PepQuery

PepQuery is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.

Inputs

• A sequence to match, one of the following:
  • A peptide string or a history dataset with a list of peptides
  • A protein string or a history dataset with a protein fasta
  • A DNA string that is at least 60 base pairs in length
• A mass spectrometry MGF file
• A reference protein fasta database, peptides matching a reference sequence will be excluded.
• An optional tags file for no-enzyme immunopeptidomics search
  • See: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf

Outputs

• PSM annotation - tabular with columns:
  • peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
• Detail - tabular with columns:
  • report_spectrum_file spectrum_title peptide modification pep_mass score
• PSM - tabular with columns:
  • peptide modification n report_spectrum_file spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
• PSM Rank - tabular with columns:
  • peptide modification n report_spectrum_file spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm
• An MGF with the best matching spectrums

The report_spectrum_file is an optional field that can be added.

The n_ptm field is added when using unrestricted modification searching (-um).