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Questions tagged [mass-spectrometry]

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Finding mutations in glycosylation sites

We are going to look at the likely N- and O- glycosylation sites within MUC16 (Q8WXI7 · MUC16_HUMAN)§ by in house long-read DNA sequencing data (PacBio). Counting the number of tandem repeats is a ...
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Mass spectrometry: How to obtain expression counts for protein

I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent. Each sample corresponds to a folder ...
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Can Maven (mass spectrometry software) read mzML files?

I did not find a documentation. Can Maven (mass spectrometry software) read mzML files?
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How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
Soerendip's user avatar
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XCMS isn't evaluating the proper peak due to retention time drift

I'd like to do a targeted screening analysis for trace contaminates. However, due to the nature of the sample preparations, the retention times I'm getting drift a lot from run to run and XCMS isn't ...
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Seeking Advice on Acquiring Clean Experimental data comprises of proteins for FDR Estimation

I am a bioinformatics student doing my research on top-down mass spectrometry-based proteomics and seeking some guidance on acquiring very clean experimental data with known true positives and false ...
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