This project is to find neutron coded pairs in MS1 spectra, as an cooperation project with Dr. Chenxi Jia.
- Add a new function to find the unlabeled peak for neutron code pair. The mono-isotope and the second isotope of the unlabeled precursor are required.
- Modify the project name as NeutronCodeFinder
Add a new parameter "NeuCode_Mass" to the config file For our method, the NeuCode_Mass is 42.3 mDa, for Coon's method it is 36.6 mDa
Cancel off the "isused" feature for every isotopic peak. Allow multiple neutron-coded peak pairs share the same peak.
The original algorithm only considered the simplest situation--the peak pair indicated the i-th and the i+1 th peaks. The new algorithm includes all the possible situations, meaning the i-th and i+n th peaks within the mass tolerance (n>1) will be considered.
default range: charge=[2,5]; Rnumber=[1,5]
allow the output of multiple R number for one PSM
(1) fix a bug when peak picking
(2) add de-noise function before peak picking (need refinement)
(3) change some default parameters in config file ##v1.0.2 (2016-9-6) (1) output R number in the pep and pepion result files
(2) output the mean mass of the neutron-coded mono-isotope peak pair (set as m) and calculate the mass of the non-coded peak pair (calculated as m-6.016254*Rnum/charge)
(1) Output the m/z when the peak intensity is the max in each XIC in pep file
(2) Add new input format: FindNeutron.exe test.config
All the 15 paramters were listed in the config file as follows:
//paramters for peak detection
MAX_CHARGE 5
SN_CUTOFF 1
PEAK_RINT_CUTOFF 0 //minimum peak relative intensity,default 0.
PEAK_INT_CUTOFF 1E5 //minimum peak absolute intensity
PEAK_TOLERANCE_PPM 10 //isotope peak mass tolerance: 10 ppm
//parameters in a neutron-coded pair
RATIO_LIMIT_LH 10 //max ratio limit for light vs heavy intensity
RATIO_LIMIT_SUM_LH 2 //the ratio limit of sumL/sumH in an XIC 2016-8-27
MIN_MASS_DIFF_IN_PAIR 5 //mDa
MAX_MASS_DIFF_IN_PAIR 100 //mDa
//paramters between neutron-coded pairs
MIN_MASS_DIFF_BETWEEN_PAIR 0 //mDa
MAX_MASS_DIFF_BETWEEN_PAIR 3 //mDa
RT_TOLERANCE 5 //max rt range when merging redundant ions, default +/-5min
ION_TOLERANCE_PPM 3 //precursor ion tolerance when merging redundant ions, default +/-3 ppm
MAX_R_NUM 3 //R number in a peptide sequence 2016-7-29
PEAKPAIR_LIMIT_mDa 10 //the tolerance of the mass diff in a peak pair and the theoretical mass diff (42.3 mDa*Rum/charge)
//raw files (one file per line)
e:\task\task_NeutronCoding_JCX\data\raw_data\20160809_SILAC.raw e:\task\task_NeutronCoding_JCX\data\raw_data\20160705_JCX_SLIAC_DDA_100per.raw
It began on 2016-6-21.
- Feature detection in MS1 spectra: find all the mono-isotopes with accurate charge, XIC and RT
- Find neutron coded peak pairs in MS1 spectra