This is the second presentation of the BITS training on 'Mass spec data processing'.
It reviews the methods for separating protein mixtures prior to further analysis.
Thanks to the Compomics Lab of the VIB for contribution.
BITS - Overview of sequence databases for mass spectrometry data analysisBITS
This is the fourth presentation of the BITS training on 'Mass spec data processing'.
It review sequences databases and their flaws in light of mass spectrometry data analysis.
Thanks to the Compomics Lab of the VIB for their contribution.
Presentation of Eugeni Belda (LABGeM-Genoscope) at the Biocuration 2012 conference (Georgetown University, Washington DC): From bacterial genome annotation to metabolic pathway curation
BITS - Overview of sequence databases for mass spectrometry data analysisBITS
This is the fourth presentation of the BITS training on 'Mass spec data processing'.
It review sequences databases and their flaws in light of mass spectrometry data analysis.
Thanks to the Compomics Lab of the VIB for their contribution.
Presentation of Eugeni Belda (LABGeM-Genoscope) at the Biocuration 2012 conference (Georgetown University, Washington DC): From bacterial genome annotation to metabolic pathway curation
RNA-seq for DE analysis: detecting differential expression - part 5BITS
Part 5 of the training sesson 'RNA-seq for differential expression analysis' considers the algorithm used for detecting differential expression between conditions. See http://www.bits.vib.be
RNA-seq for DE analysis: extracting counts and QC - part 4BITS
Part 4 of the training sesson 'RNA-seq for differential expression analysis' considers extracting the count table from a mapping, and performing QC to detect sample biases. See http://www.bits.vib.be
RNA-seq for DE analysis: the biology behind observed changes - part 6BITS
Part 6 of the training sesson 'RNA-seq for differential expression analysis' considers gene set analysis for inferring biology from RNA-seq data. See http://www.bits.vib.be
The structure of Linux - Introduction to Linux for bioinformaticsBITS
This 3th slide deck of the training 'Introduction to linux for bioinformatics' gives a broad overview of the file system structure of linux. We very gently introducte the command line in this presentation.
This 1st presentation in the training "Introduction to linux for bioinformatics" gives an introduction to Linux, and the concepts by which Linux operates.
This is the last presentation of the BITS training on 'Comparative genomics'.
It reviews tthe Contra tool for detecting common transcription factor binding sites in sequences.
Thanks to Stefan Broos of the DMBR department of VIB
BITS - Comparative genomics on the genome levelBITS
This is the third presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on the gene
Thanks to Klaas Vandepoele of the PSB department.
BITS - Comparative genomics: gene family analysisBITS
This is the second presentation of the BITS training on 'Comparative genomics'.
It reviews the different methods of investigating sequence homology on the gene family level.
Thanks to Klaas Vandepoele of the PSB department.
RNA-seq for DE analysis: detecting differential expression - part 5BITS
Part 5 of the training sesson 'RNA-seq for differential expression analysis' considers the algorithm used for detecting differential expression between conditions. See http://www.bits.vib.be
RNA-seq for DE analysis: extracting counts and QC - part 4BITS
Part 4 of the training sesson 'RNA-seq for differential expression analysis' considers extracting the count table from a mapping, and performing QC to detect sample biases. See http://www.bits.vib.be
RNA-seq for DE analysis: the biology behind observed changes - part 6BITS
Part 6 of the training sesson 'RNA-seq for differential expression analysis' considers gene set analysis for inferring biology from RNA-seq data. See http://www.bits.vib.be
The structure of Linux - Introduction to Linux for bioinformaticsBITS
This 3th slide deck of the training 'Introduction to linux for bioinformatics' gives a broad overview of the file system structure of linux. We very gently introducte the command line in this presentation.
This 1st presentation in the training "Introduction to linux for bioinformatics" gives an introduction to Linux, and the concepts by which Linux operates.
This is the last presentation of the BITS training on 'Comparative genomics'.
It reviews tthe Contra tool for detecting common transcription factor binding sites in sequences.
Thanks to Stefan Broos of the DMBR department of VIB
BITS - Comparative genomics on the genome levelBITS
This is the third presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on the gene
Thanks to Klaas Vandepoele of the PSB department.
BITS - Comparative genomics: gene family analysisBITS
This is the second presentation of the BITS training on 'Comparative genomics'.
It reviews the different methods of investigating sequence homology on the gene family level.
Thanks to Klaas Vandepoele of the PSB department.
This is the first presentation of the BITS training on 'Comparative genomics'.
It reviews the basic concepts of sequence homology on different levels.
Thanks to Klaas Vandepoele of the PSB department.
