Lecture: Mass spec Proteomics & Metabolomics

Bioconductor / CSAMA

Course material for CSAMA: Statistical Data Analysis for Genome Scale Biology

https://csama2024.bioconductor.eu/

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Lecture: Mass spec Proteomics & Metabolomics #3

Closed jorainer closed 7 years ago

jorainer commented 7 years ago

@lgatto would it be OK for you to split the lecture into 35 and 20 minute parts (first part your proteomics, second part my metabolomics)?

lgatto commented 7 years ago

In principle, I'm fine with splitting the lecture, but let's set up a table of content of the different topic that should be covered to (1) make sure there is no overlap/repetition and (2) get the time splitting right. I'll start some topics in the next post, under this issue - please add your topics and amend as appropriate.

lgatto commented 7 years ago

Brief intro on how MS works
Raw MS data (linked to the how MS works section)
MS quantitation: MS1 vs MS2, label-free vs labelled
Peptide identification and protein inference
Proteomics data processing overview
Some packages of interest (summary of above, could be joined for proteomics/metabolomics)

jorainer commented 7 years ago

had the timings wrong above, 35 + 20 is 55 mins ;) think I could reduce mine down to 15.

Title would be: Metabolomics data analysis with Bioconductor

Short intro into metabolomics
Short LCMS intro
LCMS-based data pre-processing
- Chromatographic peak detection
- Sample alignment
- Correspondence

This would describe in brief the topics of the (metabolomics part from the) afternoon workshop.

lgatto commented 7 years ago

It looks like Short LCMS intro and Brief intro on how MS works are overlapping. In my case, I would also introduce MSMS, but otherwise, I expect the content to be equivalent. My goal is to clarify how the data in an MSnExp related to what happens in the mass spec.

Are you happy with me presenting this for both of us, making sure that you add any parts that are essential for the metabolomics part?

jorainer commented 7 years ago

Fine for me if you include also the LCMS part. I had it only very very short (see also https://github.com/Bioconductor/CSAMA/blob/2017/lecture/4-thursday/lecture-14b-Metabolomics/Metabolomics.org) - eventually I'd then just keep the LCMS image to emphasize that in metabolomics we aim to identify chromatographic peaks in contrast to mass peaks.

lgatto commented 7 years ago

LC-MS is included in LC-MSMS, so yes, I fill address it. I also intend to talk about different ways to quantify MS data, including XICs. Best is probably for you to have your material at hand in case you need to clarify a few concepts, and/or amend my material once it's up.

jorainer commented 7 years ago

Fine for me. I try to keep my part as simple and short as possible (I'll not add additional things/slides - if at all I will shorten it).