I am a newcomer to LC-MS/MS data analysis and I would like to ask a question before starting the data analysis. I would like to quantify the dynamic changes in the whole proteome between two species. I have received the raw files and I have used MSconvertGUI to convert the raw format to mzML format to get started.
Considering the example below, there are two patients and the samples was ran in triplicate.
-> Should I open the files one by one on R? Is there another easier way to load all the data at once?
-> What is the better way to organize the data to compare the samples coming from the patients infected with bacteria 1 and 2?
20180202 LA 02 run01.raw; 20180202 LA 02 run02.raw ; 20180202 LA 02 run03.raw ;
20180202 LA 04 run1.raw; 20180202 LA 04 run2.raw; 20180202 LA 04 run3.raw;
Obs.: ."02" = sample that came from a patient; ."04" = sample that came from a patient
20180202 LA 03 run01.raw; 20180202 LA 03 run02.raw; 20180202 LA 03 run03.raw;
20180218 05 run01.raw; 20180218 05 run02.raw; 20180218 05 run03.raw
Obs.: ."03" = sample that came from a patient; ."05" = sample that came from a patient
I would be grateful if you could give some tips.
Thanks in advance!