Data Processing for Small Molecules

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Data Processing for Small Molecules Basic Metabolomics Workflows Metabolomics: the apogee of the

Patti, Oscar Yanes and Gary Siuzdak Molecular Cell Biology, 2012, 13, 263-269 MATTHEW BERNIER, PH.D.

METLIN > 68,000 13,048 Public, no download mzcloud > 416,000 2,975 Public, no download MoNA >

Public, downloadable GNPS > 9,000 ~2200 NP Public, downloadable ReSpect (MS n ) > 9,000 3,595

Commercial MetabolomicsWorkBench Public, no download LipidBlast 200,000 Public, downloadable Lipid

1 Data Processing for Small Molecules Basic Metabolomics Workflows Metabolomics: the apogee of the omics trilogy Gary J. Patti, Oscar Yanes and Gary Siuzdak Molecular Cell Biology, 2012, 13, MATTHEW BERNIER, PH.D. CCIC MS&P SUMMER WORKSHOP JULY 2018 Thanks to Yu Cao ESI-MS n Libraries # Spectra # Compounds Notes METLIN > 68,000 13,048 Public, no download mzcloud > 416,000 2,975 Public, no download MoNA > 236,000 69,946 Public, no download MassBank > 28,100 > 43,000 Public, downloadable HMDB 9,500 Public, downloadable GNPS > 9,000 ~2200 NP Public, downloadable ReSpect (MS n ) > 9,000 3,595 Public, downloadable NIST14 MS/MS > 234,000 9,344 Commercial Wiley MSforID > 10,000 > 1,200 Commercial MetabolomicsWorkBench Public, no download LipidBlast 200,000 Public, downloadable Lipid Maps 37,500 Public, downloadable LipidSearch >1500,000 lipid ions Commercial Database Search Progenesis QI Import Data MS + Data Alignment MS - 1

2 MS + Peak Picking MS - Adduct Selection Review Deconvolution Identify Compounds Review Compounds Pathway Analysis How do we streamline data processing? Need workflows for reproducible processing Tools making up the nodes of the workflows A workflow engine executing the nodes in a predefined order OpenMS is an open source set of tools for analyzing mass spectrometric data KNIME is the interface used to construct and execute these sequences of tools (workflows) in a convenient manner They are open-source software and freely available on all major platforms 2

PSI Standard Formats Numerous open and standardized XML formats have been proposed by the HUPO Proteomics Standards Initiative (HUPO PSI): mzml (successor of mzdata) for storing mass spectrometry

, MCP, 2013) mztab for summary information of quantitative and qualitative results, Excelcompatible TSV format (Griss et al.

, MCP,2014) Advantages Open, documented, no closedsource libraries required Will still be readable in 10 years from now Interoperable with different software packages Disadvantages Initial raw data

0 - Features Currently 185 distinct tools Utilities extract information from files, file conversion, visualization PTX identification interface to DB search engines, de novo search, RNA-protein XL

3 PSI Standard Formats Numerous open and standardized XML formats have been proposed by the HUPO Proteomics Standards Initiative (HUPO PSI): mzml (successor of mzdata) for storing mass spectrometry data mzidentml for storing peptide/protein identifications traml for storing transition and inclusion lists (Deutsch et al., MCP, 2012) mzquantml for storing quantitation results (Walzer et al., MCP, 2013) mztab for summary information of quantitative and qualitative results, Excelcompatible TSV format (Griss et al., MCP, 2014) qcml for storing and mining quality control information (Walzer et al., MCP,2014) Advantages Open, documented, no closedsource libraries required Will still be readable in 10 years from now Interoperable with different software packages Disadvantages Initial raw data conversion required (and often awkward) File size Poor support by instrument software OpenMS Features Currently 185 distinct tools Utilities extract information from files, file conversion, visualization PTX identification interface to DB search engines, de novo search, RNA-protein XL MS, protein inference, RT prediction, proteotypicity prediction PTX quantification label-free, TMT, itraq,silac, MRM, OpenSWATH (DIA), ProteinSIP (metaproteomics), RT alignment MTX quantification nontargeted metabolomics, MRM MTX identification accurate mass DB search, spectral matching, composition Miscellaneous MRM scheduling, LC-MS simulator, Röst et al., Nat. Methods, 2016, 13:741 KNIME Platform KNIME Platform KNIME Platform KNIME KoNstanz Information MinEr Visualization capabilities Data mining & advanced statistical methods 3

plotting capabilitiesof R can be used as

Finding all proteins in multiple samples

4 Statistics Workflows in KNIME KNIME permitsthe embedding of R code for advanced statistics Embedding of R scripts using the R Snippet node All plotting capabilitiesof R can be used as well Protein Identification Workflow Finding all proteins in multiple samples Mass spectra enter workflow on the left Loop nodes permit execution of parts of the workflow Identifiedproteins end up in result files (right side) 4

Workflow Repositories Other Computational Tools for

independent MS/MS experiments https://www.openms.

repository with selected example workflows (www.

engines Numerous applications,can be used to document

database search (commercial) XCMS Online Submission

5 Workflow Repositories Other Computational Tools for Metabolomics MS-DIAL Data dependent and/or independent MS/MS experiments OpenMS website contains a workflow repository with selected example workflows ( General-purpose workflow repository: Collects workflows from arbitrary workflow engines Numerous applications,can be used to document data analysis MS-FINDER GC/MS data alignment, database search (commercial) XCMS Online Submission for single or multi-group metabolomics datasets Uses the Metlin Database for feature matching Streamlined Pathway Analysis Free use 5

6 Anal. Chem. 2014, 86, Anal. Chem. 2014, 86, Thank you! Yu Cao Arpad Somogyi Vicki Wysocki Entire CCIC MSP Facility 6

Open Source Software Packages: Using and Making your conbributions. June 5, 2017 Bioinformatics MS Interest Group

Open Source Software Packages: Using and Making your conbributions June 5, 2017 Bioinformatics MS Interest Group Your hosts Meena Choi Post doc. Northeastern University Statistical methods for quantitative