BITS - Protein inference from mass spectrometry dataBITS
This is the fifth presentation of the BITS training on 'Mass spec data processing'.
It reviews the problems of determining protein sequences of mass spec data, how to deal with it, with an overview of useful tools.
Thanks to the Compomics Lab of the VIB for their contribution.
This is the third presentation of the BITS training on 'Mass spec data processing'.
It reviews the methods for matching mass spectrometry data with protein sequences, with review of useful tools.
Thanks to the Compomics Lab of the VIB for contribution.
BITS - Introduction to Mass Spec data generationBITS
This is the first presentation of the BITS training on 'Mass spec data processing'.
It reviews the basic concepts of mass spectrometry data generation.
Thanks to the Compomics Lab of the VIB for contribution.
These is the second part of the lecture slides of the BITS bioinformatics training session on the UCSC Genome Browser.
See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203990:orange-genome-browsers-ucsc-training&catid=81:training-pages&Itemid=190
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
• The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
• Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
• Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
• Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
PHP Frameworks: I want to break free (IPC Berlin 2024)Ralf Eggert
In this presentation, we examine the challenges and limitations of relying too heavily on PHP frameworks in web development. We discuss the history of PHP and its frameworks to understand how this dependence has evolved. The focus will be on providing concrete tips and strategies to reduce reliance on these frameworks, based on real-world examples and practical considerations. The goal is to equip developers with the skills and knowledge to create more flexible and future-proof web applications. We'll explore the importance of maintaining autonomy in a rapidly changing tech landscape and how to make informed decisions in PHP development.
This talk is aimed at encouraging a more independent approach to using PHP frameworks, moving towards a more flexible and future-proof approach to PHP development.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
2. introduction to proteomics
kenny helsens
kenny.helsens@ugent.be
Lennart MARTENS
lennart.martens@ebi.ac.uk
Computational Omics and Systems Biology Group
Proteomics Services Group
European Bioinformatics Institute
Department of Medical Protein Research, VIB
Hinxton, Cambridge
United Kingdom
Department of Biochemistry, Ghent University
www.ebi.ac.uk
Kenny Helsens Ghent, Belgium
BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
3. The central paradigm
- Primary structure (sequence)
…YSFVATAER…
- Secondary structure (structural elements)
- Tertiairy structure (3D shape)
- Modifications (dynamic, function)
phosphorylation
- Processing (targetting, activation)
trypsin
Adapted from the NCBI Science Primer
http://www.ncbi.nih.gov/About/primer/genetics_cell.html
platelet activity
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
4. 2D-PAGE separation of proteins (Est. 1975)
Principle
Protein A Protein B
cell lysis
protein extraction
Protein C Protein D
cells protein mixture
pI Chemistry
Mr toolbox
2D-PAGE
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
5. 2D-PAGE separation of proteins (Est. 1975)
protein
complex protein mixture
extraction
http://www.akh-wien.ac.at/biomed-research/htx/platweb1.htm
2D-PAGE separation
MS/MS analysis
100
%
pI
0 m/z
100 300 500 700 900 1100 1300 1500 1700 1900 2100
fragmentation
100
MS analysis
tryptic
%
digest
0 m/z
300 400 500 600 700 800 900 1000 1100
MW
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
7. Going gel-free in the new millennium
• ICAT (Gygi et al., 1999)
• MudPIT (Washburn et al., 2001)
• Accurate Mass Tags for proteome analysis (Conrads et al., 2000)
• Signature Peptides approach for proteomics (Ji et al., 2000)
• AA-based covalent chromatography peptide selection (Wang & Regnier, 2001)
• Affinity-based enrichment of phosphopeptides (Oda et al., 2001)
• ICAT for phosphopeptides (Zhou et al., 2001)
• Reversible biotinylation of Cys-peptides (Spahr et al., 2000)
• COFRADIC (Gevaert et al., 2002)
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
8. An overview of the pro’s and cons
• Massive increase in mixture redundancy (eg. membrane proteins)
Corresponding increase in mixture complexity (from a few
thousand proteins to hundreds of thousands of peptides!)
• Easier seperation of peptides instead of proteins
Loss of protein-level information (pI, MW, isoforms)
• Mixture complexity can be reduced by peptide selection (Cys-
peptides, Met-peptides, N-terminal peptides, phospho-peptides, …)
Again leading to reduced redundancy of the mixture
• Choice of selection technique, depending on circumstances/analyte
Massive amounts of data generated (10.000 spectra per hour)
• Additional processing information (N-terminal peptides)
Unadapted database search engines (N-terminal processing)
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
9. AN INCOMPLETE OVERVIEW
OF GEL-FREE TECHNIQUES
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
10. MudPIT: that which we call a rose…
Strong cation Reverse-phase
exchanger resin
SCX RP ESI-based MS
• Orthogonal, 2D separation of peptides
• 2D analogon: pI = SCX, Mr = RP
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
11. But what about the complexity?
e.g., Escherichia coli 4,349 predicted proteins
if 100% expressed 109,934 detectable tryptic peptides
if 50% expressed 54,967 detectable tryptic peptides
Sample complexity increased one order of magnitude!
