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. 2010 Oct;28(10):1015-7.
doi: 10.1038/nbt1010-1015.

ProHits: integrated software for mass spectrometry-based interaction proteomics

Guomin Liu, Jianping Zhang, Brett Larsen, Chris Stark, Ashton Breitkreutz, Zhen-Yuan Lin, Bobby-Joe Breitkreutz, Yongmei Ding, Karen Colwill, Adrian Pasculescu, Tony Pawson, Jeffrey L Wrana, Alexey I Nesvizhskii, Brian Raught, Mike Tyers, Anne-Claude Gingras

ProHits: integrated software for mass spectrometry-based interaction proteomics

Guomin Liu et al. Nat Biotechnol. 2010 Oct.
No abstract available

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Figures

Figure 1
Figure 1
Overview of ProHits. (a) Modular organisation of ProHits. The Data Management module backs up all raw mass spectrometry data from acquisition computers, and handles data conversion and database searches. The Analyst module organizes data by project, bait, experiment and sample (gel-free project shown; see Supplementary Fig. 8 for gel-based organization). Search results from the Data Management module are parsed to individual samples defined within the Analyst module. ProHits can handle large collaborative projects, and offers several security layers. In the Analyst module, several view, filter and export functions enable data analysis. Functions provided by external software are listed on the right. (b) ProHits Comparison page. Left: Filtered Comparison results for four human baits and one negative control (see Supplementary Fig. 17 online for unfiltered data). Display, sort, filter and literature overlap options are listed on the top; selected options in this example are shown in red. Filtered results are displayed at the bottom of the page. Columns represent individual baits. Comparison at the Experiment or Sample levels is also possible. Rows list the hits that pass selected filters. Color-coding and intensity in each cell is based in the property selected for visualization, shown for this example as total peptide numbers; mouse-overs of each cell will list all properties. A star or triangle inside the cell indicates an interaction identified in previous high-throughput (star) or low-throughput (triangle) studies in BioGRID. Each term in the hits column is hyperlinked to external databases (Entrez Gene, BioGRID or NCBI Protein) or to the list of identified peptides. Right, top: Visualization of data in Cytoscape with mass spectrometric information encoded as an edge attribute. Interactions detected for the example bait protein WASL that are not reported in BioGRID are shown as blue edges with color intensity mapped spectral counts and thickness mapped to number of unique peptides; overlap interactions detected in both the experiment and in BioGRID are shown in green; interactions detected only in BioGRID are shown in grey. Right, bottom: Example of the Peptide View for the protein WIPF3 in the WASL AP-MS experiment.
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