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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Related Experiment Video

Updated: Dec 8, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
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Spritz: A Proteogenomic Database Engine.

Anthony J Cesnik1,2,3,4, Rachel M Miller1, Khairina Ibrahim1

  • 1Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.

Journal of Proteome Research
|September 24, 2020
PubMed
Summary
This summary is machine-generated.

Researchers developed Spritz, an open-source software tool to create custom protein databases from RNA sequencing data. This enables more accurate identification of protein variants and post-translational modifications (PTMs) using mass spectrometry.

Keywords:
PTMsRNA-Seqmodificationsproteoformproteogenomicssample-specificsequence variationstop-downtranscriptomics

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Genomics

Background:

  • Proteoforms, differing in amino acid sequence or post-translational modifications (PTMs), are crucial for cellular function.
  • Accurate identification and quantification of proteoforms in diverse samples by mass spectrometry (MS) require sample-specific protein databases.
  • Existing methods may not fully capture the complexity of proteoforms in genetically varied samples.

Purpose of the Study:

  • To develop an open-source software tool, Spritz, for generating customized protein databases tailored to specific biological samples.
  • To enable the annotation of sequence variations and PTMs within these databases.
  • To facilitate the identification of variant proteoforms and their modifications using MS.

Main Methods:

  • Developed Spritz, an open-source software tool with a graphical user interface (Windows) and cross-platform scripts.
  • Integrated approximately 20 tools to construct proteogenomic databases from raw RNA sequencing data.
  • Annotated sequence variations against the Ensembl reference genome and transferred PTMs from UniProt.
  • Incorporated PTMs discovered via bottom-up MS and MetaMorpheus for global PTM discovery.

Main Results:

  • Demonstrated the utility of sample-specific databases for identifying variant peptides and modified variant peptides.
  • Successfully identified variant proteoforms using bottom-up and top-down proteomic data from Jurkat T lymphocytes.
  • Identified phosphorylated variant sites using phosphoproteomic data from U2OS osteosarcoma cells.

Conclusions:

  • Spritz facilitates the creation of comprehensive, sample-specific protein databases from RNA sequencing data.
  • These databases significantly enhance the identification of variant proteoforms and their PTMs.
  • The software provides a valuable tool for proteogenomic research, improving the accuracy of proteoform analysis.