Exercise:AntigenProcessing - Revision history

Carol: /* Data Collection: Get the Data and Filter It */

2026-09-23T09:57:47Z

Data Collection: Get the Data and Filter It

← Older revision		Revision as of 11:57, 23 September 2026
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	In addition, inspect the column containing the '''MHC Types present in the host'''.		In addition, inspect the column containing the '''MHC Types present in the host'''.

	*'''Q5: Which alleles are expressed in the ~~patient~~ used for this assay?'''		*'''Q5: Which alleles are expressed in each of the patients used for this assay?'''
	BAD LUCK! It seems that IEDB missed the annotation of the specific alleles for each peptide, we can only read "HL-DR" on MHC restriction. This is insufficient for our purpose, so we will need to traceback the original data from the original publication. Find it. look for table 1 and table 2. Luckily your friend ChatGPT can do the tedious work for ~~you separating the~~ peptides ~~into five files, and can also read~~ the ~~paper for you~~ to ~~tell~~ you ~~which HLA alleles has each patient~~. Try to do this prompt with your favourite LLM-friend.'''		BAD LUCK! It seems that IEDB missed the annotation of the specific alleles for each peptide, we can only read "HL-DR" on MHC restriction. This is insufficient for our purpose, so we will need to traceback the original data from the original publication. Find it. look for table 1 and supplementary table 2 in the original paper. Luckily your friend ChatGPT can do the tedious work by reading table 1 to find the hla alleles for each patient and making a list of which peptides on the IEDB belong to each of the patients. There are 5 Rheumatoid Arthritis patients, so you should expect five files with peptides. Try to do this prompt with your favourite LLM-friend.'''

	Now have the grasped of how much effort takes to create a curated database. You can also observe that databases contain errors, and missing data. If you still didn't manage to ask the relevant question to your LLM sparring partner.. no worries, you can download all 5 files from DTU Learn in a zip file called Datasets_for_antigen_processing.zip		Now have the grasped of how much effort takes to create a curated database. You can also observe that databases contain errors, and missing data, like in this case for the IEDB. If you still didn't manage to ask the relevant question to your LLM sparring partner.. no worries, you can download all 5 files from DTU Learn in a zip file called Datasets_for_antigen_processing.zip

Carol: /* GibbsCluster */

2026-09-22T20:34:23Z

GibbsCluster

← Older revision		Revision as of 22:34, 22 September 2026
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	Click '''Submit'''.		Click '''Submit'''.

			To save you some time I have performed two searches:
			In the first one all the peptides from the different patients have been combined:
			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2E38A000C5E087D058D4B&wait=20

			In the second one only the peptides from patient RA 2 have been included:
			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2E615000C60D27CDD1E9F&wait=20

	*'''Q10: Does the number of clusters found by GibbsCluster correspond to the number of HLA alleles in your sample?'''		*'''Q10: Does the number of clusters found by GibbsCluster correspond to the number of HLA alleles in your sample?'''

Carol: /* GibbsCluster */

2026-09-22T20:23:30Z

GibbsCluster

← Older revision		Revision as of 22:23, 22 September 2026
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	*'''Q11: Can you identify other differences between the GibbsCluster solution and the MHCMotifDecon solution?'''		*'''Q11: Can you identify other differences between the GibbsCluster solution and the MHCMotifDecon solution?'''

	~~---~~		== Conclusion ==

	You should now have experience with two different approaches for analysing complex immunopeptidomics datasets:		You should now have experience with two different approaches for analysing complex immunopeptidomics datasets:

Carol: /* MHCMotifDecon */

2026-09-22T19:53:05Z

MHCMotifDecon

← Older revision		Revision as of 21:53, 22 September 2026
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	Run MHCMotifDecon again with this additional alleles.		Run MHCMotifDecon again with this additional alleles.

	*'''Q9: How many peptides are now associated with HLA-~~DRB4~~? Where did these peptides come from?'''		*'''Q9: How many peptides are now associated with HLA-DRB3,4 and 5? Where did these peptides come from?'''

	https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2D94E000C4F404E837EBC&wait=20		https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2D94E000C4F404E837EBC&wait=20

Carol: /* MHCMotifDecon */

2026-09-22T19:47:27Z

MHCMotifDecon

← Older revision		Revision as of 21:47, 22 September 2026
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	If you want to learn more about this topic, search for '''HLA-DR linkage disequilibrium'''.		If you want to learn more about this topic, search for '''HLA-DR linkage disequilibrium'''.

	~~Having this information~~, ~~extend~~ the ~~HLA typing of~~ the ~~experiment~~ by ~~including:~~		To predict which alleles are in linkage disequilibrium with your HLA-DRB1 alleles, you can use the following server. Make sure that you input the patients information on the right format by looking at the test example.

