Mass Spectrometry

AQUA™ Peptides

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

View additional information on the Protein AQUA Strategy and Protein AQUA Applications and Protein AQUA References.

This method was developed by Dr. Steve Gygi and colleagues at Harvard Medical School [Stemmann O., Zou H., Gerber S. A., Gygi S. P., Kirschner M. W.; Dual inhibition of sister chromatid separation at metaphase, Cell 2001, Dec 14, 107: 715-726]. Limited use of this method is permitted under a licensing arrangement with Harvard Medical School.


We are pleased to announce the launch of its AQUA Peptide Library. Select from a library of over 300 readily available AQUA Peptides for even greater convenience and value.

Browse The AQUA Peptide Library
Choose from the three methods below:


Download Sequences and Protein IDs
Want associated protein information?


AQUA Library
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AQUA Library
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View by Sequence and Product Number
Want to browse the AQUA Peptide Library catalog listings?

View the online catalog of AQUA Library Peptides

Can't find your AQUA of interest in the library?
Take advantage of our Custom AQUA Peptide Design Tool page.

Custom Peptides and Custom AQUA™ Peptides

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.
  • To meet the specific demands of AQUA experimentation, custom AQUA™ peptides are available using fully labeled 98 atom% 13C and 98 atom% 15N enriched amino acids, with one labeled amino acid per peptide.
  • For both unlabeled and isotopically labeled custom peptides, we offer the following modifications:  phosphorylation (Ser, Thr, Tyr), carboxymethylation (Cys), carbamidomethylation (Cys), hydroxyproline, and N-terminal biotin.
  • Custom peptides and custom AQUA™ peptides up to 30 amino acids long can be synthesized.
  • Standard synthesis amount is 5 x 1 nmol (quantified using AAA).

