Download the latest version of the CDF C Library: Here's an easy to follow guide if you didn't even know what the CDF file format was before you found this question on SO.ġ. So having used the scan filter on MSCovert to convert my APD.raw files to mzML as suggested, I now have a scan 1 and a scan2 files for each, to the best of my knowledge these represent MS1 in scan 1 and MSe in scan 2 (is this correct? if not can anyone point me in the direction of something to read to understand this better as the waters handbooks are pretty dry!)Īlso I would like to use XCMS online, but does XCMS understand/ can i make it understand what each file represents so for example say i am uploading for a pairwise comparision of x vs y, 10 repeats of each, and a scan 1 and a scan 2 for each file.The answer by is correct, but it assumes that you have already installed the CDF C Library. I am still not sure about a few thing and given that i am confident i am not alone i have a few questions. New update, I have checked my spectrums and scan numbers, i am confident they are correct. They should always be correct regarding the masses but you still need to centroid first. Do this with a few scans just to be sure. If not you probably got uncalibrated data. If they are exactly the same to at least 4 digits you are OK. Then you open the extract same spectrum in for example mzMine (the mzML file of course). The way to check if things worked is to open the centroided raw file in masslynx and open a few ms spectra. It is by far easiest for your down-stream work to have each scanEvent (function in Waters language) in separate files. Remember to use the scanEvent filter when you use msconvert. If that doesn't work try the lockmassRefiner filter. You can start by trying converting your centroided files with msconvert (to mzML since that is the newer format) without any special parameters. The new set of files will have the files centroided (be sure that your originals are not already centroided) but you still need to check the accurate mass issue.
#Cdf files windows#
To centroid a whole file or a set of files you use "Tools" -> "Accurate mass measure" -> "Automatic peak detection" from the main windows of masslynx. You will need to check the masses masslynx is showing and comparing to the converted file to understand if things were converted correctly. From my short tests it appears that some newer versions of masslynx will do the conversion correctly without this now.ī) Some files now seem to have the correction baked in. Options are:Ī) Some files will need the lockmassRefiner filter in msconvert. Now it appears that the solution depends on how the files were recorded and the version of masslynx. It used to be that msconvert were not able to use the lockmass information to calibrate the masses. You can get around it by centroiding the files in masslynx to create centroided raw files that can then be convertedĢ) Accurate mass. For waters data msconvert cannot use the Waters centroiding algorithm. If you open the _extern.inf file inside the raw folder each function is described at the bottom.įor conversion with proteowizard you have two problems:ġ) Centroiding (if your files actually were recorded in profile mode). One could be a low energy scan and the other a high energy scan, or MSE. Analyzing different functions together probably doesn't make much sense. You will need to know what is in each function/scanEvent to know what is best to do.
#Cdf files license#
has this since been updated? As a return to masslynx would be a nightmare for me as I do not have a license and would need to travel to use it!Īnyways I am feeling very lost and due to the size of the files in question trying things to see if they work takes such a long time so if anyone has any suggestions it would be much appreciated. I have tried a while ago to convert files using proteowizard but it doesn't or at least didn't seem to like waters files at the time. but others suggest using proteowizard to convert. I have seen some other threads suggesting that waters users need to go back to masslynx and make sure all their data is centrioded before they export and convert. 1.cdf and 2.cdf) is meaning that I am losing information, is this concern valid? I have been trying to use xcms online but I am worried that the division of my mass spec info (ie. raw files but it doesn't seem to like the scan filter and I have a lot to get through so moved onto my. raw data run on a ULPC water synapt G2 which I converted using databridge, this gave me four files, I think one is lock spray and one is UV data.3.cdf and 4.cdf
#Cdf files software#
I have been trying for a while now to make sense of all of the software etc.