PeptideMapper Annotation Syntax Guide

🎨 Basic Shape Annotations

K fill red - Red peptides containing lysine
C circle yellow - Yellow circles on cysteines
R square blue - Blue squares on arginines
P diamond green - Green diamonds on prolines

🌈 Colors with Transparency

K fill red50 - Semi-transparent red (50% opacity)
C circle blue25 - Mostly transparent blue (25% opacity)
R square green75 - Slightly transparent green (75% opacity)
P diamond magenta - Solid magenta (100% opacity)

Available Colors

Color	Solid	50% Opacity	25% Opacity
red	red	red50	red25
green	green	green50	green25
blue	blue	blue50	blue25
magenta	magenta	magenta50	magenta25
cyan	cyan	cyan50	cyan25
yellow	yellow	yellow50	yellow25
orange	orange	orange50	orange25
purple	purple	purple50	purple25

📍 Positioning Options

K circle red in - Red circles inside peptide rectangles
C square yellow out above - Yellow squares above peptides with lines
R diamond blue out below - Blue diamonds below peptides with lines
P circle green out - Green circles below (default direction)

Placement	Direction	Description
in	-	Inside the peptide rectangle
out	above	Above the peptide with connecting line
out	below	Below the peptide with connecting line (default)

🔤 Text Annotations - Table Data

P1 text sequence red out above L1 - Show peptide sequence at level 1
P2 text mass blue out below L2 - Show mass at level 2
P3 text mh green out above L1 - Show [M+H]+ with "+" suffix
P4 text m2h purple out below L1 - Show [M+2H]++ with "++" suffix

Keyword	Output	Description
sequence	MKWVTFISLLL	Amino acid sequence of the peptide
mass	1234.5678	Molecular mass in Daltons
mh	1235.5756+	[M+H]+ mass with "+" suffix
m2h	618.2878++	[M+2H]++ mass with "++" suffix

💬 Text Annotations - Custom Labels

P1 text "Active site" red out above L1
P5 text "Cleavage site" blue out below L2
C text "Disulfide bond" yellow out above L1
121 text "Catalytic residue" green out above L3

💡 Custom Text Tips

Always use double quotes around custom text
Multi-word labels: "Active site peptide"
Single words can omit quotes: P1 text Important red out above L1
Keep labels concise for better readability

📏 Multi-Level Text Positioning

P4 text sequence red out above L1 - Level 1 (closest to peptide)
P4 text mass blue out above L2 - Level 2 (medium distance)
P4 text "Important" green out above L3 - Level 3 (furthest from peptide)

Level	Distance	Best Use
L1	~35px	Primary data (sequence, mass)
L2	~70px	Secondary info (additional masses)
L3	~105px	Descriptive labels (function, notes)

🎯 Position-Specific Annotations

57 circle red out above - Circle at global position 57
121 diamond green out below - Diamond at global position 121
250 text "His-57" blue out above L2 - Text label at position 250

Note: Position numbers refer to the original protein sequence (1-based numbering).

🔬 Research Application Examples

Enzyme Active Site Analysis

Chymotrypsin catalytic triad annotation:

                Amino Acid Rules (one per line):
            
                57 text "His-57" red out above L2

                102 text "Asp-102" blue out above L2

                195 text "Ser-195" green out above L2

                57 circle red out above

                102 circle blue out above

                195 circle green out above

Mass Spectrometry Workflow

Highlight peptides of interest for MS analysis:

                Amino Acid Rules (one per line):
            
                P5 text mh red out above L1

                P7 text m2h blue out below L1

                P12 text mass green out above L2

                P5 fill red25

                P7 fill blue25

                P12 fill green25

Post-Translational Modifications

Common protein modifications mapping:

                Amino Acid Rules (one per line):
            
                C text "Oxidation site" yellow out below L2

                M text "Met oxidation" orange out above L1

                K text "Ubiquitination" purple out below L3

                S text "Phosphorylation" cyan out above L2

Protease Specificity Mapping

Trypsin cleavage pattern visualization:

                Amino Acid Rules (one per line):
            
                K fill red25

                R fill red25

                K text "Trypsin cut" red out below L1

                R text "Trypsin cut" red out below L1

🎪 Advanced Multi-Layered Examples

Complete Peptide Characterization

Comprehensive annotation of peptide P3:

                Amino Acid Rules (one per line):
            
                P3 fill green25

                P3 circle red in

                P3 text sequence blue out above L1

                P3 text mh purple out above L2

                P3 text "Biomarker peptide" orange out above L3

Amino Acid Property Analysis

Color-code by chemical properties:

                Amino Acid Rules (one per line):
            
                K fill blue25

                R fill blue25

                H fill blue25

                D fill red25

                E fill red25

                C circle yellow out below L1

                C text "Disulfide" yellow out below L2

Protein Domain Mapping

Map functional domains across peptides:

                Amino Acid Rules (one per line):
            
                P1 text "Signal peptide" gray out above L3

                P5 text "Binding domain" blue out above L3

                P10 text "Catalytic domain" red out above L3

                P15 text "Regulatory region" green out above L3

                P1 fill gray25

                P5 fill blue25

                P10 fill red25

                P15 fill green25

📋 Quick Reference Tables

Identifiers

Type	Example	Description
Amino Acid	K, R, C	Single letter amino acid codes
Peptide	P1, P5, P10	Peptide numbers from digestion table
Position	57, 121, 250	Global position in original protein

Shapes

Shape	Best Use	Visual Impact
fill	Grouping/highlighting peptides	High (colors entire peptide)
circle	Marking specific residues	Medium
square	Functional annotations	Medium
diamond	Special sites/modifications	Medium
text	Data display and labeling	High (informational)

PeptideMapper

🎯 General Syntax Format

Example Annotation Input: