diff --git a/refs/UP000005640_9606.fasta.gz b/refs/UP000005640_9606.fasta.gz
new file mode 100644
index 0000000..cc4b02e
Binary files /dev/null and b/refs/UP000005640_9606.fasta.gz differ
diff --git a/run_fragpipe.sh b/run_fragpipe.sh
deleted file mode 100644
index 5bd148f..0000000
--- a/run_fragpipe.sh
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/bin/bash
-
-set -e
-set -o pipefail
-
-# Set tools and input directories
-input_dir=input
-tools_dir=/fragpipe_bin/fragPipe-23.1/fragpipe/tools
-
-# Error out if no custom.fasta is provided
-if [ ! -e "$input_dir/custom.fasta" ]; then
-  echo "Error: must supply a custom.fasta file in the input directory ($input_dir)"
-  exit 1
-fi
-
-echo "Adding decoys and contaminants to FASTA files.."
-cd $input_dir
-
-# Initialize the Philosopher workspace
-$tools_dir/Philosopher/philosopher-v5.1.1 workspace --init
-
-# Add decoys and contaminants to the custom FASTA file
-gunzip -c UP000005640_9606.fasta.gz | $tools_dir/Philosopher/philosopher-v5.1.1 database --custom custom.fasta --add /dev/stdin --contam
-mv *decoys-contam-custom.fasta.fas decoys-contam-custom-canonical.fasta
-
-# Clean intermediate files
-$tools_dir/Philosopher/philosopher-v5.1.1 workspace --clean 
-
-# Return to the previous directory
-cd -
-
-# set cavatica directory
-cavatica_dir=(/home/rstudio/fragpipe/data/projects/harenzaj/proteomics)
-
-if [ ! -d $cavatica_dir ]; then
-  echo "Error: path to cavatica project directory does not exist. Confirm that proteomics cavatica project is mounted to data/ directory"
-  exit 1
-fi
-
-# check if tmp directory exists, and create it if not
-tmp_dir=(/home/rstudio/fragpipe/tmp)
-
-if [ ! -d $tmp_dir ]; then
-  mkdir -p $tmp_dir
-  echo "Temporary directory does not exist, creating..."
-fi
-
-# clear contents of tmp directory, if not already empty
-rm -rf $tmp_dir/*
-
-# copy mzML files to temporary directory, maintaining directory structure
-echo "copying mzML files to temporary directory..."
-
-if ! [[ " $* " == *" --run_subset "* ]]; then
-
-cp -R $cavatica_dir/*CBTTC_PBT_Proteome* /home/rstudio/fragpipe/tmp/
-
-else
-
-cp -R $cavatica_dir/01CBTTC_PBT_Proteome* /home/rstudio/fragpipe/tmp/
-
-fi
-
-# unzip mzML files, force overwrite if files exist
-echo "unzipping mzML files..."
-gunzip -f /home/rstudio/fragpipe/tmp/*CBTTC_PBT_Proteome*/*mzML.gz
-
-# set workflow, manifest, results and tools directories
-echo "Starting Fragpipe run..."
-
-wf=/home/rstudio/fragpipe/input/PDC000180customworkflow.workflow
-manifest=/home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest
-
-if [[ " $* " == *" --run_subset "* ]]; then
-
-grep "01CBTTC_" $manifest > /home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest_sub
-manifest=/home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest_sub
-
-fi
-
-res_dir=/home/rstudio/fragpipe/results
-tools_dir=/fragpipe_bin/fragPipe-23.1/fragpipe/tools
-
-/fragpipe_bin/fragPipe-23.1/fragpipe/bin/fragpipe --headless --workflow $wf --manifest $manifest --workdir $res_dir --config-tools-folder $tools_dir
-
-# clear tmp directory
-rm -rf $tmp_dir/*
diff --git a/tumor-enriched-splicing/input/PDC000180customworkflow.workflow b/tumor-enriched-splicing/input/PDC000180customworkflow.workflow
new file mode 100644
index 0000000..15329cf
--- /dev/null
+++ b/tumor-enriched-splicing/input/PDC000180customworkflow.workflow
@@ -0,0 +1,327 @@
+# Workflow: PDC000180customworkflow
+
+
+# Please edit the following path to point to the correct location.