AQUA™ Peptide References

  1. Harig, S., et al., Induction of cytotoxic T-cell responses against immunoglobulin V region–derived peptides modified at human leukocyte antigen-A2 binding residues.  Blood., 98(10), 2999-3005 (2001). Abstract
  2. Landesman-Bollag, E., et al., Protein kinase CK2: Signaling and tumorigenesis in the mammary gland.  Mol. Cell Biochem., 227(1-2), 153-165 (2001). Abstract
  3. von Bergwelt-Baildon, M.S., et al.,  Human primary and memory cytotoxic T lymphocyte responses are efficiently induced by means of CD40-activated B cells as antigen-presenting cells: potential for clinical application.  Blood, 99(9), 3319-3325 (2002). Abstract 
  4. Verginis, P., et al., Delineation of Five Thyroglobulin T Cell Epitopes with Pathogenic Potential in Experimental Autoimmune Thyroiditis.  J. Immunol., 169(9), 5332-5337 (2002). Abstract 
  5. Karras, E , et al., Induction of murine thyroiditis by a non dominant Ek-restricted peptide of human thyroglobulin.  Immunology, 108(4), 556-561 (2003). Abstract 
  6. Guenther, J.F., et al., Phosphorylation of soybean nodulin 26 on serine 262 enhances water permeability and is regulated developmentally and by osmotic signals.  Plant Cell, 15(4), 981-991 (2003). Abstract 
  7. Lui, W.W.Y., et al., Binding Partners for the COOH-Terminal Appendage Domains of the GGAs and γ-Adaptin.  Mol. Biol. Cell, 14(6), 2385-2398 (2003). Abstract
  8. Wilkemeyer, M.F., et al., Differential effects of ethanol antagonism and neuroprotection in peptide fragment NAPVSIPQ prevention of ethanol-induced developmental toxicity.  Proc. Nat. Acad. Sci. USA, 100(14), 8543-8548 (2003). Abstract
  9. Chan, S.-A., and Smith, C., Low frequency stimulation of mouse adrenal slices reveals a clathrin-independent, protein kinase C-mediated endocytic mechanism.  J. Physiol., 553(Pt 3), 707-717 (2003). Abstract
  10. Yu, W., et al., Enhanced transfection efficiency of a systemically delivered tumor-targeting immunolipoplex by inclusion of a pH-sensitive histidylated oligolysine peptide.  Nucleic Acids Res., 32(5), e48 (2004). Abstract
  11. Kawamoto, S., et al., The anaphylatoxin C3a downregulates the Th2 response to epicutaneously introduced antigen.  J. Clin. Invest., 114(3), 399-407 (2004). Abstract
  12. Chan, S.-A., et al., Adrenal Chromaffin Cells Exhibit Impaired Granule Trafficking in NCAM Knockout Mice.  J. Neurophysiol., 94(2), 1037-1047 (2005). Abstract
  13. Pan, C.Q., et al., Design of a Long Acting Peptide Functioning as Both a Glucagon-like Peptide-1 Receptor Agonist and a Glucagon Receptor Antagonist.  J. Biol. Chem., 281(18), 12506-12515 (2006). Abstract
  14. Zhang, L., et al., Structures of α-Type Ions Formed in the 157 nm Photodissociation of Singly-Charged Peptide Ions.  J. Am. Soc. Mass Spectrom., 17(9), 1315-1321 (2006). Abstract
  15. Mahnke, L., and Clifford, D., Cytotoxic T cell recognition of an HIV-1 reverse transcriptase variant peptide incorporating the K103N drug resistance mutation.  AIDS Res. Ther., 3, 21 (2006). Abstract 
  16. Gao, W., et al., Exosite interactions contribute to tension-induced cleavage of von Willebrand factor by the antithrombotic ADAMTS13 metalloprotease.  Proc. Nat. Acad. Sci. USA, 103(50), 19099-19104 (2006). Abstract
  17. Thompson, R.N., et al., Pregnancy block by MHC class I peptides is mediated via the production of inositol 1,4,5-trisphosphate in the mouse vomeronasal organ.  J. Exp. Biol., 210(Pt 8), 1406-1412 (2007). Abstract
  18. Peng, S., et al., HLA-DQB1*02–Restricted HPV-16 E7 Peptide–Specific CD4+ T-Cell Immune Responses Correlate with Regression of HPV-16–Associated High-Grade Squamous Intraepithelial Lesions.  Clin. Cancer Res., 13(8), 2479-2487 (2007). Abstract
  19. Borthwick, L.A., et al., The Formation of the cAMP/Protein Kinase A-dependent Annexin 2-S100A10 Complex with Cystic Fibrosis Conductance Regulator Protein (CFTR) Regulates CFTR Channel Function.  Mol. Biol. Cell, 18(9), 3388-3397 (2007). Abstract
  20. Gay, E.A., et al., Structural Determinates for Apolipoprotein E-Derived Peptide Interaction with the α7 Nicotinic Acetylcholine Receptor.  Mol. Pharmacol., 72(4), 838-849 (2007). Abstract 
  21. 21. Brun, V., et al., Isotope-labeled Protein Standards : Toward Absolute Quantitative Proteomics.  Mol. Cell. Proteomics, 6(12), 2139-2149 (2007). Abstract
  22. Minko, I.G., et al., Mutagenic potential of DNA-peptide crosslinks mediated by acrolein-derived DNA adducts.  Mutat. Res., 637(1-2), 161-172 (2008). Abstract
