Bioinformatic Tools. So you acquired data.. But you wanted knowledge. So Now What?

Transcription

1 Bioinformatic Tools So you acquired data.. But you wanted knowledge So Now What?

2 We have a series of questions What the Heck is That Ion? How come my MW does not match? How do I make a DB to search against? How Do I Search my Data? How do I Navigate through the Tower of Babel in Nomenclature? Has Anyone seen this Protein Before? How do I look at my Search Results at the Project Level rather than on a Sample Level? OK, I believe in the Integrity of my Search Results - do they tell a biological story? I have Confidence in the Integrity of my Data and I believe they tell a Biological Story Now I am only interested in quantifying a subset of proteins in my sample using MRM how do I develop methods? Will my Targeted MRM Analyses Developed be Reproducible?

3 What the Heck is That Ion?

4 How come my MW does not match? UNIMOD Protein Modifications for Mass Spectrometry

5 How do I make a DB to search against? Downloading Protein Databases from UniProt Visit Select Downloads from top left of web page From the UniProtKB select UniProtKB/Swiss-Prot FASTA This downloads a WinZip file, from which you extract the uniprot_sprot.fasta file

6 How do I make a species specific NCBI DB to search against?

7 How Do I Search my Data? Open Source MS/MS DB Search Engines (thanks to John Cottrell for this compilation) MS-Tag (Protein Prospector) Omssa PepFrag (Prowl) PepProbe Phenyx RAId_DbS X!Tandem (The GPM) XProteo

8 How do I Navigate through the Tower of Babel in Nomenclature? biodbnet Database Finder dbfind can be used when you do not know the actual type of your identifiers or when you have a mixture of different types of identifiers. The tool finds the identifier type and converts them into the selected output if the identifiers are within the network. To get a list of the identifiers and their coverage read our documentation on the network nodes Basically an Accession Number Translator between Gene ID, Ensemble Gene ID, and UniProt

9 biodbnet Try inputting the Names from the ASMS Protein Expression Set File

10 biodbnet Gene ID to Entrez Gene (active link)

11 biodbnet Gene ID to UniProt (active link)

12 Has Anyone seen this Protein Before?

13 Indeed, it has Been Seen a few times Before

14 How do I look at my Search Results at the Project Level rather than on a Sample Level? Scaffold (Proteome Software) is a free viewer which accepts results from most MS/MS DB search engines Allows detailed evaluation of qualitative results from a sample Allows detailed comparison of qualitative results across experiments Provide Gene Ontology information on the identified proteins Free Download at Mass Spec labs have to buy one license All collaborators can download for free

15 Instructions for Scaffold Download From Select Downloads Download Scaffold 3 Insure you select version appropriate for your computer You do not need to request an evaluation key as you will be using this as a viewer only (no cost) Selecting the Tour button allows you to view Flash presentations on use of this software for proteomic analyses Taking the Tours is Highly Recommended

16 Installing GO Database in Scaffold Open Scaffold 3 Under Edit, select Preferences Select GO Database From the dropdown menu select Human Only EBI, UK,~ 5 min

17 Scaffold Overview of Four Phenotypes of a Cell Line - high resolution, accurate mass LC/MS/MS dataset - all fields sorted by clicking on header

18 Scaffold Overview of Four Phenotypes of a Cell Line Note each sample was analyzed in triplicate previous slide showed a composite result

19 Details of Identification of Actin -

20 Correlation of Peptide IDs Across Experiments

21 Details of the Identification of a Peptide in a Sample

22 Details of the Identification of a Peptide in a Sample

23 Scaffold View for Sequence Homology Challenges

24 Automated Generation of Venn Diagram Overlaps between Phenotypes in Scaffold Protein Overlap State 1 State State 3 Peptide Overlap State 1 State State 3

25 Scaffold Supplemental Information - Gene Ontology Biological Function and Compartment Information from NCBI

26 OK, I believe in the Integrity of my Search Results - do they tell a biological story? STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) developed at CPR, EMBL, SIB, KU, TUD and UZH. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C., Nucleic Acids Res Jan;37(Database issue):d Epub 2008 Oct 21. Functional partnerships between proteins are at the core of complex cellular phenotypes, and the networks formed by interacting proteins provide researchers with crucial scaffolds for modeling, data reduction and annotation STRING is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available.