+# In Windows, please replace single '\' with '\\'
+database.db-path=/home/rstudio/fragpipe/tumor-enriched-splicing/input/decoys-contam-custom-canonical.fasta
+
+crystalc.run-crystalc=false
+database.decoy-tag=rev_
+diann.fragpipe.cmd-opts=
+diann.generate-msstats=true
+diann.heavy=
+diann.library=
+diann.light=
+diann.medium=
+diann.q-value=0.01
+diann.quantification-strategy=3
+diann.quantification-strategy-2=QuantUMS (high accuracy)
+diann.run-dia-nn=false
+diann.run-dia-plex=false
+diann.run-specific-protein-q-value=false
+diann.unrelated-runs=false
+diann.use-predicted-spectra=true
+diaumpire.AdjustFragIntensity=true
+diaumpire.BoostComplementaryIon=false
+diaumpire.CorrThreshold=0
+diaumpire.DeltaApex=0.2
+diaumpire.ExportPrecursorPeak=false
+diaumpire.Q1=true
+diaumpire.Q2=true
+diaumpire.Q3=true
+diaumpire.RFmax=500
+diaumpire.RPmax=25
+diaumpire.RTOverlap=0.3
+diaumpire.SE.EstimateBG=false
+diaumpire.SE.IsoPattern=0.3
+diaumpire.SE.MS1PPM=10
+diaumpire.SE.MS2PPM=20
+diaumpire.SE.MS2SN=1.1
+diaumpire.SE.MassDefectFilter=true
+diaumpire.SE.MassDefectOffset=0.1
+diaumpire.SE.NoMissedScan=1
+diaumpire.SE.SN=1.1
+diaumpire.run-diaumpire=false
+fpop.fpop-tmt=false
+fpop.label_control=
+fpop.label_fpop=
+fpop.region_size=1
+fpop.run-fpop=false
+fpop.subtract-control=false
+freequant.mz-tol=10
+freequant.rt-tol=0.4
+freequant.run-freequant=false
+ionquant.excludemods=
+ionquant.heavy=
+ionquant.imtol=0.05
+ionquant.ionfdr=0.05
+ionquant.light=
+ionquant.locprob=0.75
+ionquant.maxlfq=1
+ionquant.mbr=0
+ionquant.mbrimtol=0.05
+ionquant.mbrmincorr=0
+ionquant.mbrrttol=1
+ionquant.mbrtoprun=10
+ionquant.medium=
+ionquant.minfreq=0
+ionquant.minions=2
+ionquant.minisotopes=2
+ionquant.minscans=3
+ionquant.mztol=10
+ionquant.normalization=1
+ionquant.peptidefdr=5
+ionquant.proteinfdr=5
+ionquant.requantify=1
+ionquant.rttol=0.4
+ionquant.run-ionquant=true
+ionquant.tp=0
+ionquant.uniqueness=0
+ionquant.use-labeling=false
+ionquant.use-lfq=true
+ionquant.writeindex=0
+msbooster.predict-rt=true
+msbooster.predict-spectra=true
+msbooster.run-msbooster=true
+msbooster.use-correlated-features=false
+msfragger.Y_type_masses=
+msfragger.activation_types=all
+msfragger.allowed_missed_cleavage_1=2
+msfragger.allowed_missed_cleavage_2=2
+msfragger.calibrate_mass=2
+msfragger.check_spectral_files=true
+msfragger.clip_nTerm_M=true
+msfragger.deisotope=1
+msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
+msfragger.deneutralloss=1
+msfragger.diagnostic_fragments=
+msfragger.diagnostic_intensity_filter=0
+msfragger.digest_max_length=50
+msfragger.digest_min_length=8
+msfragger.fragment_ion_series=b,y
+msfragger.fragment_mass_tolerance=20
+msfragger.fragment_mass_units=1
+msfragger.group_variable=0
+msfragger.intensity_transform=0
+msfragger.ion_series_definitions=
+msfragger.isotope_error=-1/0/1/2/3
+msfragger.labile_search_mode=off
+msfragger.localize_delta_mass=false
+msfragger.mass_diff_to_variable_mod=0
+msfragger.mass_offsets=0
+msfragger.mass_offsets_detailed=
+msfragger.max_fragment_charge=2
+msfragger.max_variable_mods_combinations=5000
+msfragger.max_variable_mods_per_peptide=3
+msfragger.min_fragments_modelling=2
+msfragger.min_matched_fragments=4
+msfragger.min_sequence_matches=2
+msfragger.minimum_peaks=15
+msfragger.minimum_ratio=0.01
+msfragger.misc.fragger.clear-mz-hi=131.5
+msfragger.misc.fragger.clear-mz-lo=125.5
+msfragger.misc.fragger.digest-mass-hi=5000
+msfragger.misc.fragger.digest-mass-lo=200
+msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
+msfragger.misc.fragger.enzyme-dropdown-2=null
+msfragger.misc.fragger.precursor-charge-hi=4
+msfragger.misc.fragger.precursor-charge-lo=1
+msfragger.misc.fragger.remove-precursor-range-hi=1.5
+msfragger.misc.fragger.remove-precursor-range-lo=-1.5
+msfragger.misc.slice-db=1
+msfragger.num_enzyme_termini=2
+msfragger.output_format=pepXML_pin
+msfragger.output_max_expect=50
+msfragger.output_report_topN=1
+msfragger.output_report_topN_dda_plus=5
+msfragger.output_report_topN_dia1=5
+msfragger.override_charge=false
+msfragger.precursor_mass_lower=-20
+msfragger.precursor_mass_mode=selected
+msfragger.precursor_mass_units=1
+msfragger.precursor_mass_upper=20
+msfragger.precursor_true_tolerance=20
+msfragger.precursor_true_units=1
+msfragger.remainder_fragment_masses=-18.01056 79.96633
+msfragger.remove_precursor_peak=1
+msfragger.report_alternative_proteins=true
+msfragger.require_precursor=true
+msfragger.restrict_deltamass_to=all
+msfragger.reuse_dia_fragment_peaks=false
+msfragger.run-msfragger=true
+msfragger.search_enzyme_cut_1=KR
+msfragger.search_enzyme_cut_2=
+msfragger.search_enzyme_name_1=stricttrypsin
+msfragger.search_enzyme_name_2=null
+msfragger.search_enzyme_nocut_1=
+msfragger.search_enzyme_nocut_2=
+msfragger.search_enzyme_sense_1=C
+msfragger.search_enzyme_sense_2=C
+msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
+msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
+msfragger.track_zero_topN=0
+msfragger.use_all_mods_in_first_search=false
+msfragger.use_detailed_offsets=false
+msfragger.use_topN_peaks=150
+msfragger.write_calibrated_mzml=false
+msfragger.write_uncalibrated_mgf=false
+msfragger.zero_bin_accept_expect=0
+msfragger.zero_bin_mult_expect=1
+opair.activation1=HCD
+opair.activation2=ETD
+opair.filterOxonium=true
+opair.glyco_db=
+opair.max_glycans=4
+opair.max_isotope_error=2
+opair.min_isotope_error=0
+opair.ms1_tol=20
+opair.ms2_tol=20
+opair.oxonium_filtering_file=
+opair.oxonium_minimum_intensity=0.05
+opair.reverse_scan_order=false
+opair.run-opair=false
+opair.single_scan_type=false
+peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
+peptide-prophet.combine-pepxml=false
+peptide-prophet.run-peptide-prophet=false
+percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
+percolator.keep-tsv-files=false
+percolator.min-prob=0.5
+percolator.run-percolator=true
+phi-report.dont-use-prot-proph-file=false
+phi-report.filter=--sequential --picked --psm 0.05 --pep 0.05 --prot 0.05
+phi-report.pep-level-summary=false
+phi-report.philosoher-msstats=false
+phi-report.print-decoys=false
+phi-report.prot-level-summary=false
+phi-report.remove-contaminants=false
+phi-report.run-report=true
+protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5
+protein-prophet.run-protein-prophet=true
+ptmprophet.cmdline=true
+ptmprophet.run-ptmprophet=false
+ptmshepherd.adv_params=false
+ptmshepherd.annotation-common=true
+ptmshepherd.annotation-custom=false
