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DART-ID (2018) Chen, Albert & Franks, Alexander & Slavov, Nikolai

Unless otherwise specified, data used for this paper is from the updated evidence.txt file (ev_updated.txt) in ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/. The MaxQuant output files are specified in the config file, SQC.yaml, and are available in ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/. Raw files are also available in .raw and mzXML form as part of the MassIVE submission.

Figures

Figure 1:

Data

All data used for these diagrams are simulated. Values such as null distribution height and experiment shifts are exaggerated for visual clarity.

Scripts: (GitHub/Rscripts)

  • 1A: fig_scripts/fig_1a_canonical_demo.R
  • 1B: fig_scripts/fig_1b_alignment_demo_v5.R
  • 1C: fig_scripts/fig_1c_confidence_update_v2.R

Figure 2:

Data:

  • MaxQuant search results: SQC_67_95_Varied -- ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/
  • DART-ID Alignment, and results from other RT inference methods: SQC_varied_20180711_4/ -- ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/
  • iRT search and converted data: dat/irt.txt, dat/irt.xls (ftp://massive.ucsd.edu/MSV000083149/other/Rdata/)
  • R objects: error_df.RData (ftp://massive.ucsd.edu/MSV000083149/other/Rdata/)

Experiments used:

180320S_QC_SQC67A1, 180324S_QC_SQC67C10, 180324S_QC_SQC68A1, 180324S_QC_SQC68B1, 180324S_QC_SQC69A, 180324S_QC_SQC69B, 180324S_QC_SQC70A, 180324S_QC_SQC70B, 180324S_QC_SQC71A, 180324S_QC_SQC71B, 180402S_QC_SQC72A1, 180402S_QC_SQC72B1, 180402S_QC_SQC73A1, 180402S_QC_SQC73A2, 180406S_QC_SQC74A, 180406S_QC_SQC74B, 180408S_QC_SQC75A, 180408S_QC_SQC75B, 180409S_QC_SQC76A, 180409S_QC_SQC76B, 180411S_QC_SQC77A, 180411S_QC_SQC77B, 180413S_X_FP18I, 180413S_X_FP18J, 180413S_X_FP18K, 180416S_QC_SQC78A1, 180420S_QC_SQC79A, 180420S_QC_SQC79B, 180420S_QC_SQC80A, 180420S_QC_SQC80B, 180424S_QC_SQC81A, 180424S_QC_SQC81B, 180424S_X_IFN6H, 180424S_X_IFN6I, 180424S_X_IFN6J, 180424S_X_IFN6K, 180502S_QC_SQC82A, 180502S_QC_SQC82B, 180503S_QC_SQC83A, 180503S_QC_SQC83B, 180503S_QC_SQC84A, 180503S_QC_SQC84B, 180503S_QC_SQC85A1, 180503S_QC_SQC85B1, 180503S_QC_SQC86A, 180503S_QC_SQC86B

Scripts: (GitHub/Rscripts)

  • alignment_comparisons.R -- load and process alignment comparison data
  • 2A-B: fig_scripts/fig_2_alignment_comparison.R

Figure 3:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Figure 3B. Contains only the first 50 experiments (sorted chronologically, from run date) of the entire dataset, for visual clarity and space constraints. Figures 3A, C, D, and E use data from the entire set.

The proportions and magnitudes of numbers from Figure 3B. do shift when including more experiments, but not significantly.

Scripts: (GitHub/Rscripts)

  • add_percolator.R -- add results from percolator output
  • protein_quant.R -- Split data into PSM sets, get protein quantification from PSM quantification
  • 3A: fig_scripts/fig_3a_pep_scatter_v3.R
  • 3B: fig_scripts/fig_3b_protein_map_v3_4.R
  • 3C: fig_scripts/fig_3c_fdr_fold_change
  • 3D: fig_scripts/fig_3d_protein_ids_v2.R
  • 3E: fig_scripts/fig_3e_pep_dists.R

Figure 4:

Data:

  • MaxQuant search results: FP18 -- ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/FP18/
  • DART-ID alignment results: All sets: ftp://massive.ucsd.edu/MSV000083149/other/Alignments/FP_validation_allsets_20180706_1/, Set 1: ftp://massive.ucsd.edu/MSV000083149/other/Alignments/FP_validation_set1_20180706_2/, Set 2: ftp://massive.ucsd.edu/MSV000083149/other/Alignments/FP_validation_set2_20180706_1/

Scripts: (GitHub/Rscripts)

  • 4B-C: fig_scripts/fig_4_validate_new_peptides_v2.R

Figure 5:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Scripts: (GitHub/Rscripts)

  • add_percolator.R -- add results from percolator output
  • 5B-C: fig_scripts/fig_5_cv_valiation.R

Figure 6:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Manually removed experiments that were missing a significant amount of TMT quantitation, in order to lessen the amount of missing data in the final expression matrix.

