ProteinProspector

ProteinProspector performs protein identification and analysis of mass spectrometry data to support proteomic and protein–protein interaction studies.

Key Features:

• Mass spectrometry data processing: Processes LC-ESI-MS/MS datasets to assign interpretable tandem mass spectra for protein identification.
• Multidimensional chromatography integration: Supports workflows combining strong cation exchange fractionation of peptides with reverse-phase liquid chromatography.
• Instrument and geometry compatibility: Handles data from QSTAR instruments using quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry.
• Spectrum assignment confidence: Confidently assigns the majority of interpretable spectra in complex proteomic datasets.
• SearchCompare feature: Facilitates direct comparison of search results with other search engines such as Mascot.
• Developmental-version processing: Datasets can be processed using developmental versions of the software as reported in the study.

Scientific Applications:

• Proteomic identification: High-confidence protein identification from LC-ESI-MS/MS experiments.
• Protein–protein interaction analysis: Identification and analysis of interaction partners, exemplified by studies of the yeast GTPase Gsp1p.
• Comparative search validation: Validation and enhancement of protein identification accuracy via comparison with search engines like Mascot using SearchCompare.

Methodology:

Datasets were processed with a developmental version of ProteinProspector to assign tandem mass spectra, and results were compared to other search engines (e.g., Mascot) using the SearchCompare function.