Lecture: Mass spec Proteomics & Metabolomics about csama HOT 7 CLOSED

• 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)

from csama.

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.

from csama.

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.

from csama.

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.

from csama.

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?

from csama.

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.

from csama.

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).

from csama.