Example Spectronaut evidence file from the output of a label free experiment
Source:R/dataDoc.R
spectronaut_input.RdExperiment was performed by the Olsen lab and published on Nat. Commun. (citation below).
Details
Bekker-Jensen, D.B., Bernhardt, O.M., Hogrebe, A. et al. Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nat Commun 11, 787 (2020). https://doi.org/10.1038/s41467-020-14609-1
The experiment was processed using Spectronaut by the computational proteomics team at Pfizer (Liang Xue and Pierre Jean).
The experiment did not contain a global profiling run, but we show an example of extracting the unmodified peptides and using them in place of the profiling run.
Examples
head(spectronaut_input)
#> R.Condition R.FileName R.Replicate PG.Genes
#> 1 Honly 20180815_QE3_nLC3_AH_DIA_Honly_ind_01 1 DNM1L
#> 2 Honly 20180815_QE3_nLC3_AH_DIA_Honly_ind_01 1 BIN1
#> 3 Honly 20180815_QE3_nLC3_AH_DIA_Honly_ind_01 1 BIN1
#> 4 Honly 20180815_QE3_nLC3_AH_DIA_Honly_ind_01 1 KMT2D
#> 5 Honly 20180815_QE3_nLC3_AH_DIA_Honly_ind_01 1 PPP1R12A
#> 6 Honly 20180815_QE3_nLC3_AH_DIA_Honly_ind_01 1 SEC16A
#> PG.ProteinDescriptions PG.ProteinGroups PG.ProteinNames
#> 1 Dynamin-1-like protein O00429 DNM1L_HUMAN
#> 2 Myc box-dependent-interacting protein 1 O00499 BIN1_HUMAN
#> 3 Myc box-dependent-interacting protein 1 O00499 BIN1_HUMAN
#> 4 Histone-lysine N-methyltransferase 2D O14686 KMT2D_HUMAN
#> 5 Protein phosphatase 1 regulatory subunit 12A O14974 MYPT1_HUMAN
#> 6 Protein transport protein Sec16A O15027 SC16A_HUMAN
#> PEP.PeptidePosition EG.IsDecoy
#> 1 607 FALSE
#> 2 293 FALSE
#> 3 293 FALSE
#> 4 4736 FALSE
#> 5 443 FALSE
#> 6 879 FALSE
#> EG.PrecursorId
#> 1 _SKPIPIM[Oxidation (M)]PAS[Phospho (STY)]PQK_.2
#> 2 _GNKSPS[Phospho (STY)]PPDGSPAATPEIR_.3
#> 3 _GNKS[Phospho (STY)]PSPPDGSPAATPEIR_.3
#> 4 _ALS[Phospho (STY)]PVIPLIPR_.2
#> 5 _TGS[Phospho (STY)]YGALAEITASK_.2
#> 6 _AQQELVPPQQQ[Deamidation (NQ)]AS[Phospho (STY)]PPQLPK_.3
#> EG.PTMAssayCandidateScore EG.PTMAssayProbability EG.PTMLocalizationConfidence
#> 1 29.064455 0.9999999 0.9999999
#> 2 6.009665 0.4966855 0.4966855
#> 3 6.009665 0.4966855 0.4966855
#> 4 NaN NaN 1.0000000
#> 5 24.307762 0.5848936 0.5848936
#> 6 15.286304 0.3310838 0.6655419
#> EG.PTMLocalizationProbabilities
#> 1 _S[Phospho (STY): 0%]KPIPIM[Oxidation (M): 100%]PAS[Phospho (STY): 100%]PQK_
#> 2 _GNKS[Phospho (STY): 49.7%]PS[Phospho (STY): 49.7%]PPDGS[Phospho (STY): 0.3%]PAAT[Phospho (STY): 0.3%]PEIR_
#> 3 _GNKS[Phospho (STY): 49.7%]PS[Phospho (STY): 49.7%]PPDGS[Phospho (STY): 0.3%]PAAT[Phospho (STY): 0.3%]PEIR_
#> 4 _ALS[Phospho (STY): 100%]PVIPLIPR_
#> 5 _T[Phospho (STY): 41.5%]GS[Phospho (STY): 58.5%]Y[Phospho (STY): 0%]GALAEIT[Phospho (STY): 0%]AS[Phospho (STY): 0%]K_
#> 6 _AQ[Deamidation (NQ): 0%]Q[Deamidation (NQ): 0%]ELVPPQ[Deamidation (NQ): 33.1%]Q[Deamidation (NQ): 33.1%]Q[Deamidation (NQ): 33.1%]AS[Phospho (STY): 100%]PPQ[Deamidation (NQ): 0.7%]LPK_
#> EG.NormalizationFactor EG.TotalQuantity..Settings. FG.Charge F.Charge
#> 1 1558039.8 24796966912 2 2
#> 2 1766846.4 9006234624 3 3
#> 3 1766846.4 9006234624 3 3
#> 4 887979.7 26086424576 2 2
#> 5 1128734.0 98855960576 2 2
#> 6 1189332.0 356193000000 3 3
#> EG.ModifiedSequence F.FrgIon F.FrgLossType
#> 1 _SKPIPIM[Oxidation (M)]PAS[Phospho (STY)]PQK_ NA noloss
#> 2 _GNKSPS[Phospho (STY)]PPDGSPAATPEIR_ NA noloss
#> 3 _GNKS[Phospho (STY)]PSPPDGSPAATPEIR_ NA noloss
#> 4 _ALS[Phospho (STY)]PVIPLIPR_ NA noloss
#> 5 _TGS[Phospho (STY)]YGALAEITASK_ NA noloss
#> 6 _AQQELVPPQQQ[Deamidation (NQ)]AS[Phospho (STY)]PPQLPK_ NA noloss
#> F.ExcludedFromQuantification F.PeakArea
#> 1 FALSE 24796966912
#> 2 FALSE 9006234624
#> 3 FALSE 9006234624
#> 4 FALSE 26086424576
#> 5 FALSE 98855960576
#> 6 FALSE 356193000000