Experiments used for the PCA plot:

180320S_QC_SQC67C8, 180324S_QC_SQC67C10, 180324S_QC_SQC67C11, 180324S_QC_SQC67C12, 180324S_QC_SQC67C13, 180324S_QC_SQC67C14, 180324S_QC_SQC67C15, 180324S_QC_SQC67C17, 180324S_QC_SQC67C18, 180324S_QC_SQC67C19, 180324S_QC_SQC67C9, 180324S_QC_SQC68B1, 180324S_QC_SQC68C1, 180324S_QC_SQC68C2, 180324S_QC_SQC68C3, 180324S_QC_SQC68D2, 180324S_QC_SQC68D3, 180324S_QC_SQC68D4, 180324S_QC_SQC68D4_20180330185431, 180324S_QC_SQC68E2, 180324S_QC_SQC68E3, 180324S_QC_SQC68E4, 180324S_QC_SQC68E5, 180324S_QC_SQC68E6, 180324S_QC_SQC68F1, 180324S_QC_SQC68F2, 180324S_QC_SQC68F3, 180324S_QC_SQC69A, 180324S_QC_SQC69B, 180324S_QC_SQC69C, 180324S_QC_SQC69D, 180324S_QC_SQC69E, 180324S_QC_SQC69F, 180324S_QC_SQC70D_20180330082946, 180324S_QC_SQC70E, 180324S_QC_SQC71D, 180324S_QC_SQC71E2, 180402S_QC_SQC72A1, 180402S_QC_SQC72B1, 180402S_QC_SQC72B10, 180402S_QC_SQC72B11, 180402S_QC_SQC72B12, 180402S_QC_SQC72B2, 180402S_QC_SQC72B3, 180402S_QC_SQC72B7, 180402S_QC_SQC72C1, 180402S_QC_SQC72C2, 180402S_QC_SQC72C3, 180402S_QC_SQC72C4, 180402S_QC_SQC72C5, 180402S_QC_SQC72C6, 180402S_QC_SQC72C7, 180402S_QC_SQC72C8, 180402S_QC_SQC72D1, 180402S_QC_SQC72D2, 180402S_QC_SQC72D3, 180402S_QC_SQC72D4, 180402S_QC_SQC73C1, 180402S_QC_SQC73D1, 180406S_QC_SQC74A, 180406S_QC_SQC74B, 180406S_QC_SQC74B2, 180406S_QC_SQC74C, 180406S_QC_SQC74E, 180406S_QC_SQC74F, 180406S_QC_SQC74G, 180406S_QC_SQC74H, 180406S_QC_SQC74J, 180409S_QC_SQC76D, 180409S_QC_SQC76E, 180420S_QC_SQC79A, 180420S_QC_SQC79B, 180420S_QC_SQC79C, 180420S_QC_SQC79D, 180420S_QC_SQC79F, 180420S_QC_SQC80B, 180420S_QC_SQC80C, 180420S_QC_SQC80D, 180420S_QC_SQC80E, 180420S_QC_SQC80F, 180420S_QC_SQC80G, 180424S_QC_SQC81A, 180424S_QC_SQC81C, 180502S_QC_SQC82B, 180502S_QC_SQC82C, 180502S_QC_SQC82D, 180502S_QC_SQC82E, 180502S_QC_SQC82F, 180502S_QC_SQC82G, 180502S_QC_SQC82H, 180502S_QC_SQC82I, 180503S_QC_SQC83A, 180503S_QC_SQC83B, 180503S_QC_SQC84A, 180503S_QC_SQC84A2, 180503S_QC_SQC84B, 180503S_QC_SQC85A1, 180503S_QC_SQC85A2, 180503S_QC_SQC85A3, 180503S_QC_SQC85B1, 180503S_QC_SQC85B2, 180503S_QC_SQC85B3, 180503S_QC_SQC86A, 180503S_QC_SQC86B, 180503S_QC_SQC86C, 180508S_QC_SQC87A1, 180508S_QC_SQC87A10, 180508S_QC_SQC87A2, 180508S_QC_SQC87A3, 180508S_QC_SQC87A4, 180508S_QC_SQC87A5, 180508S_QC_SQC87A6, 180508S_QC_SQC87A7, 180508S_QC_SQC87A8, 180508S_QC_SQC87A9, 180508S_QC_SQC87C1, 180508S_QC_SQC87C10, 180508S_QC_SQC87C2, 180508S_QC_SQC87C3, 180508S_QC_SQC87C4, 180508S_QC_SQC87C5, 180508S_QC_SQC87C6, 180508S_QC_SQC87C7, 180508S_QC_SQC87C8, 180508S_QC_SQC87C9

The code to filter the data is found in the figure generation script(s) below.

Scripts: (GitHub/Rscripts)

  • validation_cormats.R -- helper scripts for filtering/wrangling data
  • 6A-B: fig_scripts/fig_6_cor_pca.R

Supporting Figures:

Supporting Figure 1:

Data:

All data was simulated

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_mixture_model.R

Supporting Figure 2:

Data:

  • One-piece fit: ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_linear_20180711_2
  • Two-piece fit: ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_compare_linear.R

Supporting Figure 3:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_exp_rt_variance.R

Supporting Figure 4:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_distribution_choice.R

Supporting Figure 5:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_othermethods.R

Supporting Figure 6:

Data:

  • ftp://massive.ucsd.edu/MSV000083149/updates/2019-01-21_blahoink_9a4c796d/other/dat_SQC_FDR_1/evidence.txt
  • ftp://massive.ucsd.edu/MSV000083149/updates/2019-01-21_blahoink_9a4c796d/other/SQC_include_decoy_20190109/ev_updated.txt

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_error_rates.R

Supporting Figure 7:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_rel_ratios.R

Supporting Figure 8:

Data:

  • ftp://massive.ucsd.edu/MSV000083149/updates/2019-01-21_blahoink_9a4c796d/other/iPRG2015_20181228/
  • ftp://massive.ucsd.edu/MSV000083149/updates/2019-01-21_blahoink_9a4c796d/other/PXD011654_20190120/

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_bulksets.R

Supporting Figure 9:

Data:

All data was simulated

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_bootstrap.R

Supporting Figure 10:

Data:

ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_20180815_2/ev_updated.txt

Scripts: (GitHub/Rscripts)

  • fig_scripts/sfig_peptides_per_prot.R