ProteinScape. Innovation with Integrity. Proteomics Data Analysis & Management. Mass Spectrometry

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1 ProteinScape Proteomics Data Analysis & Management Innovation with Integrity Mass Spectrometry

2 ProteinScape a Virtual Environment for Successful Proteomics To overcome the growing complexity of proteomics experiments, Brukers bioinformatics platform, ProteinScape, collects all your data and arranges it in a way that reflects the way you work. Customizable tables and viewers present the information such that the advanced data mining features help you get the maximum out of your data and sophisticated reports help you efficiently communicate your findings. ProteinScape is the key to running successful proteomics projects. The project navigation tree logically reflects the experiment design

3 Proteomics Data Handling Made Easy ProteinScape viewers enable fast and interactive evaluation and validation of proteomics data. Real-time updating of the linked displays speeds browsing and information management. Spectrum viewer Sequence viewer LC-MS survey viewer Chromatogram viewer Gel viewer Sequence editor View annotated spectra with peptide and/or glycan fragments and/or raw data Shows peptides with brackets indicating CID or ETD peptide fragments Represents the outline of the MS data of a complete LC-MS/MS data set. Parent ions for MS/MS and raw data can be shown. View extracted ion chromatograms for selected peptides View a scanned 1D or 2D gel image, format annotations and export graphic files for documentation purposes. Modify protein sequences, for theoretical digest Selection of viewers for protein identification Investigation of identification results (in the Peptide and protein perspective), here from a 1D gel workflow with Navigation Tree, gel image, protein and peptide table, Sequence Viewer, Survey viewer and spectrum.

4 Powerful Tools for Protein Analysis ProteinScape uses Mascot as search engine (other engines are supported via mzidentml) together with expert algoritms that increase the quality and reliability of protein identifications. Compiling protein lists for improved search results The ProteinExtractor compiles multiple peptide lists from a number of different techniques and instruments, significantly improving overall search results and increasing confidence in identifications. Decoy validation approaches ProteinScape supports decoy-database approaches to generate protein lists based on defined false-discovery rates. Posttranslational modifications (PTMs) Labile modifications like phosphorylation require special fragmentation techniques for optimum analysis. Electron Transfer Dissociation (ETD) fragments peptide backbones, leaving labile PTMs intact. ETD specific annotation in the Spectrum and Sequence viewers enables fast and easy interpretation of ETD analyses. Theoretical digest If the protein sequence is known the database search can be skipped, and a theoretical digest is performed instead with subsequent matching of the theoretical peptide masses to the spectra of an LC-MS/MS dataset. Using the integrated Sequence Editor, modification can be varied in a highly flexible way. Recalibration For MALDI PMF spectra, the ScoreBooster module significantly improves the identification success and the scores, by automatically recalibrating spectra based on frequently occurring background masses and removing those during the search routine. For LC-MS/MS data, all precursor and fragment masses are recalibrated based on peptide ID results. In this way, a successive search can be performed with a narrower mass tolerance window. This keeps False Discovery Rates low, even if more missed cleavages, a less specific enzyme or variable modifications are allowed. Targeted data acquisition A typical application of a scheduled precursor list (SPL) starts with an initial monitoring LC-MS/MS run, which is used to identify a comprehensive set of proteins. Information on the identified peptides is used to create an exclusion SPL for a second LC-MS/MS run, allowing a much higher protein identification rate based on newly identified peptide species. Protein and peptide tables from both runs are then combined using the ProteinExtractor, giving a search result with significantly increased protein sequence coverages. The recalibration on identified peptides shifts the maximum of the distribution of mass deviations towards zero. For a successive database search, the mass tolerance can be reduced. This leads to a significantly reduced False Discovery Rate.

5 Biological knowledge at your fingertips Once a protein is identified, ProteinScape automatically assembles information such as taxonomy, GO terms, and structure files from external databases. An interactive three-dimensional display highlights identified regions and modifications and a gene ontology overview gives information on protein function and location. Extracting Knowledge through Data Mining Managing the huge amount of data generated in proteomics projects can be a daunting task. Efficient tools are required to quickly and precisely extract information from the mass of available data. ProteinScape uses queries to search defined data subsets for spectra meeting specific protein or glycan attributes. Protein queries and searches can be compared to find species common to different data sets, a feature especially useful in method optimization. Protein quantitation ProteinScape supports a number of labeled and label-free quantitation workflows. Flexible tools for statistical analysis display results in an easy tointerpret format. Clicking on a point of interest automatically loads the associated protein or peptide data into the open viewers, giving immediate access to information on regulated species. ProteinScape supports Labelfree quantitation Non-isobaric labels (for example, ICPL, SILAC and 16O/18O) Isobaric labels (for example itraq and TMT) Gene ontology viewer displays protein function within biological processes Protocol LCA 3115 Boronic acid 3621 WGA 3160 ConA 3967 # N-glycosylated peptides Interactive Venn diagram displaying a comparison of four protein search results after enrichment of N-glycopeptides using different lectin stationary phases. Clicking an intersection displays the relevant proteins or peptides in a table. Statistical overview of entire data sets (log ratio vs peptide intensity) allowing fast detection of regulated species.

