PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration
Introduction
This vignette demonstrates how to use PepMapViz with
input files.
Accessing Input Files
The input files are stored in the inst/extdata/
directory of the package. You can access them using the
system.file() function. The example files are searching
results from PEAKS software. “Donor” column is added to plot peptides
from different donors.
# Access the input files
input_file_folder <- system.file("extdata", package = "PepMapViz")
# Read the input files
resulting_df <- combine_files_from_folder(input_file_folder)
head(resulting_df)## Peptide -10LgP Mass Length Delta 1/k0 ppm
## <char> <num> <num> <num> <num> <num>
## 1: ADYEKHKVYAC(+57.02)EVTHQG 26.08 2033.927 17 0 0.5
## 2: ADYEKHKVYAC(+57.02)EVTHQG 43.32 2033.927 17 0 3.0
## 3: ADYEKHKVYAC(+57.02)EVTHQGLS 37.61 2234.043 19 0 2.3
## 4: ADYEKHKVYAC(+57.02)EVTHQGLS 26.73 2234.043 19 0 4.4
## 5: ADYEKHKVYAC(+57.02)EVTHQGLS 44.82 2234.043 19 0 2.3
## 6: ADYEKHKVYAC(+57.02)EVTHQGLSSPV 29.12 2517.196 22 0 9.7
## m/z z RT 1/k0 Range Area Intensity Scan Precursor Id
## <num> <num> <num> <char> <num> <num> <num> <num>
## 1: 509.4939 4 31.9954 0.8114-0.8215 5554.165 73379.20 1591380 58236
## 2: 678.9911 3 31.9985 0.9191-0.9292 1305.469 18703.08 1591376 58232
## 3: 745.6968 3 39.5249 0.9050-0.9151 2653.591 38730.42 1978829 86021
## 4: 559.5256 4 39.5073 0.8272-0.8373 2627.366 78978.09 1978842 86034
## 5: 745.6968 3 39.5249 0.9066-0.9167 2653.591 38730.42 1980444 86112
## 6: 630.3182 4 48.1040 0.9272-0.9373 NA NA 2430176 122840
## Source File
## <char>
## 1: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 2: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 3: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 4: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 5: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 6: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## Accession
## <char>
## 1: A0A087WWV8|A0A087WWV8_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;Cosentyx_LC|Secukinumab_LC;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Etrolizumab_LC|Etrolizumab;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;hC6D4_LC|hC6D4.hIgG1;A0A087WTX5|A0A087WTX5_HUMAN;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## 2: A0A087WWV8|A0A087WWV8_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;Cosentyx_LC|Secukinumab_LC;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Etrolizumab_LC|Etrolizumab;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;hC6D4_LC|hC6D4.hIgG1;A0A087WTX5|A0A087WTX5_HUMAN;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## 3: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hA33_LC|hA33_LC;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 4: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hA33_LC|hA33_LC;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 5: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hA33_LC|hA33_LC;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 6: A0A087WWV8|A0A087WWV8_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Etrolizumab_LC|Etrolizumab;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hC6D4_LC|hC6D4.hIgG1;A0A087WTX5|A0A087WTX5_HUMAN;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## PTM AScore Donor
## <char> <char> <char>
## 1: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 2: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 3: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 4: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 5: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 6: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1Strip the sequence
This function takes outputs from multiple platform, a data frame with a column containing peptide sequences with modifications and converts it into a new dataframe with plain peptide sequences without modifications.