+ptmshepherd.annotation-glyco=false
+ptmshepherd.annotation-unimod=false
+ptmshepherd.annotation_file=
+ptmshepherd.annotation_tol=0.01
+ptmshepherd.cap_y_ions=
+ptmshepherd.decoy_type=1
+ptmshepherd.diag_ions=
+ptmshepherd.diagmine_diagMinFoldChange=3.0
+ptmshepherd.diagmine_diagMinSpecDiff=00.2
+ptmshepherd.diagmine_fragMinFoldChange=3.0
+ptmshepherd.diagmine_fragMinPropensity=00.1
+ptmshepherd.diagmine_fragMinSpecDiff=00.1
+ptmshepherd.diagmine_minIonsPerSpec=2
+ptmshepherd.diagmine_minPeps=25
+ptmshepherd.diagmine_pepMinFoldChange=3.0
+ptmshepherd.diagmine_pepMinSpecDiff=00.2
+ptmshepherd.glyco_adducts=
+ptmshepherd.glyco_fdr=5.00
+ptmshepherd.glyco_isotope_max=3
+ptmshepherd.glyco_isotope_min=-1
+ptmshepherd.glyco_ppm_tol=50
+ptmshepherd.glycodatabase=
+ptmshepherd.histo_smoothbins=2
+ptmshepherd.iontype_a=false
+ptmshepherd.iontype_b=true
+ptmshepherd.iontype_c=false
+ptmshepherd.iontype_x=false
+ptmshepherd.iontype_y=true
+ptmshepherd.iontype_z=false
+ptmshepherd.localization_allowed_res=
+ptmshepherd.localization_background=4
+ptmshepherd.max_adducts=0
+ptmshepherd.n_glyco=true
+ptmshepherd.normalization-psms=true
+ptmshepherd.normalization-scans=false
+ptmshepherd.output_extended=false
+ptmshepherd.peakpicking_mass_units=0
+ptmshepherd.peakpicking_minPsm=10
+ptmshepherd.peakpicking_promRatio=0.3
+ptmshepherd.peakpicking_width=0.002
+ptmshepherd.precursor_mass_units=0
+ptmshepherd.precursor_tol=0.01
+ptmshepherd.print_decoys=false
+ptmshepherd.prob_dhexOx=2,0.5,0.1
+ptmshepherd.prob_dhexY=2,0.5
+ptmshepherd.prob_neuacOx=2,0.05,0.2
+ptmshepherd.prob_neugcOx=2,0.05,0.2
+ptmshepherd.prob_phosphoOx=2,0.05,0.2
+ptmshepherd.prob_regY=5,0.5
+ptmshepherd.prob_sulfoOx=2,0.05,0.2
+ptmshepherd.remainder_masses=
+ptmshepherd.remove_glycan_delta_mass=true
+ptmshepherd.run-shepherd=false
+ptmshepherd.run_diagextract_mode=false
+ptmshepherd.run_diagmine_mode=false
+ptmshepherd.run_glyco_mode=false
+ptmshepherd.spectra_maxfragcharge=2
+ptmshepherd.spectra_ppmtol=20
+ptmshepherd.varmod_masses=
+quantitation.run-label-free-quant=false
+run-psm-validation=true
+run-validation-tab=true
+saintexpress.fragpipe.cmd-opts=
+saintexpress.max-replicates=3
+saintexpress.run-saint-express=true
+saintexpress.virtual-controls=100
+speclibgen.easypqp.extras.max_delta_ppm=15
+speclibgen.easypqp.extras.max_delta_unimod=0.02
+speclibgen.easypqp.extras.rt_lowess_fraction=0
+speclibgen.easypqp.fragment.a=false
+speclibgen.easypqp.fragment.b=true
+speclibgen.easypqp.fragment.c=false
+speclibgen.easypqp.fragment.x=false
+speclibgen.easypqp.fragment.y=true
+speclibgen.easypqp.fragment.z=false
+speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
+speclibgen.easypqp.neutral_loss=false
+speclibgen.easypqp.rt-cal=noiRT
+speclibgen.easypqp.select-file.text=
+speclibgen.easypqp.select-im-file.text=
+speclibgen.keep-intermediate-files=false
+speclibgen.run-speclibgen=false
+tab-run.delete_calibrated_mzml=false
+tab-run.delete_temp_files=false
+tab-run.sub_mzml_prob_threshold=0.5
+tab-run.write_sub_mzml=false
+tmtintegrator.add_Ref=-1
+tmtintegrator.aggregation_method=0
+tmtintegrator.allow_overlabel=true
+tmtintegrator.allow_unlabeled=false
+tmtintegrator.best_psm=true
+tmtintegrator.channel_num=TMT-11
+tmtintegrator.extraction_tool=IonQuant
+tmtintegrator.glyco_qval=-1
+tmtintegrator.groupby=-1
+tmtintegrator.log2transformed=true
+tmtintegrator.max_pep_prob_thres=0.9
+tmtintegrator.min_ntt=0
+tmtintegrator.min_pep_prob=0.9
+tmtintegrator.min_percent=0.05
+tmtintegrator.min_purity=0.5
+tmtintegrator.min_site_prob=-1
+tmtintegrator.mod_tag=none
+tmtintegrator.ms1_int=true
+tmtintegrator.outlier_removal=true
+tmtintegrator.print_RefInt=false
+tmtintegrator.prot_exclude=none
+tmtintegrator.prot_norm=1
+tmtintegrator.psm_norm=false
+tmtintegrator.quant_level=2
+tmtintegrator.ref_tag=Bridge
+tmtintegrator.run-tmtintegrator=true
+tmtintegrator.tolerance=20
+tmtintegrator.top3_pep=true
+tmtintegrator.unique_gene=0
+tmtintegrator.unique_pep=false
+tmtintegrator.use_glycan_composition=false
+workflow.description=<p style\="margin-top\: 0">Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.</p>
+workflow.input.data-type.im-ms=false
+workflow.input.data-type.regular-ms=true
+workflow.misc.save-sdrf=true
+workflow.saved-with-ver=22.0
diff --git a/tumor-enriched-splicing/input/PDC000180filesmanifest.fp-manifest b/tumor-enriched-splicing/input/PDC000180filesmanifest.fp-manifest
new file mode 100644
index 0000000..8bc0a4a
--- /dev/null
+++ b/tumor-enriched-splicing/input/PDC000180filesmanifest.fp-manifest
@@ -0,0 +1,276 @@
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F12-f10283.mzML	NCI_11plex_1_F12_f10283		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F8-f10279.mzML	NCI_11plex_1_F8_f10279		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F11-f10282.mzML	NCI_11plex_1_F11_f10282		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F6-f10277.mzML	NCI_11plex_1_F6_f10277		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F7-f10278.mzML	NCI_11plex_1_F7_f10278		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F5-f10276.mzML	NCI_11plex_1_F5_f10276		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F1-f10268.mzML	NCI_11plex_1_F1_f10268		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F2-f10270.mzML	NCI_11plex_1_F2_f10270		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F10-f10281.mzML	NCI_11plex_1_F10_f10281		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F9-f10280.mzML	NCI_11plex_1_F9_f10280		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F3-f10274.mzML	NCI_11plex_1_F3_f10274		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/01CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-1-F4-f10275.mzML	NCI_11plex_1_F4_f10275		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F5-f10314.mzML	NCI_11Plex_2_F5_f10314		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F10-f10319.mzML	NCI_11Plex_2_F10_f10319		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F2-f10311.mzML	NCI_11Plex_2_F2_f10311		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F1-f10309.mzML	NCI_11Plex_2_F1_f10309		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F3-f10312.mzML	NCI_11Plex_2_F3_f10312		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F9-f10318.mzML	NCI_11Plex_2_F9_f10318		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F12-f10321.mzML	NCI_11Plex_2_F12_f10321		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F7-f10316.mzML	NCI_11Plex_2_F7_f10316		