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Proteomics Data Analysis & Management

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. Sophisticated reports help you efficiently communicate your findings. ProteinScape is the key to running successful proteomics projects.

ProteinScape Project Navigator
The project navigation tree logically reflects the experiment design (click to enlarge)
Identification Results ProteinScape
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 (click to enlarge).

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.

Gathering Proteomics Data

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.




Selection of viewers for protein identification

Spectrum viewer View annotated spectra – with peptide and/or glycan fragments and/or raw data
Sequence viewer Shows peptides with brackets – indicating CID or ETD peptide fragments
LC-MS survey viewer 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
Chromatogram viewer View extracted ion chromatograms for selected peptides
Gel viewer View a scanned 1D or 2D gel image, format annotations and export graphic files for documentation purposes
Sequence editor Modify protein sequences, for theoretical digest

Glycopeptide analysis tools: 

  • Automatic classification of glycopeptide spectra
  • Combined glycopeptide table
  • SpectrumViewer with glycan and peptide fragment annotation

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

Powerful Tools for Protein Analysis

ProteinScape uses Mascot as search engine (other engines are supported via mzIdentML) together with expert algorithms 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 spectraof an LC-MS/MS dataset. Using theintegrated Sequence Editor, modificationcan be varied in a highly flexible way.

Reduced False Discovery Rate of Peptides
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.

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.

Interactive Venn Diagram
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 (click to enlarge)


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.

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.

Gene Ontology Viewer
Gene ontology viewer displays protein function within
biological processes
Protocol (click to enlarge).

Protein quantitation

ProteinScape supports a number of labeled and label-free quantitation workflows. Flexible tools for statistical analysis display results in an easy to interpret 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

  • Label-free quantitation
  • Non-isobaric labels (for example, ICPL, SILAC and 16O/18O)
  • Isobaric labels (for example iTRAQ and TMT)
Statistical Data Set Overview
Statistical overview of entire data sets (log ratio vs peptide
intensity) allowing fast detection of regulated species (click to enlarge).

Glycan analysis

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
ProteinScape Viewers
All required viewers for glycan analysis are provided in the Glycan
perspective (click to enlarge).


Data are searched against a database, which can be:

  • the meta-database GlycomeDB
  • Databases included in the GlycomeDB like GlycO
  • User-defined which are quick and easy to design with the Glycan Structure Editor


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
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 (click to enlarge).

GlycoQuest, the integrated search engine for glycans

GlycoQuest supports 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.

Strategies Glycoprotein Analysis
Several strategies for glycoprotein analysis are supported (click to enlarge).

Read what our customers say about ProteinScape

"I was astounded by how quick and easy it was to produce high quality glycopeptide data on the Q-TOF and use ProteinScape 4.0 for data analysis. With this system we are really getting a large step closer towards large scale and automated glycoproteomics."

Daniel Kolarich, MPI für Kolloid- und Grenzflächenforschung


"We use ProteinScape as a database for our protein samples handled by several employees, for different projects and measured on different instruments. ProteinScape simplifies our daily work by bringing together data of different formats in one universal program without the requirement for high memory capacities."

Simone Greven, Bayer Healthcare


"We use ProteinScape to help us rapidly identify glycans on erythropoietin based pharmaceuticals. The software tools enable us to create our own pharmaceutical specific glycan databases, allowing us a targeted and flexible approach to glycan discovery."

Daniel Spencer, Ludger, Specialist in biopharmaceutical glycoprofiling



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