Genoom-, proteoom- en metaboloomanalyse - Bewerkingsoverzicht

R0898021: /* 8u 9/1/2026 */

2026-01-13T09:34:13Z

8u 9/1/2026

← Oudere versie		Versie van 13 jan 2026 11:34
Regel 26:		Regel 26:
	*# This is a tryptic peptide. When this was not given, you could not finish this exercise. Why ?		*# This is a tryptic peptide. When this was not given, you could not finish this exercise. Why ?
	2. Metabolomics- Pontrelli		2. Metabolomics- Pontrelli
	* a. Open question (4 points) Log Transformation and Z-scoring need to be performed before PCA. Why is Z-scoring required before performing PCA ? ~~(Not 100 percent sure anymore):~~ Which information is retained / can be lost during Z-scoring ? In which condition can a misleading conclusion be derived ?		* a. Open question (4 points) Log Transformation and Z-scoring need to be performed before PCA. Why is Z-scoring required before performing PCA ? Which information is retained / can be lost during Z-scoring ? In which condition can a misleading conclusion be derived ?

	3. Genomics- Van Belleghem		3. Genomics- Van Belleghem
Regel 32:		Regel 32:
	*# Sequencing strategy of the first Human genome. Steps in sequencing and genome assembly (5 points)		*# Sequencing strategy of the first Human genome. Steps in sequencing and genome assembly (5 points)
	*# Limitations of the technique (cost, time, accuracy) (3 points)		*# Limitations of the technique (cost, time, accuracy) (3 points)
	*# ~~Compare with~~ modern sequencing strategies ~~(and advantages)(…)~~ (3 points)		*# How have modern sequencing strategies helped in conquering these challenges? (3 points)
	* b. Terms (9 points in total)		* b. Terms (9 points in total)
	*# ChIP-seq (mechanism, which molecules can be detected)		*# ChIP-seq (mechanism, which molecules can be detected)

R0877218: /* 8u 9/1/2026 */

2026-01-09T13:23:52Z

8u 9/1/2026

R0877218: /* 8u 9/1/2026 */

2026-01-09T13:23:07Z

8u 9/1/2026

← Oudere versie		Versie van 9 jan 2026 15:23
Regel 19:		Regel 19:
	=== 8u 9/1/2026 ===		=== 8u 9/1/2026 ===
	1. Proteomics- Temmerman		1. Proteomics- Temmerman
	* a. Open question (4 points):		* a. Open question (4 points): What are PCR based alternatives of MS for proteomics studies ? What are limitations and advantages of these techniques and compare this to Mass spec. Answer: Proximity Extension Assay; SOMAscan
	What are PCR based alternatives of MS for proteomics studies ? What are limitations and advantages of these techniques and compare this to Mass spec.
	Answer: Proximity Extension Assay; SOMAscan
	* b. Exercise question (4 points): No calculator allowed !		* b. Exercise question (4 points): No calculator allowed !
	*# i. A sequence was given (both one letter code and peptide structure of the sequence). Indicate the b2 and y2 ions of this tryptic peptide.		*# i. A sequence was given (both one letter code and peptide structure of the sequence). Indicate the b2 and y2 ions of this tryptic peptide.
Regel 28:		Regel 26:
	*# iv. This is a tryptic peptide. When this was not given, you could not finish this exercise. Why ?		*# iv. This is a tryptic peptide. When this was not given, you could not finish this exercise. Why ?
	2. Metabolomics- Pontrelli		2. Metabolomics- Pontrelli
	* a. Open question (4 points)		* a. Open question (4 points) Log Transformation and Z-scoring need to be performed before PCA. Why is Z-scoring required before performing PCA ? (Not 100 percent sure anymore): Which information is retained / can be lost during Z-scoring ? In which condition can a misleading conclusion be derived ?
	Log Transformation and Z-scoring need to be performed before PCA.
	Why is Z-scoring required before performing PCA ?
	(Not 100 percent sure anymore):
	Which information is retained / can be lost during Z-scoring ?
	In which condition can a misleading conclusion be derived ?