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F6-f10315.mzML	NCI_11Plex_2_F6_f10315		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F11-f10320.mzML	NCI_11Plex_2_F11_f10320		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F4-f10313.mzML	NCI_11Plex_2_F4_f10313		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/02CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-2-F8-f10317.mzML	NCI_11Plex_2_F8_f10317		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F6-f10340.mzML	NCI_11Plex_3_F6_f10340		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F12-f10339.mzML	NCI_11Plex_3_F12_f10339		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F1-f10327.mzML	NCI_11Plex_3_F1_f10327		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F10-f10337.mzML	NCI_11Plex_3_F10_f10337		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F11-f10338.mzML	NCI_11Plex_3_F11_f10338		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F3-f10330.mzML	NCI_11Plex_3_F3_f10330		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F8-f10335.mzML	NCI_11Plex_3_F8_f10335		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F4-f10331.mzML	NCI_11Plex_3_F4_f10331		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F7-f10334.mzML	NCI_11Plex_3_F7_f10334		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F5-f10332.mzML	NCI_11Plex_3_F5_f10332		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F9-f10336.mzML	NCI_11Plex_3_F9_f10336		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/03CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-3-F2-f10329.mzML	NCI_11Plex_3_F2_f10329		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F8-f10354.mzML	NCI_11Plex_4_F8_f10354		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F12-f10358.mzML	NCI_11Plex_4_F12_f10358		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F10-f10356.mzML	NCI_11Plex_4_F10_f10356		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F6-f10352.mzML	NCI_11Plex_4_F6_f10352		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F4-f10350.mzML	NCI_11Plex_4_F4_f10350		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F3-f10349.mzML	NCI_11Plex_4_F3_f10349		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F5-f10351.mzML	NCI_11Plex_4_F5_f10351		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F7-f10353.mzML	NCI_11Plex_4_F7_f10353		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F11-f10357.mzML	NCI_11Plex_4_F11_f10357		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F2-f10348.mzML	NCI_11Plex_4_F2_f10348		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F1-f10346.mzML	NCI_11Plex_4_F1_f10346		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/04CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-4-F9-f10355.mzML	NCI_11Plex_4_F9_f10355		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F7-z11114.mzML	NCI_11Plex_5_F7_z11114		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F11-z11118.mzML	NCI_11Plex_5_F11_z11118		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F3-z11110.mzML	NCI_11Plex_5_F3_z11110		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F6-z11113.mzML	NCI_11Plex_5_F6_z11113		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F9-z11116.mzML	NCI_11Plex_5_F9_z11116		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F12-z11119.mzML	NCI_11Plex_5_F12_z11119		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F1-z11108.mzML	NCI_11Plex_5_F1_z11108		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F8-z11115.mzML	NCI_11Plex_5_F8_z11115		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F5-z11112.mzML	NCI_11Plex_5_F5_z11112		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F4-z11111.mzML	NCI_11Plex_5_F4_z11111		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F10-z11117.mzML	NCI_11Plex_5_F10_z11117		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/05CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-5-F2-z11109.mzML	NCI_11Plex_5_F2_z11109		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F7-f10419.mzML	NCI_11Plex_6_F7_f10419		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F6-f10418.mzML	NCI_11Plex_6_F6_f10418		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F3-f10416.mzML	NCI_11Plex_6_F3_f10416		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F8-f10420.mzML	NCI_11Plex_6_F8_f10420		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F5-f10417.mzML	NCI_11Plex_6_F5_f10417		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F10-f10423.mzML	NCI_11Plex_6_F10_f10423		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F12-f10430.mzML	NCI_11Plex_6_F12_f10430		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F2-f10415.mzML	NCI_11Plex_6_F2_f10415		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F11-f10424.mzML	NCI_11Plex_6_F11_f10424		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F9-f10421.mzML	NCI_11Plex_6_F9_f10421		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F4-f10416_20180501005557.mzML	NCI_11Plex_6_F4_f10416_20180501005557		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/06CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-6-F1-f10414.mzML	NCI_11Plex_6_F1_f10414		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F9-f10408.mzML	NCI_11Plex_7_F9_f10408		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F8-f10407.mzML	NCI_11Plex_7_F8_f10407		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F1-f10400.mzML	NCI_11Plex_7_F1_f10400		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F12-f10411.mzML	NCI_11Plex_7_F12_f10411		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F11-f10410.mzML	NCI_11Plex_7_F11_f10410		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F7-f10406.mzML	NCI_11Plex_7_F7_f10406		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F6-f10405.mzML	NCI_11Plex_7_F6_f10405		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F5-f10404.mzML	NCI_11Plex_7_F5_f10404		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F2-f10401.mzML	NCI_11Plex_7_F2_f10401		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F10-f10409.mzML	NCI_11Plex_7_F10_f10409		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F3-f10402.mzML	NCI_11Plex_7_F3_f10402		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/07CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-7-F4-f10403.mzML	NCI_11Plex_7_F4_f10403		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F5-f10460.mzML	NCI_11Plex_8_F5_f10460		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F7-f10462.mzML	