Help & documentation

Using the SysQuan database

How to search the peptide database, build a selection, view assay data, and export what you need.

Quick start

  1. Search: enter proteins, genes, or peptides (or leave blank to browse everything).
  2. Filter: narrow to a specific tissue with the tissue filter.
  3. Select: tick the peptides you're interested in to add them to your cart.
  4. View: inspect MRM / PRM transitions or the MS/MS spectrum for a selection.
  5. Download: export your selection, or the whole filtered table, as CSV.

What's in the database

Each row is a peptide with its measured properties and available assays:

Uniprot
Protein identifier from UniProt.
Gene
Gene name for the protein.
Peptide
Amino-acid sequence (single-letter).
Tissue
Tissue the peptide was quantified in.
Mouse conc.
Pre-quantified concentration of the heavy reference (fmol/µg).
Incorp. %
Heavy-label (K6) incorporation efficiency, higher is better.
Missed cleav.
Internal trypsin sites not cut during digestion.
Assays
Optimized assays available: MRM, PRM, or both.
PTM
Post-translational modifications, if any.

Searching

  • Multiple terms: separate proteins/genes/peptides by spaces, commas, or new lines (up to 200).
  • Case-insensitive: partial matches work.
  • Combine: search together with the tissue filter for precise results.
  • Browse all: leave the box empty to page through everything.
P12345
All peptides from that UniProt accession.
GAPDH
All peptides from genes matching “GAPDH”.
AKEDLR
That exact peptide sequence.
P12345, GAPDH
Anything matching either term.

Cart & assay tools

Your selection is kept in the browser session, so it persists as you move between pages. With peptides selected you can view:

  • MRM assay: optimized transitions with precursor/product ions and retention times.
  • PRM-PASEF assay: transitions with ion mobility and collision-energy parameters.
  • MS/MS spectrum: the DDA library spectrum; light fragments in blue, heavy (SILAC) in red. Hover a peak for m/z, intensity, and ion annotation.

Downloads

  • Cart (CSV): your selected peptides with protein, sequence, tissue, and assay info.
  • All (CSV): the whole table for the current search and tissue filter.
  • Assay tables: expand any MRM/PRM result to download its transitions.
  • Spectral data: raw fragment m/z and intensity from the spectrum view.

CSV exports work directly in Skyline and most proteomics tools.

FAQ

Does it work with cell lines, or only tissues?

It works with cell lines, plasma, and serum, not only tissues. For the best absolute quantification, mix your sample with the most closely related K6-labelled mouse tissue standard. Matching your sample to the nearest reference tissue gives the most reliable results.

Does my cart empty when I change page?

No, it's saved in your session. The checkboxes reflect what's already in your cart, and you can keep adding from any page.

What's the difference between MRM and PRM?

MRM is the classic targeted method for triple-quadrupole instruments. PRM-PASEF runs on timsTOF instruments and adds ion-mobility separation for higher specificity.

Why do some peptides have no MRM/PRM assay?

Not every peptide has been optimized for a targeted assay yet. Those show only DDA spectral-library data.

What does incorporation rate mean?

It's the efficiency of heavy (K6) labelling in the reference. Values near 100% indicate high-quality labelling.

Need more help?

Reach the team directly and we'll get back to you.

Contact support About SysQuan