# Strip the sequence
striped_data_peaks <- strip_sequence(resulting_df, "Peptide", "Sequence", "PEAKS")
head(striped_data_peaks)## Peptide -10LgP Mass Length Delta 1/k0 ppm
## <char> <num> <num> <num> <num> <num>
## 1: ADYEKHKVYAC(+57.02)EVTHQG 26.08 2033.927 17 0 0.5
## 2: ADYEKHKVYAC(+57.02)EVTHQG 43.32 2033.927 17 0 3.0
## 3: ADYEKHKVYAC(+57.02)EVTHQGLS 37.61 2234.043 19 0 2.3
## 4: ADYEKHKVYAC(+57.02)EVTHQGLS 26.73 2234.043 19 0 4.4
## 5: ADYEKHKVYAC(+57.02)EVTHQGLS 44.82 2234.043 19 0 2.3
## 6: ADYEKHKVYAC(+57.02)EVTHQGLSSPV 29.12 2517.196 22 0 9.7
## m/z z RT 1/k0 Range Area Intensity Scan Precursor Id
## <num> <num> <num> <char> <num> <num> <num> <num>
## 1: 509.4939 4 31.9954 0.8114-0.8215 5554.165 73379.20 1591380 58236
## 2: 678.9911 3 31.9985 0.9191-0.9292 1305.469 18703.08 1591376 58232
## 3: 745.6968 3 39.5249 0.9050-0.9151 2653.591 38730.42 1978829 86021
## 4: 559.5256 4 39.5073 0.8272-0.8373 2627.366 78978.09 1978842 86034
## 5: 745.6968 3 39.5249 0.9066-0.9167 2653.591 38730.42 1980444 86112
## 6: 630.3182 4 48.1040 0.9272-0.9373 NA NA 2430176 122840
## Source File
## <char>
## 1: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 2: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 3: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 4: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 5: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 6: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## Accession
## <char>
## 1: A0A087WWV8|A0A087WWV8_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;Cosentyx_LC|Secukinumab_LC;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Etrolizumab_LC|Etrolizumab;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;hC6D4_LC|hC6D4.hIgG1;A0A087WTX5|A0A087WTX5_HUMAN;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## 2: A0A087WWV8|A0A087WWV8_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;Cosentyx_LC|Secukinumab_LC;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Etrolizumab_LC|Etrolizumab;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;hC6D4_LC|hC6D4.hIgG1;A0A087WTX5|A0A087WTX5_HUMAN;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## 3: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hA33_LC|hA33_LC;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 4: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hA33_LC|hA33_LC;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 5: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hA33_LC|hA33_LC;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 6: A0A087WWV8|A0A087WWV8_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;JNJ61178104_TNFa_HC|JNJ61178104_TNFa_Heavy_Chain;Q6PJF2|Q6PJF2_HUMAN;Lemtrada_LC|Alemtuzumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;Imfinzi_LC|Durvalumab_LC;Cosentyx_LC|Secukinumab_LC;Q6GMX0|Q6GMX0_HUMAN;Etrolizumab_LC|Etrolizumab;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;TrasBev_1cell_Tras_LC|TrasBev_1cell_Tras_Light_Chain;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_1cell_v2_Tras_LC|TrasBev_1cellv2_Tras_Light_Chain;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;hC6D4_LC|hC6D4.hIgG1;A0A087WTX5|A0A087WTX5_HUMAN;Rybrevant_Met_LC|Amivantamab_Met_Light_Chain;Humira_LC|Adalimumab_LC;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## PTM AScore Donor
## <char> <char> <char>
## 1: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 2: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 3: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 4: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 5: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## 6: Carbamidomethylation C11:Carbamidomethylation:1001.00 D1
## Sequence
## <char>
## 1: ADYEKHKVYACEVTHQG
## 2: ADYEKHKVYACEVTHQG
## 3: ADYEKHKVYACEVTHQGLS
## 4: ADYEKHKVYACEVTHQGLS
## 5: ADYEKHKVYACEVTHQGLS
## 6: ADYEKHKVYACEVTHQGLSSPVExtract modifications information
This function takes outputs from multiple platform, a data frame with a column containing modified peptide sequence with the detailed post translational modification(PTM) information and converts it into a new dataframe with plain peptide sequences and associated PTM information.
