Item card
Metabolomics and lipidomics BF
Some basic information about the module
Cycle of education:
2017/2018
The name of the faculty organization unit:
The faculty Chemistry
The name of the field of study:
Biotechnology
The area of study:
technical sciences
The profile of studing:
The level of study:
second degree study
Type of study:
full time
discipline specialities :
Laboratory diagnostics in biotechnology (DL), Pharmaceutical biotechnology (BF), process and bioprocess engineering (IP), Purification and analysis of biotechnological products (OA)
The degree after graduating from university:
Master of Science (MSc)
The name of the module department :
Department of Inorganic and Analytical Chemistry
The code of the module:
10264
The module status:
mandatory for the speciality Pharmaceutical biotechnology (BF)
The position in the studies teaching programme:
sem: 2 / W15 L30 / 3 ECTS / E
The language of the lecture:
Polish
The name of the coordinator:
Prof. Tomasz Ruman, DSc, PhD, Eng.
office hours of the coordinator:
pon - pt 10-11
semester 2:
Joanna Nizioł, DSc, PhD
The aim of studying and bibliography
The main aim of study:
Metabolomics is the systematic study of the unique chemical fingerprints that specific cellular processes leave behind. It is the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression. Metabolic profiling can give an instantaneous snapshot of the physiology of that cell/organ/organism.
The aim of this module is to transfer knowledge regarding metabolites, metabolic profiling methods and also about analysis of metabolic information derived from single compounds and from complex metabolomic profiles.
The general information about the module:
Module is realised in second semester. Contain 15 hours of lectures and 30 hours of laboratory classes. Module ends with an exam.
Teaching materials:
tr.sd.prz.edu.pl
Bibliography required to complete the module
| 1 | Robert M. Silverstein, Francis X. Webster, David J. Kiemle | Spektroskopowe metody identyfikacji związków organicznych | Wydawnictwo Naukowe PWN. | 2012 |
| 2 | W. Zielinski, A. Rajca | Metody spektroskopowe i ich zastosowanie do identyfikacji zwiazków organicznych | Wydawnictwo Naukowo Techniczne. | 1995 |
| 3 | M. Szafran, Z. Dega-Szafran | Okreslanie struktury zwiazków organicznych metodami spektroskopowymi | Wydawnictwo Naukowe PWN. | 1988 |
| 4 | L.A. Kazicyna, N.B. Kupletska | Metody spektroskopowe wyznaczania struktury zwiazków organicznych | Wydawnictwo Naukowe PWN. | 1974 |
| 5 | Walczyna, J. Sokołowski, G. Kupryszewski | Analiza zwiazków organicznych | Wydawnictwo Uniwersytetu Gdańskiego. | 1996 |
| 6 | L. Kłyszejko-Stefanowicz | Ćwiczenia z biochemii | Wydawnictwo Naukowe PWN. | 2005 |
| 7 | A. Berthillier | Chromatografia i jej zastosowanie | Wydawnictwo Naukowe PWN. | 1975 |
| 8 | A. Kraj, J. Silberring | Proteomika | Wydział Chemii UJ. | 2004 |
| 9 | A. Dubin | Wprowadzenie do chemii białek | Wydział Biotechnologii UJ. | 2003 |
| 10 | Walkowiak B. Techniki chromatografii cieczowej. Przykłady zastosowań. | Techniki chromatografii cieczowej. Przykłady zastosowań | Amersham Pharmacia Biotech. MORPOL. | 2000 |
| 11 | Kozik A., Rąpała-Kozik M., Guevara-Lora I | Analiza instrumentalna w biochemii. Wybrane problemy i metody instrumentalnej biochemii analitycznej | Instytutu Biologii Molekularnej UJ. | 2001 |
| 12 | A. Kraj, A. Drabik, J.Silberring | Proteomika i metabolomika | Wydawnictwo Uniwersytetu Warszawskiego. | 2010 |
Basic requirements in category knowledge/skills/social competences
Formal requirements:
semester registration
Basic requirements in category knowledge:
Composition of proteins and nucleic acids. Composition od function of saccharides, amino acids, peptides and other low molecular weight organics of biological origin. Basic knowledge of organic reacti
Basic requirements in category skills:
Good technical or chemical english; able of internet and literature search; laboratory practice with corrosive compounds and automatic pipettes.
