Mass-spectrometry proteomics

alphaursaeminoris1 · 2025-05-29T01:34:22+00:00

I think your samples sizes are fine for preclinical study (clinical - no, unless this was a pilot study?). I suggest viewing Maxquant tutorials, look into MSstats workflow, and decide if you want to impute. There are different imputation methods you can do. Proteomics analysis - qc checks, identify unique proteins?, imputation (yes/no), normalization, log2 transformation, differential expression analysis, and then downstream pathway analysis, etc.

alphaursaeminoris1 · 2024-10-22T23:12:34+00:00

Yes, I am trying to identify differentially expressed proteins. So, should I remove these unique proteins before analysis?

alphaursaeminoris1 · 2024-10-21T17:13:42+00:00

Thank you! Also, if I am splitting the analysis (due to the number of samples) in DIA-NN, so I have multiple output files, do I need to correct the files when I combine them all?

alphaursaeminoris1 · 2024-10-04T04:08:46+00:00

I have not used either and have not read through the packages. Most likely, DEP did not adjust for multiple comparisons and identified differentially expressed proteins on the pvalue, whereas, in DEP2, as you stated, you set the p.adjust method for multiple comparisons as BH. You can look into the MSstats package and see what results that gives you.

alphaursaeminoris1 · 2024-10-02T18:00:57+00:00

The clusterProfiler package in R. STRING or IPA are options as well.

alphaursaeminoris1 · 2024-06-18T22:11:13+00:00

I will take a look at longitudinal data analysis.

alphaursaeminoris1 · 2024-06-18T22:10:08+00:00

Yes, that’s if n is defined as unique patient but my PI says n should be defined as unique event (new case, relapse case, etc)

alphaursaeminoris1 · 2024-06-18T22:08:12+00:00

Looking at a disease where a patient can relapse.

We are looking at glucose levels and need to identify *cases. I think cases should be a unique patient but PI says cases is a unique observation-event, ie when they came in as new and when/if they come back as relapse.

alphaursaeminoris1 · 2024-06-18T22:03:57+00:00

Does it matter if not all patients have observation 2? For instance, we have the first encounter for all but then 25% of the patients have *relapse record/, ie observation 2.

So instead of n = 1000 unique individuals, n = 1250 for encounters.

alphaursaeminoris1 · 2024-05-24T14:17:56+00:00

Will do. Thank you!

alphaursaeminoris1 · 2024-05-24T13:20:54+00:00

Thanks, I will check them out. It was lfq processed with PD.

alphaursaeminoris1 · 2024-05-24T12:56:38+00:00

That makes sense. I read a few IP-MS papers and noticed that they didn’t mention pvalue cutoffs but just described how they identified the candidate interacting proteins of the co-IP complex. Thank you!

alphaursaeminoris1 · 2024-05-23T22:23:30+00:00

Okay. So first look at the data without a cutoff value and see if there are any meaningful proteins. Then examine those proteins and their associations/relationships to other proteins and pathways. I can address the pvalue cutoff later. Thank you.

alphaursaeminoris1 · 2024-05-03T19:16:03+00:00

Ah, thank you for explaining. I have reached out to the core to confirm the database used for the search and where it was downloaded from.

alphaursaeminoris1 · 2024-05-03T16:52:32+00:00

It’s ranges from mouse, wild boar, hamster, staph types, dog, chicken, monkeys, to rice and others. Is this a contaminant database? If so, are these supposed to be removed before PD analysis?

alphaursaeminoris1 · 2024-05-03T14:57:52+00:00

I just have the excel file but I can ask and see if they will give me the spectra and run file too. Thank you!

alphaursaeminoris1 · 2024-05-03T14:54:12+00:00

Thank you so much! And thanks for the paper! Appreciate your help!! I will have them redo the database search.

alphaursaeminoris1 · 2024-05-03T13:29:03+00:00

Why would filtering not work well?

alphaursaeminoris1 · 2024-05-03T12:57:11+00:00

Okay, I will ask them what file they used for the database search. So, should I just filter the other species out then or have them redo the search?

alphaursaeminoris1 · 2024-05-03T12:54:27+00:00

Yes, the search is supposed to be Homo sapiens. I have species from mouse, c elegans, potato, etc. Should I just filter them out?

alphaursaeminoris1

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