# Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computing

> **NIH NIH R01** · INSTITUTE FOR SYSTEMS BIOLOGY · 2021 · $100,000

## Abstract

Project Summary
Mass spectrometry (MS) based proteomics is currently the most widely used technology for the analysis of
complex protein mixtures. It has the ability to detect and quantify the abundance of thousands of proteins and
their variants, post-translational modifications, protein:protein and protein:drug interactions per experiment. The
Trans-Proteomic Pipeline (TPP) is a free and open-source suite of software tools for the analysis of mass
spectrometry (MS) proteomics data that has been widely used by the community for over 15 years. Our ongoing
award for the maintenance and development of the TPP has four aims in which we 1) enhance the TPP to
process datasets from emerging workflows, 2) add statistical analysis and visualization capabilities for large
datasets, 3) respond to the needs of the community with functional and usability enhancements, and 4) expand
our user base with improved training and on-line learning. Great progress has been made on these aims during
the project period. However, current development for one of the main tools that we are currently focusing on has
been severely hindered by aging computational servers purchased in 2012 and inadequate development of
computing resources. We propose to address this problem via the purchase and deployment of a pair of high-
memory, high-core count, fast-disk compute servers, substantially accelerating our development cycle so that
the algorithm development can be completed more rapidly, and the completed algorithm can be further rapidly
optimized to run with more modest hardware requirements routinely. Deployment of these machines will
streamline our software development by providing rapid feedback on software changes and further
developments and their impact on search speed and enable us to provide tools to our users more rapidly,
accelerating the progress of many other research programs that use the TPP for data processing.

## Key facts

- **NIH application ID:** 10389405
- **Project number:** 3R01GM087221-11S1
- **Recipient organization:** INSTITUTE FOR SYSTEMS BIOLOGY
- **Principal Investigator:** Eric Deutsch
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $100,000
- **Award type:** 3
- **Project period:** 2010-09-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10389405

## Citation

> US National Institutes of Health, RePORTER application 10389405, Shortening the development cycle time of Trans Proteomic Pipeline tools with high performance computing (3R01GM087221-11S1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10389405. Licensed CC0.

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