# Extract modifications information
PTM_table <- data.frame(PTM_mass = c("15.99", ".98", "57.02", "42.01"),
PTM_type = c("Ox", "Deamid", "Cam", "Acetyl"))
converted_data_peaks <- obtain_mod(
striped_data_peaks,
"Peptide",
"PEAKS",
strip_seq_col = NULL,
PTM_table,
PTM_annotation = TRUE,
PTM_mass_column = "PTM_mass"
)
head(converted_data_peaks)## Key: <PTM_mass>
## PTM_mass PTM_position reps Peptide -10LgP Mass Length
## <char> <num> <num> <char> <num> <num> <num>
## 1: <NA> NA 1 AENTLQSFRQDVDNASLAR 26.93 2134.040 19
## 2: <NA> NA 1 AKVQWKVDNALQSGN 32.89 1656.858 15
## 3: <NA> NA 1 AKVQWKVDNALQSG 24.38 1542.815 14
## 4: <NA> NA 1 AKVQWKVDNALQSGNS 46.89 1743.890 16
## 5: <NA> NA 1 AKVQWKVDNALQSGNS 42.78 1743.890 16
## 6: <NA> NA 1 AKVQWKVDNALQSGNS 39.31 1743.890 16
## Delta 1/k0 ppm m/z z RT 1/k0 Range Area Intensity
## <num> <num> <num> <num> <num> <char> <num> <num>
## 1: 0 0.9 712.3613 3 64.0846 0.9642-0.9743 802.0634 9006.403
## 2: 0 -0.1 829.4441 2 51.1203 1.0806-1.0907 1093.7975 12566.528
## 3: 0 3.9 772.4252 2 51.9183 1.0480-1.0581 NA NA
## 4: 0 6.4 872.9662 2 50.9561 1.0983-1.1084 32295.9060 333551.380
## 5: 0 6.4 872.9662 2 50.9561 1.0951-1.1051 32295.9060 333551.380
## 6: 0 6.4 872.9662 2 50.9561 1.0999-1.1100 32295.9060 333551.380
## Scan Precursor Id
## <num> <num>
## 1: 3270489 198105
## 2: 2586900 136308
## 3: 2630329 140113
## 4: 2576838 135390
## 5: 2575164 135240
## 6: 2575182 135258
## Source File
## <char>
## 1: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 2: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 3: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 4: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 5: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## 6: 20230208_TTS1_ptran0117_OBJ42352_IDB001031_9D1_Boco_IP1_L243_MAPPs_1_1_1419.d
## Accession
## <char>
## 1: B0YJC5|B0YJC5_HUMAN;Q5JVS8|Q5JVS8_HUMAN;B0YJC4|B0YJC4_HUMAN;P08670|VIME_HUMAN;Q53HU8|Q53HU8_HUMAN;B3KRK8|B3KRK8_HUMAN;V9HWE1|V9HWE1_HUMAN
## 2: A0A087WWV8|A0A087WWV8_HUMAN;S6B2A1|S6B2A1_HUMAN;S6AWF4|S6AWF4_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Q569I7|Q569I7_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;S6AWD6|S6AWD6_HUMAN;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;Lemtrada_LC|Alemtuzumab_LC;Q6PJF2|Q6PJF2_HUMAN;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;S6AWE3|S6AWE3_HUMAN;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;S6B2C3|S6B2C3_HUMAN;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;S6BGE9|S6BGE9_HUMAN;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;A0A087WTX5|A0A087WTX5_HUMAN;Humira_LC|Adalimumab_LC;S6AWD3|S6AWD3_HUMAN;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## 3: A0A087WWV8|A0A087WWV8_HUMAN;S6B2A1|S6B2A1_HUMAN;S6AWF4|S6AWF4_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;Tecentriq_LC|Atezolizumab_LC;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Q569I7|Q569I7_HUMAN;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;S6AWD6|S6AWD6_HUMAN;hA33_LC|hA33_LC;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;Lemtrada_LC|Alemtuzumab_LC;Q6PJF2|Q6PJF2_HUMAN;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;MPSK3169A_LC|MPSK3169A_LC;Keytruda_LC|Pembrolizumab_LC;Q8TCD0|Q8TCD0_HUMAN;S6AWE3|S6AWE3_HUMAN;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;S6B2C3|S6B2C3_HUMAN;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Remicade_LC|Infliximab_LC;Bococizumab_LC|Bococizumab_LC;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;S6BGE9|S6BGE9_HUMAN;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;A0A087WTX5|A0A087WTX5_HUMAN;Humira_LC|Adalimumab_LC;S6AWD3|S6AWD3_HUMAN;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN
