Processing large datasets

Some experiments can involve hundreds to thousands of MALDI-TOF MS spectra. The maximum number of spectra that Mass-Up is able to handle simultaneously depend on both the number of spectra and the size (i.ei. number of peaks) of each one.

If you are experiencing problems processing large datasets, here are some general advises to deal with them:

• The memory used by Mass-Up can be increased by editing the run.bat or run.sh that can be found the installation directory. In this file you can change the value of the MEMORY parameter. By default, this parameter is set to -Xmx2G, which means that Mass-Up will use up to 2 Gigabytes of RAM. To process large datasets, this amount can be increased up to a value near to computer's available RAM (for example, if you have 8Gb of RAM, you can set this parameter to -Xmx6G or -Xmx8G).
• Do not keep loaded spectra in Mass-Up that you don't need. If you preprocess your dataset with Mass-Up, don't keep the raw spectra in the Mass-Up's clipboard if it is not needed, because raw spectra use much more memory than the processed spectra. This is done by default by the preprocessing operations so, if you don't change this option in the operations, you don't have to worry.
• If Mass-Up can't load your raw dataset all at once, you can preprocess your spectra by batches. A raw dataset requires much more memory than a peak list. In addition, the preprocessing operations previous to peak matching can be done independently for each sample. Therefore, you can load only one batch of your samples, preprocess them and then store them. Once you have preprocessed all your dataset batchets, you can load the full preprocessed dataset (i.e. peak lists) and perform the peak matching.