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MilliporeSigma

Developed in collaboration with the Protein Quantitation Consortium, our AQUA™ Peptides enable accurate, efficient mass spectrometric quantitation of protein biomarkers.

  • Focus your analysis on significant protein biomarkers
  • Accurately quantitate low abundance proteins
  • Eliminate costly, time consuming stable isotope labeling steps
  • Measure site-specific phosphorylation states
  • Validate gene silencing at the protein level
  • Learn more on the AQUA™ Strategy and Applications
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This method was developed by Dr. Steve Gygi and colleagues at Harvard Medical School.1 Limited use of this method is permitted under a licensing arrangement with Harvard Medical School.

We offer high-purity custom peptides. Our custom peptides are stringently tested to ensure high purity (HPLC), accurate molecular weight (ESI-MS), and specific peptide content. Custom peptides are available without stable isotope labeling or with stable isotope labeling.

Designing the Optimal Sequence

Selecting an optimal AQUA™ peptide is key to your analytical success. Because your time and resources are valuable, we suggest a careful evaluation of candidate peptides. The following guidelines provide a good starting point.

Using the known specificity of trypsin and the sequence of your protein of interest, generate a complete list of its tryptic peptides. Using the guidelines below, eliminate unsuitable peptides and select peptides with optimal characteristics for AQUA™ experimentation

  • Choose a peptide that is unique to your protein of interest
  • Choose a tryptic peptide that resolves well by HPLC
  • Avoid peptides that are too hydrophilic or too hydrophobic
  • Choose a peptide that ionizes well in your MS system
  • Avoid chemically reactive residues such as Tryptophan, Methionine, Cysteine, or chemically unstable sequences such as Asp-Gly, N-term Gln, N-term Asn
  • Choose an amino acid from the available list to be isotopically labeled
  • Peptide sequence length should be limited to 15 amino acids or less

Isotopically Labeled Amino Acids

Fully Labeled,13C, 15N > 98 atom%

Mass Difference between Native Peptide and AQUA™ Peptide

L-Arginine-13C6,15N4

10 Daltons

L-Isoleucine-13C6,15N

7 Daltons

L-Leucine-13C6,15N

7 Daltons

L-Lysine-13C6,15N2

8 Daltons

L-Phenylalanine-13C9,15N

10 Daltons

L-Proline-13C5,15N

6 Daltons

L-Valine-13C5,15N

6 Daltons

AQUA™ Peptide Specifications

Amount

5 x 1 nmol (quantification by AAA)

Length

5 - 30 amino acids

Purity

>95% by RP-HPLC

Modifications

Phosphorylation (Ser, Thr, Tyr), carboxymethylated Cys,
carbamidomethylated Cys, hydroxyproline, N-terminal biotin
(inquire regarding other modifications)

Stable Isotope

Fully labeled 98 atom% 13C and 98 atom% 15N enriched amino acids,
with one labeled amino acid per peptide. Stable isotope labeled
amino acid at the C-terminal sequence position

Quality Control

All peptides by HPLC and MS; additional analysis available upon request

Format

Supplied lyophilized

Related Articles
Designing Peptides
When selecting peptides for custom synthesis, several important factors should be considered during the design process. These considerations include sequence length, solubility and sequence stability.
Solid Phase Synthesis
Peptides are manufactured using solid phase FMOC or BOC chemistry methodologies on a PEG-Polystyrene support resin. Upon synthesis completion, side chain protecting groups are removed and the peptides are simultaneously cleaved from the resin. The cleaved and deprotected peptide material is then precipitated, washed and dissolved in a buffer containing H2O/ACN/HOAC prior to lyophilization.
Handling and Storage Protocol for Synthetic Peptides
One of the most challenging aspects of working with synthetic peptides is determining the best solvent in which to dissolve the peptide. General guidelines for proper storage, handling and dissolving your synthetic peptide are provided.
Peptide Quick Tips
Peptide Quick Tips. Helpful guidelines for proper storage and resuspension of your peptide for optimal performance in your assay.
Related Product Categories
Custom Peptide Manufacturing
Custom peptides designed, synthesized, purified and modified for your research and manufacturing applications available in scalable quantities, single tube library and array formats.
Amino Acids, Resins & Reagents for Peptide Synthesis
We offer an extensive range of amino acids, resins, and reagents of unparalleled quality, including Novabiochem®, for peptide synthesis, high-throughput organic chemistry, labeling peptides, and custom manufactured products.
Custom & Predesigned RNA Oligos, siRNA Duplexes and Controls
Comprehensive portfolio of custom & predesigned RNA oligos, miRNAs, esiRNAs, siRNA duplexes and controls available in multiple formats and manufactured under ISO 9001 and ISO 13485 quality systems for research or commercial applications.
Related Applications
Peptide Synthesis
Peptide synthesis involves the formation of a peptide bond between two amino acids to create a peptide composed of a chain of multiple amino acids.
Gene Expression & Silencing
CRISPR, miRNA, siRNA, and shRNA technologies for gene expression and gene silencing applications.
Solid State Synthesis
Solid-state synthesis, also called the ceramic method, involves grinding compounds of two or more non-volatile solids, pelletizing and heating the materials to form a new solid compound with optical, conductive, or other defined properties.

Highlights

References

1.
Stemmann O, Zou H, Gerber SA, Gygi SP, Kirschner MW. 2001. Dual Inhibition of Sister Chromatid Separation at Metaphase. Cell. 107(6):715-726. https://doi.org/10.1016/s0092-8674(01)00603-1
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