R to process Netcdf file

download the ncdf package to R flowing this link http://cran.r-project.org/web/packages/ncdf/index.html
After you download the package, open R then go to "install package(s) from local zip file", open the zip file you stored. Then download the file download file here to process.

load the ncdf: library(ncdf)
to open the netcdf file: open.ncdf('filename.cdf')
> open.ncdf("C:\\Users\\MR TINH\\Desktop\\12.CDF")
[1] "file C:\\Users\\MR TINH\\Desktop\\12.CDF has 13 dimensions:"
[1] "_2_byte_string   Size: 2"
[1] "_4_byte_string   Size: 4"
[1] "_8_byte_string   Size: 8"
[1] "_16_byte_string   Size: 16"
[1] "_32_byte_string   Size: 32"
[1] "_64_byte_string   Size: 64"
[1] "_128_byte_string   Size: 128"
[1] "_255_byte_string   Size: 255"
[1] "range   Size: 2"
[1] "point_number   Size: 961761"
[1] "error_number   Size: 1"
[1] "scan_number   Size: 7028"
[1] "instrument_number   Size: 1"
[1] "------------------------"
[1] "file C:\\Users\\MR TINH\\Desktop\\12.CDF has 29 variables:"
[1] "char error_log[_64_byte_string,error_number]  Longname:error_log Missval:NA"
[1] "double a_d_sampling_rate[scan_number]  Longname:a_d_sampling_rate Missval:1e+30"
[1] "short a_d_coaddition_factor[scan_number]  Longname:a_d_coaddition_factor Missval:NA"
[1] "double scan_acquisition_time[scan_number]  Longname:scan_acquisition_time Missval:1e+30"
[1] "double scan_duration[scan_number]  Longname:scan_duration Missval:1e+30"
[1] "double inter_scan_time[scan_number]  Longname:inter_scan_time Missval:1e+30"
[1] "double resolution[scan_number]  Longname:resolution Missval:1e+30"
[1] "int actual_scan_number[scan_number]  Longname:actual_scan_number Missval:NA"
[1] "double total_intensity[scan_number]  Longname:total_intensity Missval:1e+30"
[1] "double mass_range_min[scan_number]  Longname:mass_range_min Missval:1e+30"
[1] "double mass_range_max[scan_number]  Longname:mass_range_max Missval:1e+30"
[1] "double time_range_min[scan_number]  Longname:time_range_min Missval:1e+30"
[1] "double time_range_max[scan_number]  Longname:time_range_max Missval:1e+30"
[1] "int scan_index[scan_number]  Longname:scan_index Missval:NA"
[1] "int point_count[scan_number]  Longname:point_count Missval:NA"
[1] "int flag_count[scan_number]  Longname:flag_count Missval:NA"
[1] "float mass_values[point_number]  Longname:mass_values Missval:1e+30"
[1] "float time_values[point_number]  Longname:time_values Missval:1e+30"
[1] "float intensity_values[point_number]  Longname:intensity_values Missval:1e+30"
[1] "char instrument_name[_32_byte_string,instrument_number]  Longname:instrument_name Missval:NA"
[1] "char instrument_id[_32_byte_string,instrument_number]  Longname:instrument_id Missval:NA"
[1] "char instrument_mfr[_32_byte_string,instrument_number]  Longname:instrument_mfr Missval:NA"
[1] "char instrument_model[_32_byte_string,instrument_number]  Longname:instrument_model Missval:NA"
[1] "char instrument_serial_no[_32_byte_string,instrument_number]  Longname:instrument_serial_no Missval:NA"
[1] "char instrument_sw_version[_32_byte_string,instrument_number]  Longname:instrument_sw_version Missval:NA"
[1] "char instrument_fw_version[_32_byte_string,instrument_number]  Longname:instrument_fw_version Missval:NA"
[1] "char instrument_os_version[_32_byte_string,instrument_number]  Longname:instrument_os_version Missval:NA"
[1] "char instrument_app_version[_32_byte_string,instrument_number]  Longname:instrument_app_version Missval:NA"
[1] "char instrument_comments[_32_byte_string,instrument_number]  Longname:instrument_comments Missval:NA"
 
It is said that there are 29 variables
to get the variables in netcdf: get.var.cdf(filename, "variable")
the mass spectrometry is composed of the metabolic compound form pyrolysis products, including time, intensity and mass range,
each mass spectrometry is in the 3-D matrix, time, intensity and mass, when the data is exported to AIA(type of CDF file) it expressed as scan_index presenting the number of scan/seconds.