New application-specific peptide libraries for quantitative MS workflows

by Thermo Scientific Pierce Protein Biology Team - 06/01/11

Thermo Scientific PEPotec SRM Peptide Libraries are fully synthetic, crude peptides customized for the development of mid-to high-throughput single-reaction monitoring (SRM) and multiple-reaction monitoring (MRM) assays in quantitative mass spectrometry (MS) workflows. The study of proteomes, sub-proteomes and protein pathways often requires quantitative MS analysis that depends on the identification and validation of SRM and MRM assays. PEPotec* SRM Peptide Libraries offer convenience and flexibility for developing quantitative MS approaches while accelerating biological assays by reducing the setup time of MS experiments. These peptide libraries were developed as a result of our involvement in the SRMAtlas project, which seeks to map the entire human proteome.

The standard service supplies peptides with either arginine (R) or lysine (K) as the C-terminal amino acid, which encompasses the most commonly used tryptic proteotypic peptides used for SRM assay development. Although the standard maximum peptide length is 25 amino acids, this length can be optionally increased to 30 amino acids to ensure that the vast majority of potential proteotypic peptides screened for their suitability for a reliable SRM assay are covered.


Figure 1. Targeted assay development by mass spectrometry. A key step for targeted quantitation is identifying sequence-specific or unique target peptides with sufficient signal intensity for the absolute quantitation of the target peptide(s). This step begins with a combination of peptide and spectral database searches and computational (in silico) predictions using specific programs such as Thermo Scientific Pinpoint Software to identify an initial list of potential peptides that corresponds to multiple proteins of interest. Crude peptide libraries are synthesized to screen the candidate peptides by liquid chromatography mass spectrometry (LCMS). Results are analyzed to optimize LC and MS workflows and to identify the best proteotypic sequences for target quantitation. These sequences are used to generate isotopically labeled “heavy” peptides for absolute target quantitation by LCMS.

Ordering information

The minimum order size is 24 peptides. Additional flexibility is provided through modifications (optional services) such as phosphorylations, carbamidomethylation and labeling with heavy amino acids.

For more information and to get a quote request form, please visit: or call your North American sales representative at 888-412-2225.

For Europe, call Technical Support in Ulm, Germany at +49-731-29870 or email 

General references

Prakash, A., et al. (2009). Expediting the development of targeted SRM Assays: Using data from shotgun proteomics to automate method development. J Proteome Res8(6):2733-9.

For Research Use Only. Not for use in diagnostic procedures.