Proteotypic peptides

Rapidly develop targeted mass spectrometry assays using the consensus of published literature

This rose plot enables visualization of proteotypic peptides. Each colored rose petal corresponds to a peptide and is bounded by thin gray petals, which represent tryptic cut sites. The radial magnitude of each peptide corresponds to the number of publications in which is reported. Therefore, peptides preferentially reported in MS allergen detection literature stand out as radially large rose petals.

Hover over a rose petal with your mouse to see the peptide. Click on a rose petal to see the species specificity of that peptide and add it to your cart.

Milk protein Bos d 10 (α-s2-casein)

Protein sequence:

MKFFIFTCLLAVALAKNTMEHVSSSEESIISQETYKQEKNMAINPSKENLCSTFCKEVVRNANEEEYSIGSSSEESAEVATEEVKITVDDKHYQKALNEINQFYQKFPQYLQYLYQGPIVLNPWDQVKRNAVPITPTLNREQLSTSEENSKKTVDMESTEVFTKKTKLTEEEKNRLNFLKKISQRYQKFALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL

From the above plot, 3 out of the 16 tryptic peptides within the 7 to 30 amino acid length range have clear preferential detection and use in published mass spectrometry studies. These peptides include:

• ALNEINQFYQK
• NAVPITPTLNR
• FALPQYLK

Save peptides to your cart

In the upper right of every peptide page is a button to add a peptide to your cart. If you close your browser, your cart should be preserved.

Example: add the above peptide ALNEINQFYQK to your cart by clicking below:

• Save peptide to cart

Next, you can view your cart:

• Cart: 0

Export peptides

Peptides in your cart can be easily exported in a comma separated value (csv) format that imports into Skyline, an open source, freely available software package for targeted proteomics. Once in Skyline, a targeted method in native mass spectrometry instrument format can easily be exported.

Less studied allergens

Insufficient published data for certain food allergens, such as tree nuts and wheat, implores further research before a set of proteotypic peptides are established. To accelerate this effort, the Allergen Peptide Browser includes tools for peptide selection, species specificity filtering, and method export.

1. Select abundant allergenic proteins

A pie chart representing the relative abundances of the allergens in a food highlights those that are most abundant. For some foods, this level of detail is unavailable and has been replaced with estimates of protein family fractions. Clicking on a pie segment brings you to the page for that protein.

Allergenic milk proteins

2. Filter peptides by physiochemical properties

For each protein, potential peptide targets can be filtered by physiochemical properties. The table can also be sorted by empirical count (Exp.), previous amino acid (1), subsequent amino acid (2), or by in silico prediction scores by ESP Predictor (ESP) or CONSeQuence (CONSeQ).

Milk protein: Bos d 12 (κ-casein)

Click a checkbox to exclude:

1	Peptide	2	Exp.	ESP	CONSeQ
K	SFFLVVTILALTLPFLGAQEQNQEQPIR	C	0	0.349	0.02844
K	YIPIQYVLSR	Y	5	0.413	0.46624
R	SPAQILQWQVLSNTVPAK	S	4	0.755	0.27716
K	SCQAQPTTMAR	H	0	0.314	0.3478
R	HPHPHLSFMAIPPK	K	0	0.339	0.30752

3. Check species specificity

The table below depicts select results from the BLAST query of the non-redundant protein database for the peptide YMVIQGEPGAVIR. Given that this peptide is present in soybean, rice, and hazel proteins, it is not a suitable peptide for specific allergen detection.

Species name	Common name	Accession(s)	Tax id
Oryza sativa	Rice	Q9FUD1	4530
Glycine max	Soybean	O65809	3847
Corylus avellana	Hazel	AAK01235 AAK01236	13451

4. Save peptides and export

See left / above.