Help & Documentation

1. Search: Enter proteins, genes, or peptides in the search box (or leave blank to browse all)
2. Filter: Use the tissue filter to narrow results to specific tissues
3. Select: Check the boxes next to peptides of interest to add them to your Cart
4. Analyze: View MRM transitions, PRM transitions, or MS/MS spectra for selected peptides
5. Download: Export your selections and assay data as CSV files

What is the Protein Cart?

The Protein Cart is a comprehensive database of peptides with optimized mass spectrometry assays. It aggregates data from:

• DDA (Data-Dependent Acquisition) - Peptide identification and spectral libraries
• MRM (Multiple Reaction Monitoring) - Optimized targeted assays with high sensitivity
• PRM-PASEF (Parallel Reaction Monitoring) - Advanced ion mobility-based targeted assays

Table Columns Explained

Cart Features

• Persistent Selection: Your cart selections are saved in your browser session - navigate between pages without losing your selections
• Clear Cart: Remove all selections at once with the "Clear" button
• Download Cart: Export selected peptides as a CSV file

Cart-Specific Information Tools

Understanding Peptide Spectra

The Peptide Spectra tool displays tandem mass spectrometry (MS/MS) data from our DDA spectral library:

• Light Fragments (Blue): Ions from unlabeled peptides
• Heavy Fragments (Red): Ions from isotope-labeled peptides (SILAC)
• Interactive Plot: Hover over peaks to see m/z, intensity, and ion annotation
• Selector Table: Click rows to switch between different peptides
• Download Data: Expand the table view to download raw fragment data as CSV

Available Downloads

• Download Cart (CSV): Export selected peptides with protein, sequence, tissue, and assay information
• Download All (CSV): Export the entire library table (filtered by your current search/tissue selection)
• MRM/PRM Tables: Each assay result table can be downloaded separately by expanding the "View as table" section
• Spectral Data: Raw fragment m/z and intensity data available via the expandable table in the Peptide Spectra view

Effective Searching

• Multiple Terms: Enter multiple proteins, genes, or peptides separated by spaces, commas, or semicolons (max 200 terms)
• Partial Matches: The search is case-insensitive and matches partial strings
• Combine Filters: Use search + tissue filter together for precise results
• Browse All: Leave the search box empty to see all peptides (paginated)

Example Searches

Q: Why does my cart empty when I navigate to the next page?

A: It doesn't! Your cart is saved in your browser session. The checkboxes on the current page reflect your cart contents. You can add more peptides from any page.

Q: What's the difference between MRM and PRM assays?

A: MRM (Multiple Reaction Monitoring) is a classic targeted MS method for triple quadrupole instruments. PRM-PASEF (Parallel Reaction Monitoring with PASEF) is an advanced method for timsTOF instruments that adds ion mobility separation for higher specificity.

Q: Why are some peptides missing MRM or PRM assays?

A: Not all peptides have been optimized for targeted assays. The "Optimized Assay" column shows availability. Peptides with "None" only have DDA spectral library data.

Q: What does "incorporation rate" mean?

A: Incorporation rate indicates the efficiency of heavy isotope labeling in SILAC experiments. Higher values (closer to 100%) mean better labeling quality.

Q: Can I export data for use in Skyline or other software?

A: Yes! The downloaded CSV files are compatible with most proteomics analysis tools. For Skyline, we recommend downloading the MRM or PRM transition tables.