Shedding light on complex mass spectrometry proteomics processes through advanced data mining  Wout Bittremieux.

Slides:



Advertisements
Similar presentations
Proteins: Structure reflects function….. Fig. 5-UN1 Amino group Carboxyl group carbon.
Advertisements

Review.
5’ C 3’ OH (free) 1’ C 5’ PO4 (free) DNA is a linear polymer of nucleotide subunits joined together by phosphodiester bonds - covalent bonds between.
Lectures on Computational Biology HC Lee Computational Biology Lab Center for Complex Systems & Biophysics National Central University EFSS II National.
Molecular Techniques in Molecular Systematics. DNA-DNA hybridisation -Measures the degree of genetic similarity between pools of DNA sequences. -Normally.
Exciting Developments in Molecular Biology As seen by an amateur.
You Must Know How the sequence and subcomponents of proteins determine their properties. The cellular functions of proteins. (Brief – we will come back.
Proteins. The central role of proteins in the chemistry of life Proteins have a variety of functions. Structural proteins make up the physical structure.
Chapter 27 Amino Acids, Peptides, and Proteins. Nucleic Acids.
Spectral Counting. 2 Definition The total number of identified peptide sequences (peptide spectrum matches) for the protein, including those redundantly.
Proteins account for more than 50% of the dry mass of most cells
1.What makes an enzyme specific to one type of reaction (in other words, what determines the function of a protein)? –SHAPE determines the function of.
Protein Synthesis. DNA RNA Proteins (Transcription) (Translation) DNA (genetic information stored in genes) RNA (working copies of genes) Proteins (functional.
2012 YCU Science Summer Program Lecture #6 Proteomic Approach to Protein Alterations Implicated in Aging and Geriatric Diseases Tosifusa Toda Yokohama.
How Proteins Are Made Mrs. Wolfe. DNA: instructions for making proteins Proteins are built by the cell according to your DNA What kinds of proteins are.
. Sequence Alignment. Sequences Much of bioinformatics involves sequences u DNA sequences u RNA sequences u Protein sequences We can think of these sequences.
LESSON 4: Using Bioinformatics to Analyze Protein Sequences PowerPoint slides to accompany Using Bioinformatics : Genetic Research.
AMINO ACIDS.
WSSP Chapter 8 BLASTX Translated DNA vs Protein searches atttaccgtg ttggattgaa attatcttgc atgagccagc tgatgagtat gatacagttt tccgtattaa taacgaacgg ccggaaatag.
Amino Acids are the building units of proteins
Learning Targets “I Can...” -State how many nucleotides make up a codon. -Use a codon chart to find the corresponding amino acid.
Fig Second mRNA base First mRNA base (5 end of codon) Third mRNA base (3 end of codon)
Welcome Back! February 27, 2012 Sit in any seat for today. You will have assigned seats tomorrow Were you absent before the break? Plan on coming to tutorial.
Practice Quiz (you will need your amino acid sheet for this quiz)
intro-VIRUSES Virus NamePDB ID HUMAN PAPILLOMAVIRUS 161DZL BACTERIOPHAGE GA1GAV L-A virus1M1C SATELLITE PANICUM MOSAIC VIRUS1STM SATELLITE TOBACCO NECROSIS2BUK.
Amino Acids ©CMBI 2001 “ When you understand the amino acids, you understand everything ”
Proteins.
EBI is an Outstation of the European Molecular Biology Laboratory. In silico analysis of accurate proteomics, complemented by selective isolation of peptides.
Chapter 3 Proteins.
Amino Acids  Amino Acids are the building units of proteins. Proteins are polymers of amino acids linked together by what is called “ Peptide bond” (see.
Amino acids Common structure of 19 AAs H3N+H3N+ COO - R H C Proline.
Prepared By: Syed Khaleelulla Hussaini. Outline Proteins DNA RNA Genetics and evolution The Sequence Matching Problem RNA Sequence Matching Complexity.
Proteins Tertiary Protein Structure of Enzyme Lactasevideo Video 2.
Collecting and mining mass spectrometry quality control data Wout Bittremieux, Pieter Kelchtermans, Dirk Valkenborg, Lennart Martens, Bart Goethals, Kris.
9th Benelux Bioinformatics Conference, 09/12/2014.
Peptide de novo sequencing Peptide de novo sequencing is the analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum.
Arginine, who are you? Why so important?. Release 2015_01 of 07-Jan-15 of UniProtKB/Swiss-Prot contains sequence entries, comprising
Amino acids Proof. Dr. Abdulhussien Aljebory College of pharmacy
Approaches for mass spectrometry quality control
Amino acids.
Translation PROTEIN SYNTHESIS.
Whole process Step by step- from chromosomes to proteins.
Proteins account for more than 50% of the dry mass of most cells
BIOLOGY 12 Protein Synthesis.
Protein Sequence Alignments
Proteins.
Transport proteins Transport protein Cell membrane
Cathode (attracts (+) amino acids)
THE PRIMARY STRUCTURES OF PROTEINS
Proteins account for more than 50% of the dry mass of most cells
Phosphopeptide sequencing by MALDI-TOF/TOF of the C-terminal tail of AtPIP2;1.A, MS/MS spectrum of singly phosphorylated 277SLGSFRSAANV287 (m/z ).
Chemistry 121 Winter 2016 Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)
The Interface of Biology and Chemistry
Chapter 3 Proteins.
Fig. 5-UN1  carbon Amino group Carboxyl group.
Proteins account for more than 50% of the dry mass of most cells
Proteins Genetic information in DNA codes specifically for the production of proteins Cells have thousands of different proteins, each with a specific.
After leaving the nucleus, mRNA heads to a ribosome.
Cytochrome.
The 20 amino acids.
How to Test an Assertion
Translation.
The 20 amino acids.
2D-LC-MS/MS analysis of tryptic digest of HEK293-SUMO3 cells (2 μg inj
Analysis of a tryptic digest of subunit B12 by MALDI-TOF mass spectrometry. Analysis of a tryptic digest of subunit B12 by MALDI-TOF mass spectrometry.
Example of regression by RBF-ANN
Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes 2. Proteins are.
“When you understand the amino acids,
Presentation transcript:

