Mar 01, 2022
Top-down proteomics data analysis on the NRTDP TDPortal
- 1Northwestern University
- Human BioMolecular Atlas Program (HuBMAP) Method Development Community
- Kelleher Research Group
Protocol Citation: Jeannie Camarillo, Neil Kelleher 2022. Top-down proteomics data analysis on the NRTDP TDPortal. protocols.io https://dx.doi.org/10.17504/protocols.io.bnicmcaw
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: October 16, 2020
Last Modified: March 01, 2022
Protocol Integer ID: 43300
Abstract
This method describes how to analyze data on TD Portal, a top-down proteomics search tool from the National Resource for Translational and Developmental Proteomics.
Top-down proteomics data was searched on the TD Portal (portal.nrtdp.northwestern.edu)
Raw files for analysis were selected for search using Top Down Search v. 4.0.
Search parameters:
Organism: Homo Sapiens (Human) with Curated Histones: (Taxon 9606 - June 2020)
Use Empirical P-Score: FALSE
Filter by FDR: TRUE
Create SAS Input Sheet for Quant: FALSE
Precursor Resolution: High Resolution
Fragmentation Type: Auto
Code Set: Standard 4.0.0
Include ProSight Error Tolerant Search: FALSE