	~~DRB4_0101~~		[https://services.healthtech.dtu.dk/services/HLAAssoc-1.0/ HLAAssoc]

	Run MHCMotifDecon again with this additional ~~allele~~.
			Having this information, now go back to MHC Motif Decon and extend the HLA typing of the patients.

			If everything goes bananas and you are completely lost, dont panic! Here is the output of HLAAssoc:

			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2D62B000C48502E9E90B0&wait=20


			Run MHCMotifDecon again with this additional alleles.

	*'''Q9: How many peptides are now associated with HLA-DRB4? Where did these peptides come from?'''		*'''Q9: How many peptides are now associated with HLA-DRB4? Where did these peptides come from?'''

			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2D94E000C4F404E837EBC&wait=20

	== GibbsCluster ==		== GibbsCluster ==

Carol: /* MHCMotifDecon */

2026-09-22T19:23:02Z

MHCMotifDecon

← Older revision		Revision as of 21:23, 22 September 2026
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	*'''Q7: Can you see any differences between the trash-cluster peptides and the peptides assigned to a specific allele? Explain.'''		*'''Q7: Can you see any differences between the trash-cluster peptides and the peptides assigned to a specific allele? Explain.'''

	Go back to the previous submission and modify the '''%rank threshold'''.		Go back to the previous submission and modify the '''%rank threshold''' to 2%.

	*'''Q8: What is the effect of changing the %rank threshold?'''		*'''Q8: What is the effect of changing the %rank threshold?'''

Carol: /* MHCMotifDecon */

2026-09-22T19:20:15Z

MHCMotifDecon

← Older revision		Revision as of 21:20, 22 September 2026
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	Go to the [https://services.healthtech.dtu.dk/services/MHCMotifDecon-1.2/ MHCMotifDecon server] and select '''MHC class II''' as the input type.		Go to the [https://services.healthtech.dtu.dk/services/MHCMotifDecon-1.2/ MHCMotifDecon server] and select '''MHC class II''' as the input type.

	~~For~~ this ~~exercise,~~ we will analyse all five RA patients in the same run. Upload the provided peptide file in the main input field. Each line contains the '''peptide sequence followed by the patient ID''', separated by a tab:		In this section we will analyse all five RA patients in the same run. Upload the provided peptide file in the main input field. Each line contains the '''peptide sequence followed by the patient ID''', separated by a tab:

	PEPTIDESEQUENCE RA1		PEPTIDESEQUENCE RA1
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	Press '''Submit'''. When the analysis is complete, inspect the motif deconvolution plots and peptide-count results for each patient. Peptides predicted not to bind sufficiently strongly to any of the HLA molecules supplied for that patient are assigned to the '''Trash''' cluster.		Press '''Submit'''. When the analysis is complete, inspect the motif deconvolution plots and peptide-count results for each patient. Peptides predicted not to bind sufficiently strongly to any of the HLA molecules supplied for that patient are assigned to the '''Trash''' cluster.


	If you are ''really''' struggling to get the peptides in the right format to make MHC Motif Deconvolution work.. you can get to the output shortcut here and answer the questions (this temporary link will not work more than a few hours for the exercise, so remember to download the output):		If you are ''really''' struggling to get the peptides in the right format to make MHC Motif Deconvolution work.. you can get to the output shortcut here and answer the questions (this temporary link will not work more than a few hours for the exercise, so remember to download the output):

Carol: /* MHCMotifDecon */

2026-09-22T19:10:24Z

MHCMotifDecon

← Older revision		Revision as of 21:10, 22 September 2026
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	If you are ''really''' struggling to get the peptides in the right format to make MHC Motif Deconvolution work.. you can get to the output shortcut here and answer the questions (this temporary link will not work more than a few hours for the exercise, so remember to download the output):		If you are ''really''' struggling to get the peptides in the right format to make MHC Motif Deconvolution work.. you can get to the output shortcut here and answer the questions (this temporary link will not work more than a few hours for the exercise, so remember to download the output):
	https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2CF75000C1FD0C658852D&wait=20		https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2CF75000C1FD0C658852D&wait=20


	*'''Q6: How many peptides were assigned to each of the alleles, and how many were assigned to the trash cluster?'''		*'''Q6: How many peptides were assigned to each of the alleles, and how many were assigned to the trash cluster?'''