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
12. A thought experiment seems appropriate
What happens when there are 100.000 peptides present?
How often do we need to repeat an analysis of an identical sample
in order to obtain reasonable coverage?
The explorative aspect
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
13. The explorative aspect
Complete coverage
2010
2006
2002
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
14. More coverage by reducing population size
Tissue
• Laser capture microdissection
• Flow cytometry
cells
one cell-type
• Differential Detergent
compartments fractionation
one organel / • Differential centrifugation
compartment
• Gel-filtration
proteins subset of • 1D-gel electrophoresis
• Ion-exchange
proteins
• ICAT-method
peptides subset of
• COmbined FRActional
peptides Diagonal Chromatography
Preselected, representative peptides
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
15. Peptide selection techniques: ICAT
Isotope Coded Affinity Tag
1) Modify cysteine residues using a molecule consisting of 3 parts:
• a thiol reactive group
• a biotin label
• a linker that may contain light or heavy atoms
2) Digest proteins
3) Affinity isolation of labeled cysteine-peptides
4) Use cysteine-peptides for LC-MS/MS analysis
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
16. The ICAT molecule
biotin
thiol-specific
O heavy reagent: X = deuterium
light reagent: X = hydrogen
reactive group
HN NH O X X O
X O X I
N XO OX N
S H H
X X
The linker allows differential proteome analysis!
Evoked mass difference = 8 amu’s.
From: Gygi SP et al., Nature Biotechnology, 1999
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
17. Peptide selection techniques: COFRADIC
COmbined FRActional DIagonal Chromatography
• Selection technique based on diagonal chromatography
• Versatile – requires only a specific modification that
changes chromatographic properties
• Already applied to methionine, cysteine, N-terminal,
nitrosylated, glycosylated, phosphorylated and ATP-
binding peptides
• N-terminal analysis is well-suited for detecting
proteolytic events
From: Gevaert et al., Molecular & Cellular Proteomics, 2002
Gevaert et al., Nature Biotechnology, 2003
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
18. COFRADIC in principle
AU gradient
Chemical (or enzymatic)
alteration of subset of peptides
in separate or combined
fractions
time =0
Separate and collect in fractions AU gradient
- +
Altered peptides display changed
chromatographic properties
(-, +)
Alternatively: selected peptides
are not altered (=0), while non
selected peptides are altered
time
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
19. COFRADIC in practice (I)
primary run secondary run
H H O H H O
... N C C ... ... N C C ...
Methionine COFRADIC CH2
H2O2-oxidation
CH2
(Gevaert et al., 2002) CH2 CH2
S S O
CH3 CH3
methionine methionine-sulfoxide
primary run secondary run
Ac AA1 AA2 AA3 AA4 ... Arg Ac AA1 AA2 AA3 AA4 ... Arg
N-terminal
Ac AA1 Lys AA3 AA4 ... Arg peptides Ac AA1 Lys AA3 AA4 ... Arg
NH-Ac NH-Ac
NO2
N-terminal COFRADIC
TNBS modification
H2N AA1 AA2 AA3 AA4 ... Arg NO2 N AA1 AA2 AA3 AA4 ... Arg
(Gevaert et al., 2003)
H
NO2
internal
NO2
peptides
H2N AA1 AA2 Lys AA4 ... Arg NO2 N AA1 AA2 Lys AA4 ... Arg
H
NH-Ac NH-Ac
NO2
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
20. COFRADIC in practice (II)
primary run secondary run
H H O H H O H H O
... N C C ... ... N C C ... ... N C C ...
CH2 Ellman’s reagent CH2 TCEP reduction CH2
Cysteine COFRADIC
SH S SH
S
(Gevaert et al., 2004)
cysteine cysteine
HOOC
NO2
TNB-cysteine
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
21. COFRADIC in practice (III)
~60% Detectable!
log10(Mass N-terminal Peptide)
~60% Detectable!
log10(Mass C-terminal Peptide)
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011
22. Thank you!
Questions?
Kenny Helsens BITS MS Data Processing – Protein Inference
kenny.helsens@UGent.be UGent, Gent, Belgium – 16 December 2011