27 String Startup Screen

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29 STRING Provides Protein Information and Links to Additional Information One-click link to UniProt DB For this protein the link:

30 Expanding Interactors +1

31 Millipore s Pathway Tool

32 I have Confidence in the Quality of my Data I believe they tell a Biological Story Now I am only interested in quantifying a subset of proteins in my sample

33 Will my MRM Analyses Developed in Skyline be Reproducible?

34 Proteomic Software Suites - if you only go to one site.. ProteinProspector prospector/mshome.htm These programs were developed in the UCSF Mass Spectrometry Facility, which is directed by Dr. Alma Burlingame, Professor of Chemistry and Pharmaceutical Chemistry at UCSF and funded by the NIH National Center for Research Resources.

35 Using MS-Digest to perform in-silico Digests - particularly useful for insuring coverage of a specific peptide sequence, such as in phosphorylation mapping

36 Using MS-Isotope to compare Experimental and Theoretical Isotope Distributions Resolution = 10,000 Resolution = 1,000 The advantages of high resolution mass spectrometers are clear

37 Proteomic Software Suites - if you go to two sites.. Pacific Northwest National Lab Proteomics Research Resource for Integrative Biology

38 Really Useful PNNL App Molecular Weight Calculator Tool This program can calculate the molecular weight and percent composition of chemical formulas and amino acids Provides a graphical user interface to edit the formulas and parsing options. It recognizes user-definable abbreviations, custom elemental isotopes, and can display up to 20 compounds simultaneously. It also includes a Mole/Mass Converter Formula Finder Capillary Flow Modeler Amino Acid Notation Converter Peptide Sequence Fragmentation Modeler Isotopic Distribution Calculator and last but not least built-in calculator.

39 Bioinformatics Resource Manager (PNNL) The Bioinformatics Resource Manager (BRM), developed at Pacific Northwest National Laboratory (PNNL), is a software program that provides robust middleware architecture to link scientific applications and heterogeneous data sources. - Automated data gathering - Bioinformatics tool interfaces - Data Extraction and Integration Shah AR, M Singhal, KR Klicker, EG Stephan, HS Wiley, KM Waters. "Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager." Bioinformatics (7): ;

40 Bioinformatics Resource Manager (PNNL)

41 Computational Proteomics Laboratory Fred Hutchison Cancer Research Center CPAS Computational Proteomics Analysis CPAS is a suite of database and analysis tools, originally developed in the FHCRC CPL, that manages proteomics experimental workflows and integrates database search algorithms (X!Tandem, Mascot, and Sequest) and Institute for Systems Biology (ISB) data management tools. CPAS is now distributed as part of an open source project managed by the Labkey Software Foundation.

42 Computational Proteomics Laboratory Fred Hutchison Cancer Research Center msinspect msinspect is a set of tool forcreating and managing Accurate Mass and Time databases from high-quality MS/MS identifications, matching high-resolution LC-MS peptide features to those data, and integrating the AMT results with MS/MS identifications from the same LC-MS runs The msinspect/amt platform takes the Accurate Mass and Time approach first described by the Smith laboratory and implements those ideas in an open-source, platform-independent Java software suite, with many original features that we have described in our publications.

43 Computational Proteomics Laboratory Fred Hutchison Cancer Research Center MRMer allows you to view and analyze MRM data stored in an mzxml file. General overview: MRMer reads an mzxml file and infers precursor-ion/product-ion relationships. It displays elution curves of the product ions and allows the user to select or deselect them as candidates for MRM-based assays. It also displays the elution curve of the precursor ions when MS1 scans are present in the mzxml file. MRMer's calculations can be output to a tab-delimited file. MRMer will also read a specialized tab-delimited file that defines heavy and light ion relationships in SILAC or AQUA experiments. When this file is present, MRMer calculates and displays the lightto-heavy ratio of the elution AUCs (areas under the elution curves).