Carol: /* MHCMotifDecon */

2026-09-22T19:08:52Z

MHCMotifDecon

← Older revision		Revision as of 21:08, 22 September 2026
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	For this exercise, we will analyse all five RA patients in the same run. Upload the provided peptide file in the main input field. Each line contains the '''peptide sequence followed by the patient ID''', separated by a tab:		For this exercise, we will analyse all five RA patients in the same run. Upload the provided peptide file in the main input field. Each line contains the '''peptide sequence followed by the patient ID''', separated by a tab:

	PEPTIDESEQUENCE RA1		PEPTIDESEQUENCE RA1
	PEPTIDESEQUENCE RA2		PEPTIDESEQUENCE RA2

	The server refers to the patient ID as the '''Cell_line_ID'''. This identifier allows MHCMotifDecon to keep peptides from the different patients separate during the analysis.		The server refers to the patient ID as the '''Cell_line_ID'''. This identifier allows MHCMotifDecon to keep peptides from the different patients separate during the analysis.
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	Because we are analysing multiple patients, use the section '''"If input data is for multiple cell lines"''' to upload the provided HLA allele file. The format is:		Because we are analysing multiple patients, use the section '''"If input data is for multiple cell lines"''' to upload the provided HLA allele file. The format is:

	RA1 DRB1_0402,DRB1_1104		RA1 DRB1_0402,DRB1_1104
	RA2 DRB1_0101,DRB1_0401		RA2 DRB1_0101,DRB1_0401

	Make sure that the patient IDs in the HLA file (RA1, RA2, etc.) are exactly the same as those in the peptide file. Multiple HLA alleles for the same patient are separated by commas without spaces.		Make sure that the patient IDs in the HLA file (RA1, RA2, etc.) are exactly the same as those in the peptide file. Multiple HLA alleles for the same patient are separated by commas without spaces.

Carol: /* MHCMotifDecon */

2026-09-22T19:08:36Z

MHCMotifDecon

← Older revision		Revision as of 21:08, 22 September 2026
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	== MHCMotifDecon ==		== MHCMotifDecon ==

	Go to the [https://services.healthtech.dtu.dk/~~service.php?~~MHCMotifDecon-1.2 MHCMotifDecon server].		Go to the [https://services.healthtech.dtu.dk/services/MHCMotifDecon-1.2/ MHCMotifDecon server] and select '''MHC class II''' as the input type.

	~~Enter~~ the ~~submission page and select~~ '''~~MHC class II~~'''.		For this exercise, we will analyse all five RA patients in the same run. Upload the provided peptide file in the main input field. Each line contains the '''peptide sequence followed by the patient ID''', separated by a tab:

	~~Paste the list of peptides into the input window. The input should contain only '''one column of peptide sequences'''.~~		PEPTIDESEQUENCE RA1
			PEPTIDESEQUENCE RA2

	~~Scroll down and select~~ the '''~~HLA-DR alleles~~''' ~~expressed by~~ the ~~cell line for which~~ the ~~immunopeptidomics assay was performed~~.		The server refers to the patient ID as the '''Cell_line_ID'''. This identifier allows MHCMotifDecon to keep peptides from the different patients separate during the analysis.

	~~Press~~ '''~~Submit~~'''.		Because we are analysing multiple patients, use the section '''"If input data is for multiple cell lines"''' to upload the provided HLA allele file. The format is:

	'''Note:''' ~~Be aware that~~ HLA alleles ~~are entered into this software using a particular naming format~~. For example:		RA1 DRB1_0402,DRB1_1104
			RA2 DRB1_0101,DRB1_0401

			Make sure that the patient IDs in the HLA file (RA1, RA2, etc.) are exactly the same as those in the peptide file. Multiple HLA alleles for the same patient are separated by commas without spaces.

			'''Note:''' MHCMotifDecon uses a specific notation for HLA alleles. For example:

	HLA-DRB1*01:01 → DRB1_0101		HLA-DRB1*01:01 → DRB1_0101

			Under '''Additional configuration''', keep the default MHC class II peptide-length range ('''12–21 amino acids''') and the default '''%Rank threshold''' for the first analysis. Select '''Include peptide count histogram''' so that the number of peptides assigned to each HLA molecule can be easily compared.

			Press '''Submit'''. When the analysis is complete, inspect the motif deconvolution plots and peptide-count results for each patient. Peptides predicted not to bind sufficiently strongly to any of the HLA molecules supplied for that patient are assigned to the '''Trash''' cluster.


			If you are ''really''' struggling to get the peptides in the right format to make MHC Motif Deconvolution work.. you can get to the output shortcut here and answer the questions (this temporary link will not work more than a few hours for the exercise, so remember to download the output):
			https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi?jobid=6AB2CF75000C1FD0C658852D&wait=20


	*'''Q6: How many peptides were assigned to each of the alleles, and how many were assigned to the trash cluster?'''		*'''Q6: How many peptides were assigned to each of the alleles, and how many were assigned to the trash cluster?'''