Basic requirements in category social competences:
effective collaboration with team members
Module outcomes
| MEK | The student who completed the module | Types of classes / teaching methods leading to achieving a given outcome of teaching | Methods of verifying every mentioned outcome of teaching | Relationships with KEK | Relationships with OEK |
|---|---|---|---|---|---|
| MEK01 | know physical background of methods: NMR, FTIR, MS | lectures | written exam |
K-W01++ K-U02+++ |
W01 U02 |
| MEK02 | can work with biomacromolecules without its decomposition; can perform analyses and results interpretation | Lectures | colloquium |
K-W08+ K-U09+++ K-K02+ |
W05 U09 K03 |
The syllabus of the module
| Sem. | TK | The content | realized in | MEK |
|---|---|---|---|---|
| 2 | TK01 | W01-W05 | MEK01 MEK02 | |
| 2 | TK02 | W06-W10 | MEK02 | |
| 2 | TK03 | W11-15 | MEK02 | |
| 2 | TK04 | L04 | MEK02 | |
| 2 | TK05 | L05 | MEK02 | |
| 2 | TK06 | L06 | MEK02 |
The student's effort
| The type of classes | The work before classes | The participation in classes | The work after classes |
|---|---|---|---|
| Lecture (sem. 2) | The preparation for a test:
9.00 hours/sem. |
contact hours:
15.00 hours/sem. |
complementing/reading through notes:
2.00 hours/sem. Studying the recommended bibliography: 3.00 hours/sem. |
| Laboratory (sem. 2) | The preparation for a Laboratory:
3.00 hours/sem. The preparation for a test: 4.00 hours/sem. |
contact hours:
30.00 hours/sem. |
Finishing/Making the report:
2.00 hours/sem. |
| Advice (sem. 2) | |||
| Exam (sem. 2) | The preparation for an Exam:
12.00 hours/sem. |
The way of giving the component module grades and the final grade
| The type of classes | The way of giving the final grade |
|---|---|
| Lecture | exam |
| Laboratory | colloquium |
| The final grade |
Sample problems
Required during the exam/when receiving the credit
(-)
Realized during classes/laboratories/projects
(-)
Others
(-)
Can a student use any teaching aids during the exam/when receiving the credit : no
The contents of the module are associated with the research profile yes
| 1 | B. Gutarowska; M. Komar; S. Manente; J. Nizioł; T. Ruman; S. Socci; J. Szulc | Microbial biodeterioration of historic wood based on classical and omics methods with model studies | 2025 |
| 2 | J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman | Untargeted metabolomic profiling of serum and urine in kidney cancer: a non-invasive approach for biomarker discovery | 2025 |
| 3 | M. Misiorek; T. Ruman | Application of mass spectrometry for imaging the distribution of primary and secondary metabolites in the storage root of red radish | 2025 |
| 4 | S. Krupa; J. Nizioł; T. Ruman; W. Szuberla | Advances in metallic nanostructures-assisted laser desorption/ionization mass spectrometry imaging of biological samples: A review | 2025 |
| 5 | S. Krupa; J. Nizioł; T. Ruman; W. Szuberla | Analysis of the spatial distribution of metabolites in Aloe vera leaves by mass spectrometry imaging and UHPLC-UHRMS | 2025 |
| 6 | T. Branysova; B. Gutarowska; M. Komar; J. Nizioł; K. Olejnik; A. Płaza-Altamer; T. Ruman; T. Stryszewska; M. Sypka; J. Szulc | Biochemical and chemical markers associated with biodeterioration agents isolated from archive audio-visual materials | 2025 |
| 7 | T. Grzyb; B. Guratowska; S. Krupa; J. Nizioł; T. Ruman; J. Szulc | 3D Mass Spectrometry Imaging as a Novel Screening Method for Evaluating Biocontrol Agents | 2025 |
| 8 | T. Grzyb; S. Krupa; J. Nizioł; T. Ruman; W. Szuberla; J. Szulc | Direct 3D Mass Spectrometry Imaging Analysis of Environmental Microorganisms | 2025 |
| 9 | A. Kołodziej; Z. Krupa; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman | Untargeted metabolomics of bladder tissue using liquid chromatography and quadrupole time-of-flight mass spectrometry for cancer biomarker detection | 2024 |