NCI_11Plex_8_F7_f10462		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F1-f10456.mzML	NCI_11Plex_8_F1_f10456		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F4-f10459.mzML	NCI_11Plex_8_F4_f10459		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F10-f10465.mzML	NCI_11Plex_8_F10_f10465		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F8-f10463.mzML	NCI_11Plex_8_F8_f10463		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F6-f10461.mzML	NCI_11Plex_8_F6_f10461		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F9-f10464.mzML	NCI_11Plex_8_F9_f10464		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F3-f10458.mzML	NCI_11Plex_8_F3_f10458		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F11-f10466.mzML	NCI_11Plex_8_F11_f10466		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F12-f10467.mzML	NCI_11Plex_8_F12_f10467		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/08CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-8-F2-f10457.mzML	NCI_11Plex_8_F2_f10457		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F3-z11239.mzML	NCI_11Plex_9_F3_z11239		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F1-z11237.mzML	NCI_11Plex_9_F1_z11237		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F8-z11244.mzML	NCI_11Plex_9_F8_z11244		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F2-z11238.mzML	NCI_11Plex_9_F2_z11238		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F12-z11248.mzML	NCI_11Plex_9_F12_z11248		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F6-z11242.mzML	NCI_11Plex_9_F6_z11242		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F5-z11241.mzML	NCI_11Plex_9_F5_z11241		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F4-z11240.mzML	NCI_11Plex_9_F4_z11240		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F11-z11247.mzML	NCI_11Plex_9_F11_z11247		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F10-z11246.mzML	NCI_11Plex_9_F10_z11246		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F9-z11245.mzML	NCI_11Plex_9_F9_z11245		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/09CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-9-F7-z11243.mzML	NCI_11Plex_9_F7_z11243		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F9-f10507.mzML	NCI_11Plex_10_F9_f10507		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F3-f10501.mzML	NCI_11Plex_10_F3_f10501		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F2-f10500.mzML	NCI_11Plex_10_F2_f10500		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F11-f10509.mzML	NCI_11Plex_10_F11_f10509		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F5-f10503.mzML	NCI_11Plex_10_F5_f10503		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F12-f10510.mzML	NCI_11Plex_10_F12_f10510		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F1-f10499.mzML	NCI_11Plex_10_F1_f10499		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F8-f10506.mzML	NCI_11Plex_10_F8_f10506		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F7-f10505.mzML	NCI_11Plex_10_F7_f10505		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F6-f10504.mzML	NCI_11Plex_10_F6_f10504		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F10-f10508.mzML	NCI_11Plex_10_F10_f10508		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/10CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-10-F4-f10502.mzML	NCI_11Plex_10_F4_f10502		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F7A-z11339.mzML	NCI_11Plex_11_F7A_z11339		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F1A-z11333.mzML	NCI_11Plex_11_F1A_z11333		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F11A-z11343.mzML	NCI_11Plex_11_F11A_z11343		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F2A-z11334.mzML	NCI_11Plex_11_F2A_z11334		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F10A-z11344.mzML	NCI_11Plex_11_F10A_z11344		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F4A-z11336.mzML	NCI_11Plex_11_F4A_z11336		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F6A-z11338.mzML	NCI_11Plex_11_F6A_z11338		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F3A-z11335.mzML	NCI_11Plex_11_F3A_z11335		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F8A-z11340.mzML	NCI_11Plex_11_F8A_z11340		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F12A-z11342.mzML	NCI_11Plex_11_F12A_z11342		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F5A-z11337.mzML	NCI_11Plex_11_F5A_z11337		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/11CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-11-F9A-z11341.mzML	NCI_11Plex_11_F9A_z11341		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F6-f10507.mzML	NCI_11Plex_12_F6_f10507		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F7-f10508.mzML	NCI_11Plex_12_F7_f10508		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F10-f10511.mzML	NCI_11Plex_12_F10_f10511		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F1-f10502.mzML	NCI_11Plex_12_F1_f10502		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F2-f10503.mzML	NCI_11Plex_12_F2_f10503		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F12-f10513.mzML	NCI_11Plex_12_F12_f10513		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F9-f10510.mzML	NCI_11Plex_12_F9_f10510		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F8-f10509.mzML	NCI_11Plex_12_F8_f10509		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F3-f10504.mzML	NCI_11Plex_12_F3_f10504		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F5-f10506.mzML	NCI_11Plex_12_F5_f10506		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F11-f10512.mzML	NCI_11Plex_12_F11_f10512		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/12CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-12-F4-f10505.mzML	NCI_11Plex_12_F4_f10505		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F4A-z11350.mzML	NCI_11Plex_13_F4A_z11350		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F6A-z11352.mzML	NCI_11Plex_13_F6A_z11352		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F9A-z11355.mzML	NCI_11Plex_13_F9A_z11355		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F2A-z11348.mzML	NCI_11Plex_13_F2A_z11348		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F8A-z11354.mzML	NCI_11Plex_13_F8A_z11354		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F1A-z11347.mzML	NCI_11Plex_13_F1A_z11347		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F3A-z11349.mzML	NCI_11Plex_13_F3A_z11349		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F5A-z11351.mzML	