# Development of Trans Proteomic Pipeline, an Analysis Suite for Mass Spectrometry

> **NIH NIH R01** · INSTITUTE FOR SYSTEMS BIOLOGY · 2021 · $524,789

## Abstract

Project Summary
Mass spectrometry (MS) based proteomics is a key technology for the identification, quantification and
comparison of proteins and their post-translational modifications across all aspects of biology. MS datasets
have been growing ever larger with the advancement of instrumentation, as has the archive of experimental
data available for re-analysis and comparison. In order to meet the needs of the proteomics community for
coping with big data, we have been developing our end-to-end suite of data processing and analysis tools,
called the Trans-Proteomic Pipeline (TPP). This project will advance the widely used TPP software suite to
become even more useful to its user community, enabling them to perform their analyses even faster with less
human effort, and adding capabilities that are currently not possible or are only in testing stages. We will add
full end-to-end TPP support for the data independent acquisition (DIA) workflows, such as SWATH-MS, and
proteogenomics workflows, such as RNA-seq assisted proteomics. The TPP already has partial support for
these workflows, but needs additional finishing, hardening, and extension to high capacity cloud computing
platforms to become truly useful to all our users. As protein abundance quantification becomes even more
essential to more experiments, we will enhance our existing tools for isotopic and isobaric labeled data as well
as label-free data, and build a new analysis workbench that will give our users access to advanced statistical
analysis and comparison routines that already exist but are difficult for many users to handle. In addition to
bundling this statistical software, we will build a framework that allows users to take their quantitative results
from any of the traditional workflows or new workflows, transform them into the formats that the statistical
packages require, and then visualize and interactively explore the outputs of statistical analysis, so trends can
be uncovered and outliers verified in the original data.
A substantial number of smaller enhancements to the TPP suite will be made to make the tools smarter so that
users are relieved of the burden setting parameters and shepherding data through various tools. We will
develop new modes of operation for existing tools to be able to handle challenges presented by our users
based on the feedback we receive from them. We will continue our many outreach efforts, which include
teaching software courses several times per year, hosting workshops and booths at scientific conferences to
meet with and gain feedback from our users, and develop many more publicly available tutorials and recipes
for using the tools and applications to various circumstances. We will of course continue to disseminate the
advancements of the TPP with articles in the literature and with presentations at scientific conferences. In
summary, this proposed program will continue to advance the TPP as the preeminent free and open-source
end-to-end software ...

## Key facts

- **NIH application ID:** 10155495
- **Project number:** 5R01GM087221-11
- **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:** $524,789
- **Award type:** 5
- **Project period:** 2010-09-01 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10155495

## Citation

> US National Institutes of Health, RePORTER application 10155495, Development of Trans Proteomic Pipeline, an Analysis Suite for Mass Spectrometry (5R01GM087221-11). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10155495. Licensed CC0.

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