Does anyone know how to analyze LCMS data? I'm looking for guidance on how to identify differentially expressed genes and glycoproteins. How can I determine which glycoproteins are upregulated and downregulated?
Hi,
Although I am not sure I'm able to help you out, there are a few questions I have:
What machine did you use to generate the MS data?
Did you try to use the software provided with the machine to analyze your MS data?
What was your experimental setup, i.e. what are you comparing, how many groups of samples, how many replicates per sample, what kind of controls were included, did you use some kind of labeling to facilitate protein quantitation, etc.
I assume that peptide mixtures were analyzed?
Typically, LC-MS raw data is searched against a database to allow for qualitative protein identification. In addition, the number of peptides retrieved per protein could be somewhat indicative of its abundance, just like sequence coverage, although there are a lot of restrictions and considerations you'll need to take into account when (quantitatively) interpreting your data, especially when you're interested in low abundant proteins.
Post-translational modifications, such as glycosylation, add a whole new level of complexity to your (quantitative) analysis.
Perhaps, some additional information might enable the community to help you out (better).
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