PeptideMapper by Rob Beynon

Accepts .fasta, .fas, .fa, .txt files

Show annotations for all peptides (ignore mass filter)

Apply Rules Clear Rules

Format: Identifier shape color[opacity] [placement] [direction] [level]

Identifiers:
• Amino acid letter (K, R, C, etc.)
• Position number (121, 45, etc.)
• Peptide number (P1, P4, P10, etc.)

Shapes:
• fill - Colors entire peptide
• circle - Circle marker
• square - Square marker
• diamond - Diamond shape marker
• text - Text label (see below)

Text Content (for text shape):
• sequence - Shows peptide sequence
• mass - Shows mass in Da
• mh - Shows [M+H]+ mass with "+" suffix
• m2h - Shows [M+2H]++ mass with "++" suffix
• "Custom text" - Any text in quotes

Colors with Transparency:
red, green, blue, magenta, cyan, yellow, orange, purple, white, black
• red - 100% opacity (solid)
• red50 - 50% opacity (semi-transparent)
• blue25 - 25% opacity (mostly transparent)

Placement:
• in - Inside peptide rectangle (default)
• out - External with connecting line

Direction (for 'out' only):
• above - Above the peptide
• below - Below the peptide (default)

Levels (for text 'out' only):
• L1 - Closest to peptide (default)
• L2 - Medium distance
• L3 - Furthest from peptide

Examples:
K fill red - Red peptides containing K
C circle yellow out below - Yellow dots below cysteines
P4 text sequence red out above L1 - Show peptide sequence
P5 text mass blue out below L2 - Show mass at level 2
P6 text mh green out above L1 - Show [M+H]+ with "+" suffix
P7 text m2h purple out below L1 - Show [M+2H]++ with "++" suffix
121 text "Catalytic" green out above L3 - Custom text at level 3
C text "S-S bond" purple out below L1 - Custom cysteine labels

Multi-level example:
P4 text sequence red out above L1
P4 text mass blue out above L2
P4 text "Active site" purple out above L3