| 10 | B. Guratowska; A. Kuźniar; J. Nizioł; A. Nowak; M. Okrasa; T. Ruman; M. Ryngajłło; J. Szulc | Uncontrolled Post-Industrial Landfill—Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment—A Case Study | 2024 |
| 11 | J. Nizioł; A. Płaza-Altamer; T. Ruman | Analysis of mycotoxins using laser desorption/ionization mass spectrometrywithinfrared pulsed fiber laser-produced silver-109-nanoparticles | 2024 |
| 12 | P. Antos; M. Balawejder; B. Kusz; T. Ruman; J. Szulc; K. Tereszkiewicz | Ozonation procedure for removal of mycotoxins in maize: A promising screening approach for improvement of food safety | 2024 |
| 13 | V. Copie; A. Kołodziej; Z. Krupa; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman; B. Tripet | Metabolomic profiling of human bladder tissue extracts | 2024 |
| 14 | Z. Krupa; J. Nizioł; T. Ruman | Direct Three-Dimensional Mass Spectrometry Imaging with Laser Ablation Remote Atmospheric Pressure Photoionization/Chemical Ionization | 2024 |
| 15 | Z. Krupa; M. Misiorek; J. Nizioł; T. Ruman | Infrared Laser-Based Selected Reaction Monitoring Mass Spectrometry Imaging of Banana (Musa spp.) Tissue—New Method for Detection and Spatial Localization of Metabolites in Food | 2024 |
| 16 | A. Arendowski; A. Kołodziej; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman | Monoisotopic silver nanoparticles-based mass spectrometry imaging of human bladder cancer tissue: Biomarker discovery | 2023 |
| 17 | A. Kołodziej; A. Nieczaj; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman | Untargeted urinary metabolomics for bladder cancer biomarker screening with ultrahigh-resolution mass spectrometry | 2023 |
| 18 | A. Kołodziej; Z. Krupa; J. Nizioł; A. Płaza-Altamer; T. Ruman | Infrared pulsed fiber laser-produced gold and silver-109 nanoparticles for laser desorption/ionization mass spectrometry of steroid hormones | 2023 |
| 19 | M. Dudek; B. Gutarowska; M. Komar; J. Nizioł; P. Nowicka-Krawczyk; T. Ruman | Biodeterioration potential of algae on building materials - Model study | 2023 |
| 20 | S. Kuberski; A. Kuźniar; J. Nizioł; A. Nowak; I. Nowak; M. Okrasa; T. Ruman; B. Szponar; J. Szulc | Biological and chemical contamination of illegal, uncontrolled refuse storage areas in Poland | 2023 |
| 21 | V. Copie; A. Kołodziej; A. Nieczaj; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman; B. Tripet | Targeted and untargeted urinary metabolic profiling of bladder cancer | 2023 |
| 22 | A. Kołodziej; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman | Untargeted ultra-high-resolution mass spectrometry metabolomic profiling of blood serum in bladder cancer | 2022 |
| 23 | A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman | Infrared pulsed fiber laser-produced silver-109 nanoparticles for laser desorption/ionization mass spectrometry of 3-hydroxycarboxylic acids | 2022 |
| 24 | A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman | Infrared pulsed fiber laser-produced silver-109-nanoparticles for laser desorption/ionization mass spectrometry of amino acids | 2022 |
| 25 | A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman | Infrared pulsed fiber laser-produced silver-109-nanoparticles for laser desorption/ionization mass spectrometry of carboxylic acids | 2022 |
| 26 | A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman | Laser Ablation Synthesis in Solution and Nebulization of Silver-109 Nanoparticles for Mass Spectrometry and Mass Spectrometry Imaging | 2022 |
| 27 | A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman | Laser generated gold nanoparticles for mass spectrometry of low molecular weight compounds | 2022 |
| 28 | A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman | Obrazowanie tkanek za pomocą spektrometrii mas z laserową desorpcją/jonizacją | 2022 |
| 29 | B. Gutarowska; M. Komar; P. Konca; J. Nizioł; P. Nowicka-Krawczyk; T. Ruman | Metabolomic analysis of photosynthetic biofilms on building façades in temperate climate zones | 2022 |