NCI_11Plex_13_F5A_z11351		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F11A-z11357.mzML	NCI_11Plex_13_F11A_z11357		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F12A-z11358.mzML	NCI_11Plex_13_F12A_z11358		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F10A-z11356.mzML	NCI_11Plex_13_F10A_z11356		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/13CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-13-F7A-z11353.mzML	NCI_11Plex_13_F7A_z11353		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F5-f10534.mzML	NCI_11Plex_14_F5_f10534		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F10-f10539.mzML	NCI_11Plex_14_F10_f10539		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F3-f10532.mzML	NCI_11Plex_14_F3_f10532		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F1-f10530.mzML	NCI_11Plex_14_F1_f10530		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F4-f10533.mzML	NCI_11Plex_14_F4_f10533		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F2-f10531.mzML	NCI_11Plex_14_F2_f10531		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F9-f10538.mzML	NCI_11Plex_14_F9_f10538		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F12-f10541.mzML	NCI_11Plex_14_F12_f10541		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F11-f10540.mzML	NCI_11Plex_14_F11_f10540		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F6-f10535.mzML	NCI_11Plex_14_F6_f10535		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F8-f10537.mzML	NCI_11Plex_14_F8_f10537		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/14CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-14-F7-f10536.mzML	NCI_11Plex_14_F7_f10536		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F4-m17230.mzML	NCI_11plex_15_F4_m17230		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F3-m17229.mzML	NCI_11plex_15_F3_m17229		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F11-m17237.mzML	NCI_11plex_15_F11_m17237		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F6-m17232.mzML	NCI_11plex_15_F6_m17232		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F2-m17228.mzML	NCI_11plex_15_F2_m17228		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F12-m17238.mzML	NCI_11plex_15_F12_m17238		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F9-m17235.mzML	NCI_11plex_15_F9_m17235		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F5-m17231.mzML	NCI_11plex_15_F5_m17231		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F1-m17227.mzML	NCI_11plex_15_F1_m17227		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F8-m17234.mzML	NCI_11plex_15_F8_m17234		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F7-m17233.mzML	NCI_11plex_15_F7_m17233		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/15CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-15-F10-m17236.mzML	NCI_11plex_15_F10_m17236		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F8-m17247.mzML	NCI_11plex_16_F8_m17247		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-16-F2-f10573.mzML	NCI_11Plex_16_F2_f10573		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F12-m17251.mzML	NCI_11plex_16_F12_m17251		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F9-m17248.mzML	NCI_11plex_16_F9_m17248		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F6-m17245.mzML	NCI_11plex_16_F6_m17245		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F7-m17246.mzML	NCI_11plex_16_F7_m17246		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-16-F1-f10572.mzML	NCI_11Plex_16_F1_f10572		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F4-m17243.mzML	NCI_11plex_16_F4_m17243		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F10-m17249.mzML	NCI_11plex_16_F10_m17249		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F11-m17250.mzML	NCI_11plex_16_F11_m17250		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F5-m17244.mzML	NCI_11plex_16_F5_m17244		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/16CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-16-F3-m17242.mzML	NCI_11plex_16_F3_m17242		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F8-m17260.mzML	NCI_11plex_17_F8_m17260		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F10-m17262.mzML	NCI_11plex_17_F10_m17262		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F2-m17254.mzML	NCI_11plex_17_F2_m17254		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F7-m17259.mzML	NCI_11plex_17_F7_m17259		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F5A-m17257.mzML	NCI_11plex_17_F5A_m17257		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F11-m17263.mzML	NCI_11plex_17_F11_m17263		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F1-m17253.mzML	NCI_11plex_17_F1_m17253		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F6-m17258.mzML	NCI_11plex_17_F6_m17258		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F3-m17255.mzML	NCI_11plex_17_F3_m17255		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F12-m17264.mzML	NCI_11plex_17_F12_m17264		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F4-m17256.mzML	NCI_11plex_17_F4_m17256		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/17CBTTC_PBT_Proteome_HMS_20180626/NCI-11plex-17-F9-m17261.mzML	NCI_11plex_17_F9_m17261		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F5-f10520.mzML	NCI_11Plex_18_F5_f10520		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F8-f10523.mzML	NCI_11Plex_18_F8_f10523		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F11-f10526.mzML	NCI_11Plex_18_F11_f10526		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F1-f10516.mzML	NCI_11Plex_18_F1_f10516		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F2-f10517.mzML	NCI_11Plex_18_F2_f10517		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F6-f10521.mzML	NCI_11Plex_18_F6_f10521		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F10-f10525.mzML	NCI_11Plex_18_F10_f10525		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F3-f10518.mzML	NCI_11Plex_18_F3_f10518		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F9-f10524.mzML	NCI_11Plex_18_F9_f10524		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F12-f10527.mzML	NCI_11Plex_18_F12_f10527		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F7-f10522.mzML	NCI_11Plex_18_F7_f10522		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/18CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-18-F4-f10519.mzML	NCI_11Plex_18_F4_f10519		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F7-f10550.mzML	