SpikeTides™ - Synthetic Proteotypic Peptides: light – heavy – quantified

SpikeTides™ represent fully synthetic customized peptides, which terminate as native C-terminal heavily labeled or light Arg or Lys peptides or consist of a tryptic fragment that is fused to a proprietary JPT-tag. The latter tagged peptides enable a cost efficient access to quantified proteotypic peptides. JPT has developed a synthesis technology that enables ultra-fast, highly parallel and inexpensive synthesis of small scale peptides that are ideally suited for proteome wide profiling using SRM/MRM proteomic assays.
The sequences can be selected from bioinformatic prediction (i.e. Peptide Sieve) or from proteomic data repositories such as the Peptide Atlas (http://www.peptideatlas.org) that predict proteotypic peptides corresponding to peptides will be obtained from tryptic digestion of native proteomes.

Available SpikeTides™ Proteotypic Peptides Options:

Large Scale and purified heavily labeled peptides are available as Maxi SpikeTides™ upon request

SpikeTides™ Proteotypic Peptides

SpikeTides™_L Proteotypic Peptides

SpikeTides™_TQ Proteotypic Peptides

SpikeTides™_TQL Proteotypic Peptides

Benefits of SpikeTides™ Proteotypic Peptides

• Thousands of SpikeTides™ for MRM assays
• Unmatched turnaround times (10 000 peptides per week!)
• Delivery in ready-to-use microtiter plates
• Aliquotation and mixing service available
• SpikeTides™ approach is more robust than other peptide assays and more cost effective than AAA
• Is fully compatible with downstream analyses like MS and HPLC
• Enables chemical barcoding of complex SpikeTides™ mixtures within the JPT-tag

Applications for SpikeTides™ Proteotypic Peptides

• Optimization and validation of SRM assays
• Relative and absolute quantification of proteins
• Selection of best proteotypic peptides showing high mass spectrometry signal response
• Find predominant peptide fragments specific for your proteotypic peptide to be used in MRM transition
• Develop kits to quantify entire proteomic pathways

Background

Peptide quantification is a prerequisite in many areas of proteomics. One approach for unambiguous quantitative analysis of targeted proteins in complex mixtures is the use of tandem mass spectrometry to monitor one or more proteotypic peptide(s) from one protein of interest by a selected reaction monitoring (SRM) assay or by parallel analysis of many proteotypic peptides by a multiple reaction monitoring (MRM) assay. Absolute quantification is performed by the use of stable isotope-labeled proteotypic peptides as internal standards. These standards have to be purified to high level enabling subsequent AAA or alternative peptide quantification method (LavaPep, Ninhydrin, Lowry). This results in prices of several hundred US$ / € per peptide. JPT overcomes this situation by attaching a small chemical tag (which is cleavable by trypsin or other proteases) to the proteotypic peptide (proteotypic peptide + tag = SpikeTides™. Within the sample spiked with the appropriate SpikeTides™ (or mixture of SpikeTides™) the used protease (mostly trypsin) will cleave the peptide-tag bond releasing the desired proteotypic peptide and the JPT-tag in a 1:1 ratio.

Testimonials for SpikeTides™ Proteotypic Peptides:

"My unit at the Banting and Best Department of Medical Research, University of Toronto Centre for Cellular and Biomolecular Research (CCBR) works on the systematic identification and quantification of proteins and protein complexes on a global level. In addition we have started to perform targeted proteomics to study protein regulation within pathways, e.g. signaling pathways during stem cell fate decision. For this we used JPT's various SpikeTides™ peptide products to build LC-MRM assays in a fast and cost efficient manner. More recently we also found new ways of using low cost SpikeTides™ as quantitative peptide standards in order to quantify protein targets more accurately. We are currently in the process of validating this technology for the accurate quantification of various predicted microRNA targets."
Prof. Andrew Emili (Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada)

“We at the ETH successfully apply JPT’s unpurified isotope- and non-labeled peptide libraries for proteome-wide SRM assays allowing us to identify and quantify proteins spanning a broad range of abundances, including proteins not previously detectable. With the ability to produce large numbers of affordable small scale proteotypic peptides we envision for the first time the development of assays for the quantitative analysis for any proteinof interest and covering of whole proteomes.”
Paola Picotti, PhD (Institute of Molecular Systems Biology, ETH Zürich, Switzerland)

Selected References for SpikeTides™ Proteotypic Peptides:

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry
Ludwig et al., Mol. Cell. Proteomics (2012)
SpikeTides™—Proteotypic Peptides for Large-Scale MS-Based Proteomics
Schnatbaum et al., Nature Methods (2011)
mProphet: Automated Data Processing and Statistical Validation for Large-scale SRM Experiments
Reiter et al., Nature Methods (2011)
ATAQS: A computational Software Tool for High Throughput Transition Optimization and Validation for Selected Reaction Monitoring Mass Spectrometry
Brusniak et al., BMC Bioinformatics (2011)
Comprehensive Quantitative Analysis of Central Carbon and Amino-Acid Metabolism in Saccharomyces Cerevisiae Under Multiple Conditions by Targeted Proteomics
Costenoble et al.,Mol Syst Biol. 2011
A Quantitative Targeted Proteomics Approach to Validate Predicted microRNRNA Targets in C. elegans
Jovanovic et al., Nature Methods (2010)
Synthetic 1 Peptide Arrays for Pathway-Level Protein Monitoring by Liquid Chromatography-Tandem Mass Spectrometry
Hewel et al., Mol. Cell. Proteomics (2010)
High-throughput Generation of Selected Reaction-Monitoring Assays for Proteins and Proteomes
Picotti et al., Nature Methods (2009)
Full Dynamic Range Proteome. Analysis of S. cerevisiae by Targeted Proteomics
Picotti et al., Cell (2009)

More references under JPT Publications/Literature