  23. Toropygin, I.Y., et al., The N-domain of angiotensin-converting enzyme specifically hydrolyzes the Arg-5-His-6 bond of Alzheimer’s Aβ-(1-16) peptide and its isoAsp-7 analogue with different efficiency as evidenced by quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.  Rapid Commun. Mass Spectrom., 22(2), 231-239 (2008). Abstract
  24. Atlante, A., et al., A peptide containing residues 26-44 of tau protein impairs mitochondrial oxidative phosphorylation acting at the level of the adenine nucleotide translocator.  Biochim. Biophys Acta, 1777(10), 1289-1399 (2008). Abstract
  25. Li, N., et al., Absolute Difference of Hepatobiliary Transporter Multidrug Resistance-Associated Protein (MRP2/Mrp2) in Liver Tissues and Isolated Hepatocytes from Rat, Dog, Monkey, and Human.  Drug. Metab. Dispos., 37(1), 66-73 (2009). Abstract
  26. deWilde, A., et al., Tryptic peptide analysis of ceruloplasmin in dried blood spots using liquid chromatography-tandem mass spectrometry: application to newborn screening.  Clin. Chem., 54(12), 1961-1968 (2008). Abstract 
  27. Velez, J.C.Q., et al., Angiotensin I Is Largely Converted to Angiotensin (1-7) and Angiotensin (2-10) by Isolated Rat Glomeruli.  Hypertension, 53, 790-797 (2009). Abstract
  28. Singh, S., et al., FLEXIQuant: A novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides.  J. Proteome Res., 8(5), 2201-2210 (2009). Abstract
  29. Zhou, Y., et al., Calmodulin Mediates the Ca2+-Dependent Regulation of Cx44 Gap Junctions.  Biophys. J., 96(7), 2832-2848 (2009). Abstract
  30. Tribulatti, M.V., et al., Galectin-8 provides costimulatory and proliferative signals to T lymphocytes.  J. Leukoc. Biol., 86(2), 371-380 (2009). Abstract
  31. Li, H., et al.,  Proximal glycans outside of the epitopes regulate the presentation of HIV-1 envelope gp120 helper epitopes.  J. Immunol., 182(10), 6369-6378 (2009). Abstract
  32. Zhang, L., and Reilly, J.P., Radical-Driven Dissociation of Odd-Electron Peptide Radical Ions Produced in 157 nm Photodissociation.  J. Am. Soc. Mass Spectrom., 20(7), 1378-1390 (2009). Abstract
  33. Wehling-Henricks, M., et al., Loss of positive allosteric interactions between neuronal nitric oxide synthase and phosphofructokinase contributes to defects in glycolysis and increased fatigability in muscular dystrophy.  Hum. Mol. Genet., 18(18), 3439-3451 (2009). Abstract
  34. Loit, E., et al., Identification of three wheat globulin genes by screening a Triticum aestivum BAC genomic library with cDNA from a diabetes-associated globulin.  BMC Plant Biol., 9:93 (2009). Abstract
  35. Richardson, A., et al., Intracellular delivery of bovine lactoferricin’s antimicrobial core (RRWQWR) kills T-leukemia cells.  Biochem. Biophys. Res. Commun., 388(4), 736-741 (2009). Abstract
  36. Le Bihan, T., et al., Quantitative analysis of low-abundance peptides in HeLa cell cytoplasm by targeted liquid chromatography/mass spectrometry and stable isotope dilution: emphasising the distinction between peptide detection and peptide identification.  Rapid Commun. Mass Spectrom., 24(7), 1093-1104 (2010). Abstract
  37. Rosario, M., et al., Novel Recombinant Mycobacterium bovis BCG, Ovine Atadenovirus, and Modified Vaccinia Virus Ankara Vaccines Combine To Induce Robust Human Immunodeficiency Virus-Specific CD4 and CD8 T-Cell Responses in Rhesus Macaques.  J. Virol., 84(12), 5898-5908 (2010). Abstract
  38. Kolypetri, P., et al., Iodine content of thyroglobulin in NOD.H2h4 mice developing iodine-accelerated autoimmune thyroiditis.  Hormones, 9(2), 151.160 (2010). Abstract
  39. Mc Guire, C., et al., Oligodendrocyte-Specific FADD Deletion Protects Mice from Autoimmune-Mediated Demyelination.  J. Immunol., 185(12), 7646-7653 (2010). Abstract
  40. Gomez, J.A., et al., Cell-Penetrating Penta-Peptides (CPP5s): Measurement of Cell Entry and Protein-Transduction Activity.  Pharmaceuticals, 3(12), 3594-3613 (2010). Abstract
  41. Yan, W., et al., Index-ion Triggered MS2 Ion Quantification: A Novel Proteomics Approach for Reproducible Detection and Quantification of Targeted Proteins in Complex Mixtures.  Mol. Cell. Proteomics, 10(3), M110.005611 (2011). Abstract
  42. Kettenbach, A.N., et al., Absolute quantification of protein and post-translational modification abundance with stable isotope–labeled synthetic peptides.  Nat. Protoc., 6(2), 175-186 (2011). Abstract
  43. Prabakaran, S., et al., Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions.  Mol. Syst. Biol., 7, 482 (2011). Abstract
  44. Bucher, J., et al., A systems biology approach to dynamic modeling and inter-subject variability of statin pharmacokinetics in human hepatocytes.  BMC Syst. Biol., 5, 66 (2011). Abstract
