Bruker Daltonics GmbH & Co. KG
IP2 - Integrated Proteomics Pipeline
Table of Contents
Bruker Daltonics GmbH & Co. KG
IP2 - Integrated Proteomics Pipeline
1.General Information
1.1 System Overview
1.2 3rd Party Software Integrated into the IP2
1.3 Points of Contact
2. System Summary
2.1 System Summary
3.Getting Started
3.1 Logging On
3.2 System Menu
3.3 Changing User Id and Password
3.4 Exit System
3.5 Administration Account
3.6 Command line System Management
4.Protein Database Management
4.1 Database View
4.2 Upload Database
5. Upload Spectral Files
5.1 Upload Spectral files
5.2 IP2Daemon for batch file uploading
5.3 Batch Spectra Upload
6.Project management
6.1 Project management
7. Protein Identification
7.1 ProLuCID Search Engine
7.2 Comet Search Engine
7.3 Protein Identification Results
7.4 Delta mass Plotter
7.5 PSM Score Distribution
7.6 Search a protein throughout a project
7.7 Correct mass in spectra
7.8 Batch search
7.9 Download sqt files
8. Quantification
8.1 MS1-based Analysis(SILAC, 15N, Dimethyl, etc)
8.2 15N Enrichment Calculation
8.3 Isobaric labeling(e.g.TMT)
8.4 Isobaric labeling N-plex Analysis
8.5 Site Specific tag Analysis
8.6 Targeted Quantitative Analysis
9. Post-Translational Modification
9.1 Background and Description
9.2 Analysis of Localization Score
9.3 Validation of Phosphopeptides and Phosphorylation Sites
9.4 Comparison of Phosphopeptides
9.5 Quantitation of Phosphopeptides
9.6 Kinase Enrichment Analysis with Phosphosites
10. Statistical Analysis With Multiple Data Sets
10.1 Identification Compare
10.2 Identification Stat Compare (label-free analysis using spectral count)
10.3 Quantification Compare (SILAC, 15N, Dimethyl, etc)
10.4 Quantification Compare Isobaric (TMT, iTRAQ, etc)
10.5 Quantitative Regression
10.6 Label-free Analysis using XIC
11. Quality Control Tool
11.1 Spectral Quality Control
11.2 Delta mass Plotter
11.3 PSM Score Distribution
11.4 Additional Quality control
12. Gene ontology
12.1 Gene ontology
13. Additional Tools
13.1 Proteome Discoverer Compatibility
13.2 Batch Generation of Fragment ion Annotation Images
13.3 Export data for other tools (e.g skyline)
13.4 Fractional analysis
13.5 Reactome Pathway Analysis
13.6 Clustering Analysis
13.7 Thermal Proteome Profile (TPP) Temperature Range (TR)
14. For your Publications
14.1 For your Publications
15. IP2 Troubleshooting
15.1 Server
15.2 Search
16. Appendix
16.1 IP2 FAQ
16.2 unique group filter
17. IP2 Development Kit (IDK)
17.1 IP2 IDK (API)
18. Upgrade IP2 -
18.1 IP2 Upgrade setps
18.2 IP2 Rollback
Download as PDF
17. IP2 Development Kit (IDK)
17.1
API
Usage
16.2 unique group filter
17.1 IP2 IDK (API)
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