How to Use

Step-by-step guide for Proteomics Enzyme Picker

Overview

Proteomics Enzyme Picker helps you find the best enzyme for targeted peptide measurement by LC-MS. It analyzes your target protein sequence and recommends optimal enzymes based on peptide length, presence of basic residues (K/R), and uniqueness in proteome databases.

Use case: When designing PRM/MRM assays for specific proteins, this tool helps you choose the best enzyme to generate peptides that are optimal for LC-MS detection.

1Enter Protein Sequence

Paste your full protein sequence in the input field. The sequence should contain only standard amino acid letters (A-Z).

Example:

MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVV...
Tip: You can copy the sequence from UniProt or other protein databases.

2Enter Target Subsequence

Enter the specific region of the protein you want to target. This is the subsequence that must be included in the resulting peptide.

  • Minimum 3 amino acids required
  • The target must exist within your protein sequence
  • Can include post-translational modification sites you want to monitor

3Select Uniqueness Database

Choose one or more proteome databases to check peptide uniqueness. You can select multiple databases - peptides must be unique across all selected databases.

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Human (Swiss-Prot)

Human reference proteome

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Mouse (Swiss-Prot)

Mouse reference proteome

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Rat (Swiss-Prot)

Rat reference proteome

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Custom FASTA

Upload your own file

Tip: When selecting multiple databases, peptides are checked against the combined set. This is useful for cross-species studies.

4Select Enzymes

Choose which enzymes to include in the analysis. The system automatically generates meaningful enzyme combinations from your selection. Single enzymes receive a bonus score for simplicity.

Available Enzymes (+10 simplicity bonus for single use)

  • • Trypsin - Cleaves after K, R (not before P)
  • • LysC - Cleaves after K (including KP)
  • • ArgC - Cleaves after R (including RP)
  • • GluC (E) - Cleaves after E (not before P)
  • • GluC (DE) - Cleaves after D, E (not before P)
  • • AspN - Cleaves before D
  • • Chymotrypsin - Cleaves after F, Y, W, L
  • • rChymoSelect - Cleaves after Y, F, L
  • • ProAlanase - Cleaves after P, A

Auto-Generated Combinations

Sequential digestion combinations are automatically calculated from your selected enzymes. The system intelligently filters out redundant combinations and only shows combinations that produce different results than single enzymes.

5Run Analysis & Review Results

Click "Run Analysis" to process your input. Results are ranked by LC-MS suitability score.

Result Information

  • ScoreOverall LC-MS suitability (0-100)
  • PeptideThe digested peptide containing your target
  • LengthNumber of amino acids
  • UniqueWhether the peptide is unique in the database

Pro Tips

  • Peptides with 8-25 amino acids are ideal for LC-MS
  • Peptides containing K or R have better ionization efficiency
  • Unique peptides are essential for accurate quantification
  • Single enzymes get a +10 simplicity bonus over sequential digestions
  • Use the "Load Demo" button to quickly test with sample data