/issue-with-convertprositcsvtolibrary-completes-successfully-but-produces-0-bytes-of-data/11027)
**Author:** [@prao123](https://help.galaxyproject.org/u/prao123)\ **Replies:** 1\ **Last updated:** [October 20, 2023, 10:12pm UTC](https://help.galaxyproject.org/t/issue-with-convertprositcsvtolibrary-completes-successfully-but-produces-0-bytes-of-data/11027 "2023-10-20T22:12:45Z")
Hello, When executing the tool “PrositCSV to Library” (converts a csv file format to a DLIB spectral library file) , the tool completes but the output is 0 bytes of data. I have tried it with a couple of different data… --- ## [Issue running DIA-NN: Errors out with "command not found"](https://help.galaxyproject.org/t/issue-running-dia-nn-errors-out-with-command-not-found/10995)
**Author:** [@prao123](https://help.galaxyproject.org/u/prao123)\ **Replies:** 4\ **Last updated:** [October 19, 2023, 8:10pm UTC](https://help.galaxyproject.org/t/issue-running-dia-nn-errors-out-with-command-not-found/10995 "2023-10-19T20:10:12Z")
Hello, I am trying to run a dataset of DIA data through DIA-NN. The tool gives me a “command not found” error. Below is the command which it runs and the error produced: mkdir ./input\_data && mkdir ./tmp && ln -s '/da… --- ## [SignalP output from InterProScan](https://help.galaxyproject.org/t/signalp-output-from-interproscan/10791)
**Author:** [@TRT](https://help.galaxyproject.org/u/TRT)\ **Replies:** 2\ **Last updated:** [September 14, 2023, 6:53am UTC](https://help.galaxyproject.org/t/signalp-output-from-interproscan/10791 "2023-09-14T06:53:17Z")
Hi, I’m annotation a set of protein sequences for presence or absence of signal peptide with SignalP through InterProScan. It is the first time I’m doing this. Everything seems to work ok, however in the output there is… --- ## [AlphaFold2 Error - Could not find HHsearch database /data/pdb70/pdb70](https://help.galaxyproject.org/t/alphafold2-error-could-not-find-hhsearch-database-data-pdb70-pdb70/8593)
**Author:** [@sunag\_parasu](https://help.galaxyproject.org/u/sunag_parasu)\ **Replies:** 10\ **Last updated:** [May 12, 2023, 1:35pm UTC](https://help.galaxyproject.org/t/alphafold2-error-could-not-find-hhsearch-database-data-pdb70-pdb70/8593 "2023-05-12T13:35:57Z")
I tried running a FASTA sequence on AlphaFold2 and it showed me this error: E0902 16:02:23.065268 22797118093120 hhsearch.py:56\] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): Fi… --- ## [Adding new aa modification (D4-Lysine) to MetaNovo tool](https://help.galaxyproject.org/t/adding-new-aa-modification-d4-lysine-to-metanovo-tool/9924)
**Author:** [@qcsciphi](https://help.galaxyproject.org/u/qcsciphi)\ **Replies:** 1\ **Last updated:** [April 24, 2023, 9:51am UTC](https://help.galaxyproject.org/t/adding-new-aa-modification-d4-lysine-to-metanovo-tool/9924 "2023-04-24T09:51:55Z")
Dear Galaxu.eu admin and/or specialists, Thanks for your constant support of the Galaxy server and tools. I am dealing with proteo-genomics and using the MetaNovo tool on Galaxy.eu. However a SILAC proteomic data sourc… --- ## [Spectral library for serum data](https://help.galaxyproject.org/t/spectral-library-for-serum-data/9847)
**Author:** [@Akhila\_B\_Rai](https://help.galaxyproject.org/u/Akhila_B_Rai)\ **Replies:** 1\ **Last updated:** [April 19, 2023, 7:19pm UTC](https://help.galaxyproject.org/t/spectral-library-for-serum-data/9847 "2023-04-19T19:19:36Z")
Hi, I wanted to know whether we can use tissue spectral library for serum DIA data? Thanks, Akhila [Next page](https://help.galaxyproject.org/tag/proteomics/228.md?match_all_tags=true&page=1&tags%5B%5D=proteomics)