6 GlycoQuest, Integrated Search Engine for Glycans One of the most important classes of posttranslational modifications is glycosylation. Glycans are very difficult to investigate manually so ProteinScape provides the following analysis and automation tools: the search engine GlycoQuest Glycan search result tables Spectrum Viewer for glycan annotation Glycan Structure Editor GlycoQuest GlycoQuest is a built-in glycan search engine supporting several kinds of glycans: Released glycans, free or reduced Labeled glycans Derivatized glycans e.g by permethylation Glycan moieties of glycopeptides As with protein database searches, search parameters like glycan composition range, mass tolerances, databases, etc. are defined and stored in a search method. Databases Data are searched against a database, which can be: the meta-database GlycomeDB 1 Databases included in the GlycomeDB like GlycO User-defined which are quick and easy to design with the Glycan Structure Editor All required viewers for glycan analysis are provided in the Glycan perspective. Accurate mass CID, MS ETD analysis or TOF/TOF TOF-TOF MS/MS acquisition by CID/ETD ProteinScape powered by GlycoQuest Several strategies for glycoprotein analysis are supported. Glycan search results The presentation is similar to that of protein search results: a table of glycans is displayed above a table of fragments. Selecting an entry automatically updates the integrated Glycan Structure viewer displaying structural and chemical information, as well as the Spectrum viewer showing the glycan fragment annotation. N-glycan MS/MS spectrum obtained after tryptic digestion and PGC-LC separation. The spectrum was acquired on an amazon speed ETD in negative mode. 1 developed at the German Cancer Research Center in Heidelberg. It currently contains around 35,000 glycan structures).

7 Glycopeptide Analysis The investigation of glycopeptides is even more challenging than the analysis of single glycans since additional steps like detection of glycopeptide MS/ MS spectra in LC-MS/MS data and the determination of the peptide masses are required. ProteinScape meets these challenges in a unique way. Its effective combination of spectra classification algorithms, the determination of the masses of the peptide and glycan moieties and our integrated search engine makes it a must-have tool for the analysis of glycoproteins. Glycopeptide analysis tools: Automatic classification of glycopeptide spectra Combined glycopeptide table SpectrumViewer with glycan and peptide fragment annotation Glycoprotein Glycoprotein Tryptic Protein Digest Tryptic Protein Digest LC-MS/MS LC-MS/MS Data Processing Data Processing Spectra classification incl. peptide mass determination Spectra classification Glycan ID Peptide ID (GlycoQuest) (Mascot) incl. peptide mass determination Glycan ID (GlycoQuest) high collision energy N high collision energy low collision energy N Peptide ID N N Peptide ID Glycan ID 4.0 Peptide ID (Mascot) Glycopeptides can be easily identified on a Bruker QTOF mass spectrometer (e.g. impact II), applying different collision energies. This allows the directed fragmentation of the peptide and the glycan part and thus the identification of the complete glycopeptide. 4.0 N low collision Glycan Glycopeptide spectra classification ProteinScape searches for characteristic patterns in the MS/MS spectra. For glycopeptides the peptide moiety masses are determined simultaneously. Only glycopeptide spectra are submitted to the GlycoQuest search for glycan identification. Combined glycopeptide table After the protein and glycan database search, these search results are combined to one glycoprotein table, where glycan and peptide information is linked. x10 5 E E b Q Y N S T R 6.0 y Y T S N Y Q E E The SpectrumViewer Allows the fast and simple verification of the ID results for complete glycopeptides. Intensity y (4) b (6) y (9) m/z Cmpd 907, AutoMSn( ), 22.8 min [Cmpd 907, AutoMSn( ), 22.8 min] Identification result for a glycopeptide of an example protein. The glycopeptide table shows the combined glycan and peptide information from the glycopeptide. The Spectrum Viewer presents the glycan and the peptide annotation. Both viewers can be used for QTOF as well as for MALDI spectra.

8 Bruker Daltonics is continually improving its products and reserves the right to change specifications without notice. BDAL , Technical Specifications Client/Server based architecture ProteinScape Server with a central server and five or more clients ProteinScape Workstation, with the whole system installed on a single PC Database management User management with read/write access administration Project-oriented data management Database structure reflecting laboratory workflow, including separation protocols, free text notes etc. Protein database search features ProteinExtractor compilation of protein lists from different origins Decoy validation Automatic triggering of searches Second-round searches Support of different fragmentation types, e.g. CID, ETD, ECD, etc. Automatic result assessment Protein quantitation Labelfree quantitation Various isobaric and non-isobaric labels, e.g. SILAC Alternatively augmented by 3rd party packages Skyline and MaxQuant. Advanced result processing Export in different formats for seamless knowledge transfer Simple and comparative queries for data mining Interactive viewers Gel viewer LC-MS survey viewer Spectrum viewer Protein sequence viewer 3D protein structure viewer Glycan structure viewer Quantitation statistics viewer Venn diagram viewer Chromatography Viewer Sequence Editor Histogram Viewer Report Templates Peptides and proteins: search parameters, ID results, quantitation results Glycans and glycopeptides: search parameters, ID results Publication-ready report generation Glycan Analysis Pre-search spectra classification GlycoQuest glycan search engine Linked result tables Glycan-related viewers Dedicated glycan queries and reports Supported mass spectrometers All Bruker MS systems Thermo MS systems via dta, mgf Waters MS systems via pkl, mgf ABI MS systems via mgf For research use only. Not for use in diagnostic procedures. Bruker Daltonik GmbH Bremen Germany Phone +49 (0) Fax +49 (0) Bruker Daltonics Inc. Billerica, MA USA Phone +1 (978) Fax +1 (978)

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