The aim of studying and bibliography

The main aim of study: Introduction of basics of chemical analysis. Modern and classical methods of biomolecules isolation, purification and analysis. Basic knowledge of proteomics is also discussed. New methods of protein post-translational modifications determination. Application of NMR, FTIR, MS, CD, XRD, fluorescence and other methods etc along with various purification techniques (electrophoresis, chromatography etc.). Methods dedicated for small molecules (for example metabolites) and biomacromolecules.

The general information about the module: Module is realized in 5th semester. Contain 15hours of lectures and 15 hours of laboratory classes. Module ends with written colloquium.

Teaching materials: tr.sd.prz.edu.pl

Bibliography required to complete the module

Bibliography to self-study

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 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 PRK
01	know physical background of methods: NMR, FTIR, MS	lectures	written exam	K_W04+ K_W05+ K_W10+ K_U03+	P6S_UK P6S_WG
02	can work with biomolecules and biomacromolecules	laboratory classes	written colloquium	K_W10+ K_U03+ K_U09+++ K_K03+	P6S_KR P6S_UK P6S_UO P6S_UW P6S_WG
03	Knows the strengths and weaknesses of analytical methods, is able to choose a method for a research problem	lecture	written exam	K_W04+ K_U03+ K_U09+++	P6S_UK P6S_UO P6S_UW P6S_WG
04	Can analyze and interpret the results of instrumental analytical results	laboratory classes	colloquium	K_W10++ K_U03+ K_U09+++ K_K03+	P6S_KR P6S_UK P6S_UO P6S_UW P6S_WG

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
5	TK01	basics of MS, NMR and FTIR	W01-W05	MEK01 MEK02
5	TK02	fluorescent methods, electrophoresis, X-ray diffraction	W06-W10	MEK02
5	TK03	biomolecule separation methods - chromatography, electrophoresis etc. advanced microsopic methods	W11-15	MEK02
5	TK04	Mass spectrometry of small biomolecules	L1-3	MEK01 MEK02 MEK03 MEK04
5	TK05	Mass spectrometry of biomacromolecules	L4-6	MEK01 MEK02 MEK03 MEK04
5	TK06	NMR spectroscopy of biomolecules	L7-9	MEK01 MEK02 MEK03 MEK04
5	TK07	Analysis of recombinant human insulin by Tricine-SDS-PAGE electrophoresis: preparation of solutions, gels, performance of electrophoresis, staining of insulin in the gel.	L10-15	MEK02 MEK04

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 5)	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: 15.00 hours/sem.
Laboratory (sem. 5)	The preparation for a Laboratory: 2.00 hours/sem. The preparation for a test: 2.00 hours/sem.	contact hours: 15.00 hours/sem.	Finishing/Making the report: 2.00 hours/sem.
Advice (sem. 5)
Exam (sem. 5)	The preparation for an Exam: 15.00 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	Final grade K = 0,5wW+ 0,5wL, where W - lecture grade (lecture material colloquium/exam grade) L - laboratory colloquium grade w - factor of positive grade session number - 1 for first, 0.9 for second, 0.8 for third Positive grade - min 50% of maximum points; every 10% more - grade rises of 0.5 up to 5.0

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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	M. Dudek; B. Gutarowska; M. Komar; J. Nizioł; P. Nowicka-Krawczyk; T. Ruman	Biodeterioration potential of algae on building materials - Model study	2023
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Laser generated gold nanoparticles for mass spectrometry of low molecular weight compounds	2022
17	A. Kołodziej; J. Nizioł; A. Płaza-Altamer; T. Ruman	Obrazowanie tkanek za pomocą spektrometrii mas z laserową desorpcją/jonizacją	2022
18	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
19	B. Gutarowska; T. Ruman; J. Szulc	Metagenomika i metabolomika – nowoczesne metody systemowe w identyfikacji mikroorganizmów oraz metabolitów odpowiedzialnych za niszczenie obiektów zabytkowych	2022
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	M. Misiorek; J. Nizioł; T. Ruman	Zastosowanie spektometrii mas do obrazowania rozmieszczenia flawonoidów w owocu truskawki	2021
29	A. Arendowski; J. Nizioł; K. Ossoliński; T. Ruman	Gold nanostructures - assisted laser desorption/ionization mass spectrometry for kidney cancer blood serum biomarker screening	2020
30	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
31	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
32	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
33	B. Guratowska; J. Karbowska-Berent; T. Kozielec; T. Ruman; J. Szulc	Analyses of microorganisms and metabolites diversity on historic photographs using innovative methods	2020
34	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
35	B. Gutarowska; I. Jablonskaja; E. Jabłońska; J. Karbowska-Berent; T. Ruman; J. Szulc	Metabolomics and metagenomics characteristic of historic beeswax seals	2020
36	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
37	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
38	A. Arendowski; J. Kucharz; J. Nizioł; A. Ossolińska; K. Ossoliński; T. Ossoliński; T. Ruman; P. Wiechno	Mass spectrometry-based metabolomic profiling of prostate cancer-a pilot study	2019
39	J. Cebulski; M. Kus-Liśkiewicz; T. Ruman; M. Stompor; D. Szmuc; K. Szmuc; Ł. Szyller; S. Wołowiec; I. Zawlik	Silver nanoparticles deposited on calcium hydrogenphosphate - silver phosphate matrix; biological activity of the composite	2019
40	M. Misiorek; J. Nizioł; T. Ruman	Mass spectrometry imaging of low molecular weight metabolites in strawberry fruit (Fragaria x ananassa Duch.) cv. Primoris with 109Ag nanoparticle enhanced target	2019