The following contains source code is from the manuscript "Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry Based Workflow".

Some possible analyses are included below:

1. Compute pariwise overlaps across peptide features

   • With IM python featureDensity.py allPeptides.txt True mzrtim_ovlps.npy --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
   • No IM python featureDensity.py allPeptides.txt False mzrt_ovlps.npy --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768

2. Compute overlaps between isolation windows and peptide features

   • With IM python cofragmentationRates.py allPeptides.txt 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d True cofragIm.npy --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768

   • No IM python cofragmentationRates.py allPeptides.txt 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d False cofragNoIm.npy --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768

3. Compute the Precursor Ion Fraction (PIF) of targeted peptides

   1. Fetch Isolation Window Feature Mapping python fetchIsolationWindowFeatureMapping.py allPeptides.txt 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d pasefMsmsScans.txt featureWindowMapping.pkl --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768

   2. Compute PIF python computePIF.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d featureWindowMapping.pkl pifComputations.pkl

   3. Compute PIF Top Scans python computePIFTopScans.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d featureWindowMapping.pkl pifComputationsTopScans.pkl

4. Compute the Precursor Ion Fraction of untargeted peptides

   1. Fetch Isolation Window Feature Mapping python fetchUntargetedIsolationWindowFeatureMapping.py allPeptides.txt 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d/ untargetedFeatureWindowMapping.pkl --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768
   2. Compute PIF python computePIF.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d untargetedFeatureWindowMapping.pkl untargetedPifComputations.pkl

5. Predict Identification Rates using PIF python pifToIdentifications.py pifComputations.pkl pifComputationsTopScans.pkl allPeptides.txt evidence.txt 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768

6. Predict Degree of cofragmentation in theoretical windows

   1. Create Theoretical windows python fetchUntargetedIsolationWindowFeatureMapping.py allPeptides.txt 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d untargetedFeatureWindowMapping.pkl --rawFile 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768

   2. Compute PIF python computePIF.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d UntargetedFeatureWindowMapping.pkl UntargetedPifComputations.pkl

7. Perform Post-Acqusition Extraction of high quality TOF pushes

   • We found that this does not have a huge impact on identifications. The scripts are here to see our methodology.
   1. Fetch MS2 scans from the .d file and merge (Control File) python fetchMS2Scans.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d MS2-Frames.mzML python mergeMS2Scans.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d MS2-Frames.mzML MS2-Frames-Merged.mzML
   2. Fetch (Based on post acquisition extraction) and merge python fetchMS2ScansExtract.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d MS2-Frames-Extract.mzML pifComputationsTopScans.tsv 13 python mergeMS2Scans.py 20180819_TIMS2_12-2_AnBr_SA_200ng_HeLa_50cm_120min_100ms_11CT_2_A1_01_2768.d MS2-Frames.mzML MS2-Frames-Merged-Extract.mzML

Furthermore python scripts can be called directly in the imMQExplorer python functions

If used please cite the following manuscript: Charkow and Rost, “Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry Based Workflow. doi:https://doi.org/10.1021/acs.analchem.1c01399”