NCI_11Plex_19_F7_f10550		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F10-f10553.mzML	NCI_11Plex_19_F10_f10553		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F11-f10554.mzML	NCI_11Plex_19_F11_f10554		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F3-f10546.mzML	NCI_11Plex_19_F3_f10546		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F5-f10548.mzML	NCI_11Plex_19_F5_f10548		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F9-f10552.mzML	NCI_11Plex_19_F9_f10552		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F4-f10547.mzML	NCI_11Plex_19_F4_f10547		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F12-f10555.mzML	NCI_11Plex_19_F12_f10555		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F8-f10551.mzML	NCI_11Plex_19_F8_f10551		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F1-f10544.mzML	NCI_11Plex_19_F1_f10544		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F2-f10545.mzML	NCI_11Plex_19_F2_f10545		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/19CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-19-F6-f10549.mzML	NCI_11Plex_19_F6_f10549		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F6-f10563.mzML	NCI_11Plex_20_F6_f10563		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F8-f10565.mzML	NCI_11Plex_20_F8_f10565		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F12-f10569.mzML	NCI_11Plex_20_F12_f10569		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F2-f10559.mzML	NCI_11Plex_20_F2_f10559		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F3-f10560.mzML	NCI_11Plex_20_F3_f10560		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F10-f10567.mzML	NCI_11Plex_20_F10_f10567		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F5-f10562.mzML	NCI_11Plex_20_F5_f10562		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F9-f10566.mzML	NCI_11Plex_20_F9_f10566		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F11-f10568.mzML	NCI_11Plex_20_F11_f10568		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F7-f10564.mzML	NCI_11Plex_20_F7_f10564		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F4-f10561.mzML	NCI_11Plex_20_F4_f10561		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/20CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-20-F1-f10558.mzML	NCI_11Plex_20_F1_f10558		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F10-m17285.mzML	NCI_11Plex_21_F10_m17285		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F9-m17284.mzML	NCI_11Plex_21_F9_m17284		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F1-m17276.mzML	NCI_11Plex_21_F1_m17276		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F6-m17281.mzML	NCI_11Plex_21_F6_m17281		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F5-m17280.mzML	NCI_11Plex_21_F5_m17280		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F3-m17278.mzML	NCI_11Plex_21_F3_m17278		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F7-m17282.mzML	NCI_11Plex_21_F7_m17282		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F12-m17287.mzML	NCI_11Plex_21_F12_m17287		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F8-m17283.mzML	NCI_11Plex_21_F8_m17283		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F11-m17286.mzML	NCI_11Plex_21_F11_m17286		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F4-m17279.mzML	NCI_11Plex_21_F4_m17279		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/21CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-21-F2-m17277.mzML	NCI_11Plex_21_F2_m17277		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F1-m17289.mzML	NCI_11Plex_22_F1_m17289		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F4-m17292.mzML	NCI_11Plex_22_F4_m17292		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F3-m17291.mzML	NCI_11Plex_22_F3_m17291		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F11-m17299.mzML	NCI_11Plex_22_F11_m17299		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F9-m17297.mzML	NCI_11Plex_22_F9_m17297		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F10-m17298.mzML	NCI_11Plex_22_F10_m17298		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F5-m17293.mzML	NCI_11Plex_22_F5_m17293		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F2-m17290.mzML	NCI_11Plex_22_F2_m17290		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F12-m17300.mzML	NCI_11Plex_22_F12_m17300		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F8-m17296.mzML	NCI_11Plex_22_F8_m17296		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F6-m17294.mzML	NCI_11Plex_22_F6_m17294		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/22CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-22-F7-m17295.mzML	NCI_11Plex_22_F7_m17295		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F8-m17322.mzML	NCI_11Plex_23_F8_m17322		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F9-m17323.mzML	NCI_11Plex_23_F9_m17323		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F7-m17321.mzML	NCI_11Plex_23_F7_m17321		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F3-m17317.mzML	NCI_11Plex_23_F3_m17317		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F2-m17316.mzML	NCI_11Plex_23_F2_m17316		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F1-m17315.mzML	NCI_11Plex_23_F1_m17315		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F4-m17318.mzML	NCI_11Plex_23_F4_m17318		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F11-m17325.mzML	NCI_11Plex_23_F11_m17325		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F10-m17324.mzML	NCI_11Plex_23_F10_m17324		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F5-m17319.mzML	NCI_11Plex_23_F5_m17319		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F12-m17326.mzML	NCI_11Plex_23_F12_m17326		DDA
+/home/rstudio/fragpipe/tumor-enriched-splicing/tmp/23CBTTC_PBT_Proteome_HMS_20180626/NCI-11Plex-23-F6-m17320.mzML	NCI_11Plex_23_F6_m17320		DDA
diff --git a/tumor-enriched-splicing/run_fragpipe.sh b/tumor-enriched-splicing/run_fragpipe.sh
new file mode 100644
index 0000000..716dc5c
--- /dev/null
+++ b/tumor-enriched-splicing/run_fragpipe.sh
@@ -0,0 +1,118 @@
+#!/bin/bash
+
+set -e
+set -o pipefail
+
+# Set tools and input directories
+input_dir=input
+tools_dir=/fragpipe_bin/fragPipe-22.0/fragpipe/tools/
+
+# Error out if no custom.fasta is provided
+if [ ! -e "$input_dir/custom.fasta" ]; then
+  echo "Error: must supply a custom.fasta file in the input directory ($input_dir)"
+  exit 1
+fi
+
+echo "Adding decoys and contaminants to FASTA files.."
