MRMAssayDB is a web-based application that integrates these repositories into a single resource. It maps and links the targeted assays, annotates the proteins with information from UniProtKB, KEGG pathways, and Gene Ontologies, and provides several visualization options on the peptide and protein level. Currently MRMAssayDB contains >500K assays covering more than 38K proteins from 72 organisms; >13.5k of these proteins are present in > 2.3k KEGG biological pathways corresponding to > 300 master pathways, and mapping to >13k GO biological processes. MRMAssayDB allows comprehensive searches for a targeted-proteomics assay depending on the user’s interests, by using target-protein name or accession number, or using annotations such as subcellular localization, biological pathway, or disease or drug associations. The user can see how many data repositories include a specific peptide assay, and the commonly used transitions for each peptide in all empirical data from the repositories.

he use of stable-isotope labeled (SIS) peptides in MRM experiments is a key factor contributing to high-accuracy quantitative measurements. MRM experiments are also amenable to high degrees of multiplexing, allowing hundreds of peptides to be quantitated in a single LC/MS run. Laboratories who routinely perform such analyses can therefore quickly amass inventories of hundreds to thousands of SIS peptides, which can have hundreds of metadata points associated with each one. PeptideTracker is software for tracking all of the information associated with each SIS peptides within a laboratory. The software is based on a relational database with a Web interface. Hierarchical permission schemes permit access restrictions based upon assigned roles. The structure of the software tool was built to reflect the actual workflow of peptides as they move though the laboratory from synthesis to optimization on MS instruments to the creation of SIS peptide mixtures. Data and metadata pertaining to the SIS peptides, mixtures and the corresponding experiments has been written so that reports can be queried and formatted for output in formats that are best suited to the function of particular laboratory members.  The software is not only a repository to store all information about SIS peptides; it also allows exporting the optimization parameters of each peptide so they can be used for designing MRM assays.

Selecting the most appropriate surrogate peptides to represent a target protein is a major component of experimental design in Multiple Reaction Monitoring (MRM). Our software PeptidePicker with its v-score remains distinctive in its approach of integrating information about the proteins, their tryptic peptides, and the suitability of these peptides for MRM that is available online. PeptidePicker Library is a compiled a list of all possible surrogate peptides of the human proteome. Using our stringent selection criteria, the list includes 165k suitable MRM peptides covering 17k proteins of the human reviewed proteins in UniProtKB. Compared to average of 2-4min per protein for retrieving and integrating the information, the precompiled list includes all peptides available instantly. This allows a more cohesive and faster design of a multiplexed MRM experiment and provides insights into evidence for a protein’s existence. The Library is available for download as well as for direct online search using our MADpipe software.