Jun 16, 2026
Mass spectrometry data comparison and Venn diagram analysis
- Elisabeth Holzer1
- 1Laboratory of Sascha Martens, Max Perutz Labs, University of Vienna, Austria
Protocol Citation: Elisabeth Holzer 2026. Mass spectrometry data comparison and Venn diagram analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.14egnr24ql5d/v1
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
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Created: August 06, 2025
Last Modified: June 16, 2026
Protocol Integer ID: 224299
Keywords: ASAPCRN, protein overlap between different mass spectrometry dataset, different mass spectrometry dataset, mass spectrometry data comparison, protein overlap, absence of each protein, venn diagram analysis, protein, dataset, countif function, excel
Funders Acknowledgements:
Aligning Science Across Parkinson’s (ASAP)
Grant ID: ASAP-000350
DOC Fellowship (Austrian Academy of Sciences)
Abstract
To assess protein overlap between different mass spectrometry datasets., the datasets were organized in three separate columns in Excel. Using the COUNTIF function, the presence or absence of each protein across the lists was evaluated.
Guidelines
Formula Examples (Microsoft Excel):
- Proteins only in column A, not in B or C:
=IF(AND(COUNTIF(B:B, A2)=0, COUNTIF(C:C, A2)=0), 1, 0)
- Proteins shared between column A and B (regardless of C):
=IF(COUNTIF(B:B, A2)>0, 1, 0)
- Proteins shared between column A and B but not in C:
=IF(AND(COUNTIF(B:B, A2)>0, COUNTIF(C:C, A2)=0), 1, 0)
- Proteins present in all three columns:
=IF(AND(COUNTIF(B:B, A2)>0, COUNTIF(C:C, A2)>0), A2, "")
Organize Data
Place each protein list (1000 entries per dataset) in separate columns (e.g., columns A, B, and C).
Apply COUNTIF Logic
Use COUNTIF to determine whether a protein in one column appears in the others.
Create Binary Matrix
Use formulas to assign a binary presence (1) or absence (0) for each protein's appearance in the other datasets.
Summarize Overlap
Sum binary values to count in how many datasets each protein is present.
Generate Venn Diagram Input
Use these counts to define overlap sets for Venn diagram plotting.