User guide

---

Implementation

PeptideTracker refers to the set of flat files which are available via web interface. All the routines in this database are implemented in python 2.7. The user web interface was developed in the Django 1.8.11 framework.

The metadata from UniProt are automatically retrieved using a Python tool.

All peptides in the database are available as Stable Isotope Labeled heavy standards (SIS) that are ready for use in LC-MRM/MS methods. All peptides have been rigorously characterized for purity and concentration by CZE and AAA, and LC retention times and MRM/MS transitions are known. Concentration ranges for many peptides were also determined in representative samples.

---

Searching

Basic

The database can be searched using the 'search' field located on the bottom of home page. Searching PeptideTracker can be performed in a following way:

1. User needs to select search type by selecting option from Any or Protein or UniProtKB Accession

2. Then typing in Protein name or UniProtKB Accession or or Gene name or Petidetracker ID or peptide sequence or organism name in the search field, and pressing 'submit'.

Advanced

A dedicated advanced search is available where it is possible to select one or more fields to restrict the search. The advanced search option is likely to become more relevant as the database becomes populated with Peptidetracker results investigating the same peptide, but are sourced from various organisms or proteins.

User can retrieve the corresponding PeptideTracker entries to work with them on this website.

Enter parameter, separated by a '|' or each line having one entry, into the specific form field. For example, search for one or more UniProtKB Accession(s) (UniProtKB Accession Number field):
P09958|P23188

OR simply type:
P09958
P23188

And it will show Peptidetracker results related to specified UniProtKB Accession(s).

---

Data Submission

The database is open to submissions from the community and researchers are encouraged to submit their data to peptidetracker using the online submission interface. Those users with a peptidetracker account can use their existing online credentials to login and deposit data. After login the depositor has access to an online submission form to be filled in with the required fields.

Depositors are required to fill out required fields with information before uploading their data. Submissions are manually curated by experts in the field and after that, data are considered for deposition. The peptidetracker crew may contact the submitters requesting additional data and information if requires.

---

RESTful services

This section describes how to programmatically access data and services from peptidetracker.proteincentre.com.

Basic

The base restful url (basic) for peptidetracker is : http://peptidetracker.proteincentre.com/rest/api/

It takes the following arguments: searchtype(Any or Protein or UniProtKB Accession) and searchterm(Protein name or UniProtKB Accession or Gene name or Petidetracker ID or peptide sequence or organism name) as a required parameter in the following format searchtype=Any&searchterm=PEP2014043010.

Therefore a sample query would look like http://peptidetracker.proteincentre.com/rest/api/?searchtype=Any&searchterm=PEP2014043010

A csv file with the Peptidetracker results will be returned.

Advanced

The base restful url (advanced) for peptidetracker is : http://peptidetracker.proteincentre.com/rest/api/advanced/

It takes the following multiple arguments:
protein(Protein name)
uniprotkb(UniProtKB Accession Number)
gene(Gene Name)
pepid(Peptidetracker ID)
pepseq(Peptide sequence)
org(Organism)

Therefore a sample query would look like:
http://peptidetracker.proteincentre.com/rest/api/advanced/?protein=&uniprotkb=&gene=&pepid=&pepseq=MLDGEVTDAVEAR&org=. A csv file with the Peptidetracker results will be returned for specified peptide sequence.
http://peptidetracker.proteincentre.com/rest/api/advanced/?protein=&uniprotkb=&gene=&pepid=PEP2014092224&pepseq=&org=Mus musculus. A csv file with the Peptidetracker results will be returned for specified Peptidetracker ID and Organism name.

User can retrieve the corresponding PeptideTracker entries to download them on this website.

Enter parameter, separated by a '|', into the specific parameter field. For example, search for one or more UniProtKB Accession(s) (uniprotkb field):
http://peptidetracker.proteincentre.com/rest/api/advanced/?protein=&uniprotkb=P09958|P23188&gene=&pepid=&pepseq=&org=. A csv file with the Peptidetracker results will be returned for specified UniProtKB Accession Number(s).

---

PeptideTracker Statistics

Species Amino acids Molecular weight

---

Cite

Mohammed, Y., Bhowmick, P., Smith, D. S., Domanski, D., Jackson, A. M., Michaud, S. A., Malchow, S., Percy, A. J., Chambers, A. G., Palmer, A., Zhang, S., Sickmann, A. and Borchers, C. H. (2016), PeptideTracker: A knowledgebase for collecting and storing information on protein concentrations in biological tissues. Proteomics.