Shedding light on complex mass spectrometry proteomics processes through advanced data mining  Wout Bittremieux

Molecular biology Wout Bittremieux – Faculty of Science Research Day 2017

Proteins Wout Bittremieux – Faculty of Science Research Day 2017

A protein sequence MGASYLR Methionine Glycine Alanine Serine Tyrosine Leucine Arginine Met Gly Ala Ser Tyr Leu Arg M G A S Y L R MGASYLR Wout Bittremieux – Faculty of Science Research Day 2017

Mass spectrum identification SLEDLDKEMADYFEK Wout Bittremieux – Faculty of Science Research Day 2017

Quality control Wout Bittremieux – Faculty of Science Research Day 2017

Quality control Target: peppermint icicles Result: peppermint … euh ... erm Wout Bittremieux – Faculty of Science Research Day 2017

Do you already use quality control tools? Wout Bittremieux – Faculty of Science Research Day 2017

How important is quality control for … ? Wout Bittremieux – Faculty of Science Research Day 2017

Quality control metrics Wout Bittremieux – Faculty of Science Research Day 2017

Outlier detection

Outlier detection Wout Bittremieux – Faculty of Science Research Day 2017

Outlier detection Wout Bittremieux – Faculty of Science Research Day 2017

Spectrum identification Wout Bittremieux – Faculty of Science Research Day 2017

Spectral library searching ??? peptide peptide peptide peptide peptide peptide peptide peptide peptide Wout Bittremieux – Faculty of Science Research Day 2017

ANN spectral library search Retrieve candidates in logarithmic time Does not depend on precursor mass Tunable precision-performance trade-off Wout Bittremieux – Faculty of Science Research Day 2017

ANN spectral library search Wout Bittremieux – Faculty of Science Research Day 2017

Conclusions Mass spectrometry data is highly complex Advanced data mining techniques to uncover novel biological knowledge Many more opportunities! Wout Bittremieux – Faculty of Science Research Day 2017

Acknowledgments

Feedback: Privacy Policy Feedback
Do Not Sell My Personal Information
About project: SlidePlayer Terms of Service

© 2025 SlidePlayer.com. Inc. All rights reserved.