Proteomics - DIA-NN - PTM_SEA & others

[ravi]

Dear Madam/Sir,

I am trying to do Proteome analysis from DIA-NN outputs based on cancer and normal tissues (n = 12). Initially I could finish differentially expressed proteins and Cytoscape for enriched and PPI analysis.

However, I would like to do further.

I received the following files from our collaborator.

2025-058_withNorm_MBR_report.pg_matrix.tsv

2025-058_withNorm_MBR_report.pr_matrix.tsv

I have the following columns in the pg_matrix file:

Protein.Group
Protein.Names
Genes
First.Protein.Description
N.Sequences
N.Proteotypic.Sequences
D:\DIA\2025-058\20260206_QE2_HTSPAL_ESI12cmRT_sand_AcOH_PE_2025_058_e01_DIA.raw.dia
D:\DIA\2025-058_\20260206_QE2_HTSPAL_ESI12cmRT_sand_AcOH_PE_2025_058_e02_DIA.raw.dia
D:\DIA\2025-058_\20260206_QE2_HTSPAL_ESI12cmRT_sand_AcOH_PE_2025_058_e03_DIA.raw.dia

..............remaining sample columns with data.

May I know if I could use PTM_SEA and other relevant modules to conduct further analyses? I looked into the PTM_SEA module, but couldn't find documentation.

Your expert reply will be very helpful in planning my next steps.

Thank you,

Ravi.

[D R Mani]

Hello Ravi,

PTM-SEA is meant for pathway enrichment in site-level phosphoproteomics data. Since you are working only at the protein level, you will not be able to run PTM-SEA. You can find minimal documentation at https://proteogenomics.shinyapps.io/ptmsigdb. Your best bet is to look at the Krug et al paper (https://www.mcponline.org/content/18/3/576).

Best, 

Mani

D. R. Mani, Ph.D.

Director of Computational Proteomics, Proteomics Platform 

Broad Institute of MIT and Harvard, Cambridge, MA 02142

man...@broadinstitute.org | 617.714.7483

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