Manual
User manual for QPMASS
(Version 1.0)
1 Software configuration requirements
QPMASS is developed on Windows operation system, and following are the basic requirements for the computer software and hardware:
(1) 64 bit Windows 7 operating system or its later version;
(2) CPU quad core or above, and dominant frequency more than 2 GHz;
(3) Memory over 4 Gb;
(4) Hard disk space above 100 Gb.
2 Installing QPMASS
(1) Copy the folders of "armadillo-4.320.1" and "netcdf-cxx-4.2" to the C: drive root directory;
(2) Double click the file of "netCDF4.4.1-NC4-64.exe" to set up. The path of "C:\ProgramFiles\netCDF 4.4.1" should be changed into "C:\netCDF 4.4.1";
(3) Double click "MainMFC.exe" in the folder of "QPmass_V1.0", then you will see the Graphical User Interface of QPMASS.
3 Introduction of QPMASS parameters
mzMin: minimum m/z
mzMax: maximum m/z
elu/csv: They are optional parameters for whether processing deconvolution data from AMDIS or ChromaTOF. If elu=1 and csv=0, it means processing deconvolution data from AMDIS. When elu=0 and csv=1 applied, deconvolution data from ChromaTOF will be analyzed. Note that *.csv file should include following information: the Compound Name, R.T.(min), Quant Mass, Area, and Mass Spectra (relative intensity) (Supplemental Table 3). The order of these five columns cannot be changed, and the names of raw data and deconvolution data are case sensitive.
top_n: The number of top ions, which gives a range to choose optimal quantative ion. For example, top_n=20 means choosing the quantative ion from the top 20 ions.
slaveCounts: The number of computer thread choose to processing data. Note that the setting of this parameter should depend on the personal computer configuration.
fileType: It is an optional parameter for raw data file type. fileType = 1 means importing the raw data file netCDF from ChromaTOF; while fileType = 2 stands for importing mzXML format (.txt) files of the raw data. *.txt format file is converted by MSConvert after setting the "output format" as "text"，and inputing ".txt" for "Extension" (For more detailed information about MSConvert, please visit http://proteowizard.sourceforge.net/tools.shtml).
sourcePath: The path of deconvolution results from AMDIS or ChromaTOF. For example: D:\demo_data
cdfPath, mzxmlPath: The path of raw data file convert from ChromaTOF and MsConvert. For example: D:\demo_data
gap: This parameter is the value of penalty for dynamic programming.
cutoff (s): It is a peak retention time threshold parameter to prevent the alignment of distant peaks. The values for this parameter should be chosen based on user’s knowledge of retention shifts and instrumental conditions.
peakthreshold: It is used to filter peaks that only present in a small number of samples, and cannot be aligned for most samples. If the 'peakThreshold' is set to 80%, for example, peaks that are not present in 80% of the samples (in a processing subgroup) are filtered from the QPMASS alignment results.
mzthreshold: It is used to reduce background noise. If the m/z of an ion fragment below the set value, this fragment will be filtered.
backFill: It is an optional parameter for whether conduct backfill procedure. 1 means choosing to backfill; 0 stands for this step will be skipped.
dtRange (s): It gives a range of retention time to calculate similarity in the backfill procedure. If the retention time beyond the given dtRange, this peak will not be aligned. The value of this parameter is typically 6 seconds.
simThreshold: The similarity of mass spectrum of peaks. If the similarity below the set value, these peaks will not be aligned. Typically, this value is under 0.5.
areaTol: It is used to verify the boundary of the peak in the quantificantion. The value of this parameter is typically 0.15-0.2.
4 Running QPMSS
After setting above parameters, clicking “run”, there will pop up a window where you can choose just doing alignment or quantity, or both alignment and quantity as needed. Then enter the code of each option, and press "enter", QPMASS will work.
5 Results
(1) The alignment results are saved in the file of "QPmass\Pmass_data\Result_files\dataset_mz.txt";
(2) The peak area data are saved in the file of "QPmass\Pmass_data\Result_files\Whole_method2.csv".
6 Common problems and solutions
If QPMASS cannot work normally, please check the data file which need to be processed by QPMASS as the following steps:
(1) Check the file name of deconvolution data and raw data file format. The names of deconvolution and raw data must be consistent. Note that the file names are case sensitive, and cannot contain spaces.
(2) Check the total ion chromatogram of raw data. In the process of large-scale GC-MS data, it is unavoidable to make mistakes during data collection, which makes a certain sample cannot be aligned with other samples. When this situation is encountered, users can delete those problematic data.
(3) Make sure that the folders in which the deconvolution data (.csv or .elu) and raw data (.cdf or .txt) were saved do not contain any other files. Otherwise, QPMASS cannot work correctly.
If you have any problem when using QPMASS, please contact the corresponding author: Xiaoquan Qi (xqi@ibcas.ac.cn).