	3. Genomics- Van Belleghem		3. Genomics- Van Belleghem
Regel 44:		Regel 37:
	*# ii. Photolithography (mechanism, in which biological process is this used ?)		*# ii. Photolithography (mechanism, in which biological process is this used ?)
	*# iii. Retrotransposons (origin, mechanism, genome content)		*# iii. Retrotransposons (origin, mechanism, genome content)


	===21/01/2025===		===21/01/2025===

R0877218: /* Examenvragen */

2026-01-09T13:22:05Z

Examenvragen

← Oudere versie		Versie van 9 jan 2026 15:22
Regel 19:		Regel 19:
	=== 8u 9/1/2026 ===		=== 8u 9/1/2026 ===
	1. Proteomics- Temmerman		1. Proteomics- Temmerman
	a. Open question (4 points):		* a. Open question (4 points):
	What are PCR based alternatives of MS for proteomics studies ? What are limitations and advantages of these techniques and compare this to Mass spec.		What are PCR based alternatives of MS for proteomics studies ? What are limitations and advantages of these techniques and compare this to Mass spec.
	Answer: Proximity Extension Assay; SOMAscan		Answer: Proximity Extension Assay; SOMAscan
	b. Exercise question (4 points): No calculator allowed !		* b. Exercise question (4 points): No calculator allowed !
	i. A sequence was given (both one letter code and peptide structure of the sequence). Indicate the b2 and y2 ions of this tryptic peptide.		*# i. A sequence was given (both one letter code and peptide structure of the sequence). Indicate the b2 and y2 ions of this tryptic peptide.
	ii. Spectrum was given. Indicate which peaks correspond to the b2 and y2 ion.		*# ii. Spectrum was given. Indicate which peaks correspond to the b2 and y2 ion.
	iii. Annotate all the other peaks needed to get the peaks for y2 and b2 ions, when no sequence was given and sequencing de novo		*# iii. Annotate all the other peaks needed to get the peaks for y2 and b2 ions, when no sequence was given and sequencing de novo
	iv. This is a tryptic peptide. When this was not given, you could not finish this exercise. Why ?		*# iv. This is a tryptic peptide. When this was not given, you could not finish this exercise. Why ?
	2. Metabolomics- Pontrelli		2. Metabolomics- Pontrelli
	a. Open question (4 points)		* a. Open question (4 points)
	Log Transformation and Z-scoring need to be performed before PCA.		Log Transformation and Z-scoring need to be performed before PCA.
	Why is Z-scoring required before performing PCA ?		Why is Z-scoring required before performing PCA ?
Regel 36:		Regel 36:

	3. Genomics- Van Belleghem		3. Genomics- Van Belleghem
	a. Open Question: Human genome project		* a. Open Question: Human genome project
	i. Sequencing strategy of the first Human genome. Steps in sequencing and genome assembly (5 points)		*# i. Sequencing strategy of the first Human genome. Steps in sequencing and genome assembly (5 points)
	ii. Limitations of the technique (cost, time, accuracy) (3 points)		*# ii. Limitations of the technique (cost, time, accuracy) (3 points)
	iii. Compare with modern sequencing strategies (and advantages)(…)		*# iii. Compare with modern sequencing strategies (and advantages)(…) (3 points)
	(3 points)		* b. Terms (9 points in total)
	b. Terms (9 points in total)		*# i. ChIP-seq (mechanism, which molecules can be detected)
	i. ChIP-seq (mechanism, which molecules can be detected)		*# ii. Photolithography (mechanism, in which biological process is this used ?)
	ii. Photolithography (mechanism, in which biological process is this used ?)		*# iii. Retrotransposons (origin, mechanism, genome content)
	iii. Retrotransposons (origin, mechanism, genome content)

R0877218: /* Examenvragen */

2026-01-09T13:19:58Z

Examenvragen

@@ Regel 17: / Regel 17: @@
 ==Examenvragen==
 ===21/01/2025===
 SVB

R0898021: /* Vakinformatie */

2026-01-04T15:04:25Z

Vakinformatie

← Oudere versie		Versie van 4 jan 2026 17:04
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	2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.		2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.

	2025-2026: De eerste zes hoorcolleges worden gegevens door Prof. Van Belleghem (genomics, transcriptomics, interactomics), de volgende vier door Prof. Temmerman (MS, proteomics, peptidomics) en de laatse twee door Prof. Pontrelli (metabolomics). Er zijn ook oefenzittingen en case studies.		2025-2026: De eerste zes hoorcolleges worden gegevens door Prof. Van Belleghem (genomics, transcriptomics, interactomics), de volgende vier door Prof. Temmerman (MS, proteomics, peptidomics) en de laatse twee door Prof. Pontrelli (metabolomics). Er zijn ook oefenzittingen en case studies. Op het examen zijn er twee theorie delen (elk 40%) en een oefening (20%). Je moet slagen voor het theorie deel van Van Belleghem en het theorie deel van Temmerman/Pontrelli om voor het vak te kunnen slagen.

	ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm		ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm

R0898021: /* Vakinformatie */

2026-01-04T15:00:36Z

Vakinformatie

← Oudere versie		Versie van 4 jan 2026 17:00
Regel 11:		Regel 11:

	2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.		2024-2025: Het vak wordt gegeven door Van Belleghem (genomics) en Temmerman (proteomics en metabolomics). Voor het deel van Temmerman waren er opnames van prof Schoofs en Landuyt, vanwege Temmerman haar zwangerschap. Ze was er wel voor vragen te beantwoorden. Alles is gesloten boek, geschreven examen.

			2025-2026: De eerste zes hoorcolleges worden gegevens door Prof. Van Belleghem (genomics, transcriptomics, interactomics), de volgende vier door Prof. Temmerman (MS, proteomics, peptidomics) en de laatse twee door Prof. Pontrelli (metabolomics). Er zijn ook oefenzittingen en case studies.

	ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm		ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/n/G0G57AN.htm

R0793161: /* 21/01/2025 */

2025-01-27T19:31:34Z

21/01/2025

← Oudere versie		Versie van 27 jan 2025 21:31
Regel 18:		Regel 18:
	SVB		SVB
	* Open question about pangenome analysis including 50 genomes of Arabidopsis individuals from different environments and locations (11 points in total)		* Open question about pangenome analysis including 50 genomes of Arabidopsis individuals from different environments and locations (11 points in total)
	*# Explain the concept of a pangenome analysis and explain the state of the art sequencing technique that can be used in detail (7 points)		*# Explain the concept of a pangenome analysis and explain the state of the art sequencing technique that can be used in detail (6 points)
	*# Comparison of pangenomes to high quality reference genome of Arabidopsis reveals accessory sequences and structural variants. Can you explain what is causing these accessory sequences and structural variants? (3 points)		*# Comparison of pangenomes to high quality reference genome of Arabidopsis reveals accessory sequences and structural variants. Can you explain what is causing these accessory sequences and structural variants? (3 points)
	*# Can you think of at least 2 techniques that can be used to study the functionality of these accessory sequences? (2 points)		*# Can you think of at least 2 techniques that can be used to study the functionality of these accessory sequences? (2 points)

R0793161: /* 21/01/2025 */

2025-01-27T19:31:03Z

21/01/2025

← Oudere versie		Versie van 27 jan 2025 21:31
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	* MS spectrum: Label the axes. Which peptides in spectrum? Identify which peaks belong to which peptides. (4 points)		* MS spectrum: Label the axes. Which peptides in spectrum? Identify which peaks belong to which peptides. (4 points)
	* Are the following statements true or false. Explain briefly (1 point)		* Are the following statements true or false. Explain briefly (1 point)
	*# peptide mass ~~fingerprint ?~~		*# peptide mass fingerprinting can be combined with shotgun proteomics
	*# peptide mass ~~fingerprint~~ requires MS/MS		*# peptide mass fingerprinting requires MS/MS data

	===01/02/2024===		===01/02/2024===

R0793161: /* 21/01/2025 */

2025-01-27T19:30:36Z

21/01/2025

← Oudere versie		Versie van 27 jan 2025 21:30
Regel 21:		Regel 21:
	*# Comparison of pangenomes to high quality reference genome of Arabidopsis reveals accessory sequences and structural variants. Can you explain what is causing these accessory sequences and structural variants? (3 points)		*# Comparison of pangenomes to high quality reference genome of Arabidopsis reveals accessory sequences and structural variants. Can you explain what is causing these accessory sequences and structural variants? (3 points)
	*# Can you think of at least 2 techniques that can be used to study the functionality of these accessory sequences? (2 points)		*# Can you think of at least 2 techniques that can be used to study the functionality of these accessory sequences? (2 points)
	* Terms (~~each term is~~ 3 points so 9 points in total)		* Terms (3 points/term so 9 points in total)
	*# ATAC-seq		*# ATAC-seq
	*# AP-MS		*# AP-MS