I am working on proteomics. Due to non-availability of nanoLCMS, I have conducted a ESI-MS analysis of a test sample. I have identified the proteins using XTandem. I am planning to quantify relative abundance of peptides/proteins on the basis of mz value. It would be a great favor, if I am provided a reference for this.
Best Regards
There is a group that has developed a set of tools and workflows for direct infusion shotgun proteome analysis. Their software is publicly available on GitHub.
Jiang, Yuming & Hutton, Alexandre & Cranney, Caleb & Meyer, Jesse. (2022). Label-Free Quantification from Direct Infusion Shotgun Proteome Analysis (DISPA-LFQ) with CsoDIAq Software. Analytical Chemistry. 95. 10.1021/acs.analchem.2c02249.
Cranney, Caleb & Meyer, Jesse. (2021). CsoDIAq Software for Direct Infusion Shotgun Proteome Analysis. Analytical Chemistry. XXXX. 10.1021/acs.analchem.1c02021.
GitHub - xomicsdatascience/zoDIAq: Cosine Similarity Optimization for DIA qualitative and quantitative analysis (https://github.com/xomicsdatascience/zoDIAq)
Hi Tehzeeb,
Using XTandem, are you able to match any IDs in the test sample?
The only quantifiable entity in your results is Intensity of a particular species at a particular m/z
You can utilize the XCalibur or the analytical software for your mass spectrometer to integrate area under curve of the particular species at particular m/z in your mixture.
Good luck,
Hediye
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