Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications

Dain R Brademan,Nicholas M Riley,Nicholas W Kwiecien,Joshua J Coon

doi:10.1074/mcp.tir118.001209

Dain R Brademan, Nicholas M Riley + Show 2 more

Open Access

https://doi.org/10.1074/mcp.tir118.001209

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Abstract

Here we present IPSA, an innovative web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. A tool for the scientific community, IPSA can visualize peptides collected using a wide variety of experimental and instrumental configurations. Annotated spectra are customizable via a selection of interactive features and can be exported as editable scalable vector graphics to aid in the production of publication-quality figures. Single spectra can be analyzed through provided web forms, whereas data for multiple peptide spectral matches can be uploaded using the Proteomics Standards Initiative file formats mzTab, mzIdentML, and mzML. Alternatively, peptide identifications and spectral data can be provided using generic file formats. IPSA provides supports for annotating spectra collecting using negative-mode ionization and facilitates the characterization of experimental MS/MS performance through the optional export of fragment ion statistics from one to many peptide spectral matches. This resource is made freely accessible at http://interactivepeptidespectralannotator.com, whereas the source code and user guides are available at https://github.com/coongroup/IPSA for private hosting or custom implementations.

Highlights

Upload data using generic or standard file formats mzTab, mzIdentML, or mzML. Annotation support for peptides collected using negative-mode ionization
Researchers have developed a wide variety of search algorithms and related computational tools to rapidly translate this large volume of experimental data to peptide spectral matches (PSMs), where peptide sequences are assigned to spectra to identify the proteins present in a sample (10 –16)
Powerful for the platforms for which they were designed, many of these tools are inseparable from their respective analytical pipelines; data visualization in MaxQuant is only available following processing with the integrated Andromeda search engine, for example. Their purview is limited, and facile spectral annotation is restricted to only those search algorithms packaged in a pipeline with a developed annotator. This restriction poses a problem for numerous applications, especially for alternative peptide fragmentation methods such as ultraviolet photodissociation (UVPD), collisionally supplemented electron-transfer dissociation (EThcD), or activated-ion electron-transfer dissociation (AI-ETD) (28 –30)

Summary

Introduction

Upload data using generic or standard file formats mzTab, mzIdentML, or mzML. Annotation support for peptides collected using negative-mode ionization. Powerful for the platforms for which they were designed, many of these tools are inseparable from their respective analytical pipelines; data visualization in MaxQuant is only available following processing with the integrated Andromeda search engine, for example Their purview is limited, and facile spectral annotation is restricted to only those search algorithms packaged in a pipeline with a developed annotator. This restriction poses a problem for numerous applications, especially for alternative peptide fragmentation methods such as ultraviolet photodissociation (UVPD), collisionally supplemented electron-transfer dissociation (EThcD), or activated-ion electron-transfer dissociation (AI-ETD) (28 –30).

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