Scoring Guide
Understanding the LC-MS suitability scoring system
Scoring Overview
The LC-MS suitability score ranges from 0 to 100 and is calculated based on four main factors:
Length Score
Max points
K/R Bonus
Max points
Uniqueness
Max points
Simplicity
Max points
Total Score = Length + K/R Bonus + Uniqueness + Simplicity (capped at 100)
Length Score (max 30 points)
Peptide length affects ionization efficiency and chromatographic behavior. Optimal peptides should be between 8-25 amino acids.
| Peptide Length | Score | Reason |
|---|---|---|
| 8-25 amino acids | 30 pts | Ideal range for LC-MS detection |
| < 8 amino acids | 30 - (8-length)×3 | Too short: poor retention, less specific |
| > 25 amino acids | 30 - (length-25)×3 | Too long: may not ionize well |
Example: A 10 amino acid peptide scores 30 points (ideal range). A 5 amino acid peptide scores 30 - (8-5)×3 = 21 points.
K/R Bonus Score (max 10 points)
Peptides containing Lysine (K) or Arginine (R) have improved ionization efficiency due to their basic side chains.
| Condition | Score | Reason |
|---|---|---|
| Contains K orR | +10 pts | Better ionization efficiency |
| No K or R in sequence | 0 pts | Lower charge state |
Note: The position of K/R does not matter - anywhere in the peptide sequence provides the ionization benefit.
Uniqueness Score (max 50 points)
Unique peptides are essential for accurate protein quantification.
| Status | Score | Description |
|---|---|---|
| Unique | +50 pts | Found in only one protein |
| Non-unique | -20 to -30 pts | Found in multiple proteins |
Formula: Non-unique = -20 + max(-10, (occurrences - 2) × -2)
Enzyme Simplicity Score (max 10 points)
Single enzyme digestions are preferred for simpler and more reproducible workflows.
| Digestion Type | Score | Reason |
|---|---|---|
| Single Enzyme | +10 pts | Simpler workflow, more reproducible |
| Sequential Digestion | 0 pts | More complex workflow |
Example Calculation
Peptide: PEPTIDESEQUENCEK
Length: 16 aa | Contains K | Unique: Yes | Single Enzyme: Trypsin