The data generated will be specific to the exact instrument and method used which generated it. Contact the professionals at the laboratory which generated the data to review it with you.

We use the "Excalibur" software from Thermo to analyse our .raw files. I'm not sure if there are other softwares able to open that format. However it is possible to export the data from .raw files into other formats. Again this can be done with the Excalibur software which should be the one the lab you got the data from also uses. So you can ask them to give you the data in a format that you can handle. Or as Bill suggested review the data with that lab together which might be good idea anyway depending on how familiar you are with LCMS spectroscopy.

Dear Sujitha Balaji,

Since you have been using a Thermo Orbitrap instrument, I assume that the data are recorded as Excalibur .Raw files. Data processing is then best done in Excalibur to take advantage of the high mass accuracy and all the other features of the Orbitrap. But if you need some other way to analyse the data using other software, you may consider to export the data as NetCDF file. This is an option in the Excalibur program. The NetCDF format is a general data format, which can be read by many other data processing packages, including statistical tools like R. There are already complete R-pacakages to do what you want to do. Example: http://www.bioconductor.org/help/course-materials/2014/BioC2014/Gatto.html. But first of all, you need to formulate what it is that you want to extract from the data. I hope this may be helpful. Kind regards, Harrie Verhoeven.

To read it you will have to convert it using MSConvert, which is a free download. If you convert the data into any of the open MS data standards, mzML, mzData, mzXML, you can load the runs into another open source data analysis package (e.g., OpenMS, or mzMine) for further processing. My opinion is mzMine is easier to use than OpenMS or XCMS (R-based). If the data was acquired in centroid mode, you will have a bunch of centroids that represent the peaks found in the profile data. If the data was acquired in profile mode, you will have to centroid it for further analysis. If you have to centroid the data, there are a myriad of decisons to make (see link). Once centroided, there are another myriad of decisions to make for further analysis. It is difficult to pick up all the nuances without some training.

Method Mass Spectral Data Processing

Hi All, thanks for your responses. I dont have access to Excalibur. Please suggest me any software which is user friendly and free also

Contact the professionals at the laboratory which generated the data to review it with you.

See my response above about MSConvert. It is free and relatively easy to use. Beyond that the data analysis can be done with OpenMS, mzMine, or XCMS. I recommend mzMine as the most user friendly of these options.

my lc-ms run was only for 3 min. Do you think it is still fine?? Instrument- orbitrap elite