  45. Santhoskumar, P., et al., αA-Crystallin Peptide 66SDRDKFVIFLDVKHF80 Accumulating in Aging Lens Impairs the Function of α-Crystallin and Induces Lens Protein Aggregation.  PLoS One, 6(4), e19291 (2011). Abstract 
  46. Pietras, C.O., et al., The asthma candidate gene NPSR1 mediates isoform specific downstream signalling.  BMC Pulm. Med., 11, 39 (2011). Abstract
  47. Wang, X.S., et al., Characterization of KRAS Rearrangements in Metastatic Prostate Cancer.  Cancer Discov., 1, 35-43 (2011). Abstract
  48. 48. Grisé, H., et al., A Conserved Tandem Cyclophilin-Binding Site in Hepatitis C Virus Nonstructural Protein 5A Regulates Alisporivir Susceptibility.  J. Virol., 86(9), 4811-4822 (2012). Abstract
  49. Velez, J.C.Q., et al., Enzymatic processing of angiotensin peptides by human glomerular endothelial cells.  Am. J. Physiol. Renal Physiol., 302(12), F1583-F1594 (2012). Abstract
  50. Coppinger, J.A., et al., A Chaperone Trap Contributes to the Onset of Cystic Fibrosis.  PLoS One, 7(5), e37682 (2012). Abstract
  51. Kroot, J.J.C., et al., Second Round Robin for plasma hepcidin methods: First steps toward harmonization.  Am. J. Hematol., 87(10), 977-983 (2012). Abstract
  52. Sato, Y., et al., Simultaneous Absolute Protein Quantification of Carboxylesterases 1 and 2 in Human Liver Tissue Fractions using Liquid Chromatography-Tandem Mass Spectrometry.  Drug Metab Dispos., 40(7), 1389-1396 (2012). Abstract
  53. Tumbarello, D.A., et al., β3 integrin modulates transforming growth factor beta induced (TGFBI) function and paclitaxel response in ovarian cancer cells.  Mol. Cancer, 11, 36 (2012). Abstract
  54. Stevenson, S.E., et al., Environmental Effects on Allergen Levels in Commercially Grown Non-Genetically Modified Soybeans: Assessing Variation Across North America.  Front. Plant Sci., 3, 196 (2012). Abstract
  55. van de Steeg, E., et al., Drug-Drug Interactions between Rosuvastatin and Oral Antidiabetic Drugs Occurring at the Level of OATP1B1.  Drug. Metab. Dispos., 41(3), 592-601 (2013). Abstract
  56. Schwacke, J.H., et al., Network modeling reveals steps in angiotensin peptide processing.  Hypertension, 61(3), 690-700 (2013). Abstract
  57. Wu, S., et al., CAND1 controls in vivo dynamics of the cullin 1-RING ubiquitin ligase repertoire.  Nat. Commun., 4, 1642-1650 (2013). Abstract
  58. Choudhary, S., et al., Inducible Tumor Necrosis Factor (TNF) Receptor-associated Factor-1 Expression Couples the Canonical to the Non-canonical NF-κB Pathway in TNF Stimulation.  J. Biol. Chem., 288(20), 14612-14623 (2013). Abstract
  59. Tsuchiya, H., et al., The Parallel Reaction Monitoring Method Contributes to a Highly Sensitive Polyubiquitin Chain Quantification.  Biochem. Biophys. Res. Commun., 436(2), 223-229 (2013). Abstract
  60. Peroza, E.A., et al., Metal ion release from metallothioneins: proteolysis as an alternative to oxidation.  Metallomics, 5(9), 1204-1214 (2013). Abstract
  61. Berko, D., et al., Inherent asymmetry in the 26S Proteasome Is Defined by the Ubiquitin Receptor RPN13.  J. Biol. Chem., 289(9), 5609-5618 (2014). Abstract
  62. Sato, Y., et al., Optimized Methods for Targeted Peptide-Based Quantification of Human Uridine 5'-Diphosphate-Glucuronosyltransferases in Biological Specimens Using Liquid Chromatography-Tandem Mass Spectrometry.   Drug. Metab. Dispos., 42(5), 885-889 (2014). Abstract
  63. Stecker, K., et al., Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response.  Plant Physiol., 165(3), 1171-1187 (2014). Abstract
  64. Torsetnes, S.B., et al., Multiplexing Determination of Small Cell Lung Cancer Biomarkers and Their Isovariants in Serum by Immunocapture LC-MS/MS.  Anal. Chem., 86(14), 6983-6992 (2014). Abstract
  65. Schumacher, J., et al., Differential secretome analysis of Pseudomonas syringae pv tomato using gel-free MS proteomics.  Front. Plant Sci., 5, 242 (2014). Abstract
  66. Nakayama, K., et al., The C-Terminal Fragment of Prostate-Specific Antigen, a 2331 Da Peptide, as a New Urinary Pathognomonic Biomarker Candidate for Diagnosing Prostate Cancer.  PLOS One, 9(9), e107234 (2014). Abstract:   
  67. Ohtake, F., et al., Ubiquitin acetylation inhibits polyubiquitin chain elongation.  EMBO Reports, 16(2), 192-201 (2015) Abstract
  68. Hamashima, K., et al., Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.  PLoS One, 10(1), e0116981 (2015). Abstract 
  69. Nasso, S., et al., Ariadne’s Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data.  J. Proteome Res., 14(9), 3779-3792 (2015). Abstract
  70. Yi, J., et al., Degradation and Stabilization of Peptide Hormones in Human Blood Specimens.  PLoS One, 10(7), e0134427 (2015). Abstract