+cd $input_dir
+
+# Initialize the Philosopher workspace
+$tools_dir/Philosopher/philosopher-v5.1.1 workspace --init
+
+Uniprot_canonical=/home/rstudio/fragpipe/refs/UP000005640_9606.fasta.gz
+
+# Add decoys and contaminants to the custom FASTA file
+gunzip -c $Uniprot_canonical | $tools_dir/Philosopher/philosopher-v5.1.1 database --custom custom.fasta --add /dev/stdin --contam
+#$tools_dir/Philosopher/philosopher-v5.1.1 database --custom custom.fasta --contam
+
+#mv *decoys-contam-custom.fasta.fas decoys-contam-custom-canonical.fasta
+# Remove canonica peptides annotated to genes with TESEs
+grep "^>" custom.fasta | awk -F'[:_]' '{print "GN=" $2 " "}' | sort -u > gene_symbols.txt
+
+awk 'BEGIN{while((getline k < "gene_symbols.txt") > 0){a[k]=1}}
+     /^>/{
+         keep=1
+         for (g in a) {
+             if (index($0,g)) {keep=0; break}
+         }
+     }
+     keep' *decoys-contam-custom.fasta.fas > decoys-contam-custom-canonical.fasta
+
+# Clean intermediate files
+$tools_dir/Philosopher/philosopher-v5.1.1 workspace --clean 
+
+# Return to the previous directory
+cd -
+
+# define directory to mount cavatica project; create if it does not exist
+data_dir=/home/rstudio/fragpipe/tumor-enriched-splicing/cavatica-data
+
+if [ ! -d $data_dir ]; then
+  mkdir -p $data_dir
+  echo "Creating cavatica-data directory to mount cavatica project..."
+fi
+
+# set cavatica directory
+cavatica_dir=/home/rstudio/fragpipe/tumor-enriched-splicing/cavatica-data/projects/harenzaj/proteomics
+
+if [ ! -d $cavatica_dir ]; then
+  echo "Error: path to cavatica project directory does not exist. Attempting to mount project with sbfs mount..."
+  
+  sbfs mount --profile default --project harenzaj/proteomics cavatica-data
+
+fi
+
+# check if tmp directory exists, and create it if not
+tmp_dir=(/home/rstudio/fragpipe/tumor-enriched-splicing/tmp)
+
+if [ ! -d $tmp_dir ]; then
+  mkdir -p $tmp_dir
+  echo "Temporary directory does not exist, creating..."
+fi
+
+# clear contents of tmp directory, if not already empty
+rm -rf $tmp_dir/*
+
+# copy mzML files to temporary directory, maintaining directory structure
+echo "copying mzML files to temporary directory..."
+
+if ! [[ " $* " == *" --run_subset "* ]]; then
+
+cp -R $cavatica_dir/*CBTTC_PBT_Proteome* $tmp_dir
+
+else
+
+cp -R $cavatica_dir/01CBTTC_PBT_Proteome* $tmp_dir
+
+fi
+
+# unzip mzML files, force overwrite if files exist
+echo "unzipping mzML files..."
+gunzip -f $tmp_dir/*CBTTC_PBT_Proteome*/*mzML.gz
+
+# set workflow, manifest, results and tools directories
+echo "Starting Fragpipe run..."
+
+wf=/home/rstudio/fragpipe/tumor-enriched-splicing/input/PDC000180customworkflow.workflow
+manifest=/home/rstudio/fragpipe/tumor-enriched-splicing/input/PDC000180filesmanifest.fp-manifest
+
+if [[ " $* " == *" --run_subset "* ]]; then
+
+grep "01CBTTC_" $manifest > /home/rstudio/fragpipe/tumor-enriched-splicing/input/PDC000180filesmanifest.fp-manifest_sub
+manifest=/home/rstudio/fragpipe/tumor-enriched-splicing/input/PDC000180filesmanifest.fp-manifest_sub
+
+fi
+
+res_dir=/home/rstudio/fragpipe/tumor-enriched-splicing/results-cptac-filtered-canon
+
+if [ ! -d $res_dir ]; then
+  mkdir -p $res_dir
+  echo "Creating results directory..."
+fi
+
+tools_dir=/fragpipe_bin/fragPipe-22.0/fragpipe/tools/
+
+/fragpipe_bin/fragPipe-22.0/fragpipe/bin/fragpipe --headless --workflow $wf --manifest $manifest --workdir $res_dir --config-tools-folder $tools_dir
+
+# clear tmp directory
+rm -rf $tmp_dir/*