| 30 | B. Gutarowska; T. Ruman; J. Szulc | Metagenomika i metabolomika – nowoczesne metody systemowe w identyfikacji mikroorganizmów oraz metabolitów odpowiedzialnych za niszczenie obiektów zabytkowych | 2022 |
| 31 | S. Kuberski; J. Nizioł; A. Nowak; M. Okrasa; T. Ruman; J. Szulc | Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland | 2022 |
| 32 | V. Copie; A. Kołodziej; J. Nizioł; K. Nogueira; L. Nogueira; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza-Altamer; T. Ruman; B. Tripet | Metabolomic and elemental profiling of blood serum in bladder cancer | 2022 |
| 33 | A. Arendowski; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; T. Ruman | Serum and urine analysis with gold nanoparticle-assisted laser desorption/ionization mass spectrometry for renal cell carcinoma metabolic biomarkers discovery | 2021 |
| 34 | A. Arendowski; V. Copie; J. Nizioł; K. Nogueira; L. Nogueira; K. Ossoliński; T. Ruman; B. Tripet | Metabolomic and elemental profiling of human tissue in kidney cancer | 2021 |
| 35 | A. Arendowski; V. Copie; J. Nizioł; K. Ossoliński; T. Ruman; B. Tripet | Nuclear magnetic resonance and surface-assisted laser desorption/ionization mass spectrometry-based metabolome profiling of urine samples from kidney cancer patients | 2021 |
| 36 | A. Kołodziej; T. Ruman; J. Szulc | Silver-109/Silver/Gold Nanoparticle-Enhanced Target Surface-Assisted Laser Desorption/Ionisation Mass Spectrometry—The New Methods for an Assessment of Mycotoxin Concentration on Building Materials | 2021 |
| 37 | B. Gutarowska; K. Majchrzycka; J. Nizioł; A. Nowak; M. Okrasa; T. Ruman; M. Sulyok; B. Szponar; J. Szulc | Microbiological and Toxicological Hazards in Sewage Treatment Plant Bioaerosol and Dust | 2021 |
| 38 | I. Beech; A. Drążkowska; B. Guratowska; J. Karbowska-Berent; T. Ruman; J. Sunner; J. Szulc | Metabolomics and metagenomics analysis of 18th century archaeological silk | 2021 |
| 39 | M. Misiorek; J. Nizioł; T. Ruman | Zastosowanie spektometrii mas do obrazowania rozmieszczenia flawonoidów w owocu truskawki | 2021 |
| 40 | A. Arendowski; J. Nizioł; K. Ossoliński; T. Ruman | Gold nanostructures - assisted laser desorption/ionization mass spectrometry for kidney cancer blood serum biomarker screening | 2020 |
| 41 | A. Arendowski; J. Nizioł; K. Ossoliński; T. Ruman | Screening of Urinary Renal Cancer Metabolic Biomarkers with Gold Nanoparticles-assisted Laser Desorption/Ionization Mass Spectrometry | 2020 |
| 42 | A. Arendowski; V. Copie; J. Nizioł; K. Ossoliński; T. Ruman; B. Tripet | Nuclear magnetic resonance and surface-assisted laser desorption/ionization mass spectrometry-based serum metabolomics of kidney cancer | 2020 |
| 43 | A. Kołodziej; J. Nizioł; T. Ruman | Gold and silver nanoparticles-based laser desorption/ionization mass spectrometry method for detection and quantification of carboxylic acids | 2020 |
| 44 | B. Guratowska; J. Karbowska-Berent; T. Kozielec; T. Ruman; J. Szulc | Analyses of microorganisms and metabolites diversity on historic photographs using innovative methods | 2020 |
| 45 | B. Gutarowska; A. Jachowicz; S. Kowalska; W. Machnowski; T. Ruman; A. Steglinska; J. Szulc | Beeswax-Modified Textiles: Method of Preparation and Assessment of Antimicrobial Properties | 2020 |
| 46 | B. Gutarowska; I. Jablonskaja; E. Jabłońska; J. Karbowska-Berent; T. Ruman; J. Szulc | Metabolomics and metagenomics characteristic of historic beeswax seals | 2020 |
| 47 | I. Beech; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; A. Płaza; T. Ruman; J. Sunner | Localization of Metabolites of Human Kidney Tissue with Infrared Laser-Based Selected Reaction Monitoring Mass Spectrometry Imaging and Silver-109 Nanoparticle-Based Surface Assisted Laser Desorption/Ionization Mass Spectrometry Imaging | 2020 |
| 48 | T. Ruman; J. Szulc | Laser Ablation Remote-Electrospray Ionisation Mass Spectrometry (LARESI MSI) Imaging—New Method for Detection and Spatial Localization of Metabolites and Mycotoxins Produced by Moulds | 2020 |