## 4: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;S6AWE3|S6AWE3_HUMAN;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;S6B2C3|S6B2C3_HUMAN;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Q569I7|Q569I7_HUMAN;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;S6BGE9|S6BGE9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;Lemtrada_LC|Alemtuzumab_LC;Q6PJF2|Q6PJF2_HUMAN;Humira_LC|Adalimumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;S6AWD3|S6AWD3_HUMAN;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 5: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;S6AWE3|S6AWE3_HUMAN;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;S6B2C3|S6B2C3_HUMAN;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Q569I7|Q569I7_HUMAN;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;S6BGE9|S6BGE9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;Lemtrada_LC|Alemtuzumab_LC;Q6PJF2|Q6PJF2_HUMAN;Humira_LC|Adalimumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;S6AWD3|S6AWD3_HUMAN;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## 6: Keytruda_LC|Pembrolizumab_LC;A0A087WWV8|A0A087WWV8_HUMAN;Q8TCD0|Q8TCD0_HUMAN;S6AWE3|S6AWE3_HUMAN;Imfinzi_LC|Durvalumab_LC;Q6GMX0|Q6GMX0_HUMAN;Herceptin_LC|Trastuzumab_LC;aVb8-65_LC|aVb8-65_LC|aVb8-65_Light_Chain,;S6B2C3|S6B2C3_HUMAN;Tecentriq_LC|Atezolizumab_LC;BocoBev_Boco_LC|BocoBev_Boco_Light_Chain;Tecentriq_signalseqVHS_LC|Atezolizumab_signlaseqVHS_LC;Q6PIL8|Q6PIL8_HUMAN;Q0KKI6|Q0KKI6_HUMAN;Q6P5S8|Q6P5S8_HUMAN;Q5EFE6|Q5EFE6_HUMAN;V9HW34|V9HW34_HUMAN;Remicade_LC|Infliximab_LC;Q569I7|Q569I7_HUMAN;Bococizumab_LC|Bococizumab_LC;JNJ61178104_TNFa_LC|JNJ61178104_TNFa_Light_Chain;P01834|IGKC_HUMAN;Libtayo_LC|Cemiplimab_LC;Opdivo_LC|Nivolumab_LC;A0A087WYL9|A0A087WYL9_HUMAN;S6BGE9|S6BGE9_HUMAN;Rybrevant_EGFR_LC|Amivantamab_EGFR_Light_Chain;hA33_LC|hA33_LC;Q7Z3Y4|Q7Z3Y4_HUMAN;TrasBev_2cell_Tras_LC|TrasBev_2cell_Tras_Light_Chain;A0A087WTX5|A0A087WTX5_HUMAN;Herceptin_signalseqVHS_LC|Trastuzumab_signalseqVHS_LC;Tecentriq_signalseqNAYA_LC|Atezolizumab_signalseqNAYA_LC;Herceptin_signalseqNAYA_LC|Trastuzumab_signalseqNAYA_LC;Lemtrada_LC|Alemtuzumab_LC;Q6PJF2|Q6PJF2_HUMAN;Humira_LC|Adalimumab_LC;Ly3415244_LC2|Ly3415244_Light_Chain_2;BocoBev_Bev_LC|BocoBev_Bev_Light_Chain;A0A087X130|A0A087X130_HUMAN;Praluent_LC|Alirocumab_LC;S6AWD3|S6AWD3_HUMAN;A0A087WZW8|A0A087WZW8_HUMAN;KLK5KLK7_KLK5_LC|KLK5KLK7_KLK5_Light_Chain;METMab_LC|Onartuzumab;A0A075B6H6|A0A075B6H6_HUMAN;MPSK3169A_LC|MPSK3169A_LC
## PTM AScore Donor Sequence PTM_type
## <char> <char> <char> <char> <char>
## 1: D1 AENTLQSFRQDVDNASLAR <NA>
## 2: D1 AKVQWKVDNALQSGN <NA>
## 3: D1 AKVQWKVDNALQSG <NA>
## 4: D1 AKVQWKVDNALQSGNS <NA>
## 5: D1 AKVQWKVDNALQSGNS <NA>
## 6: D1 AKVQWKVDNALQSGNS <NA>Match peptide sequence with provided sequence and calculate positions
This function matches peptide sequences from the ‘peptide_data’ data frame to corresponding provided whole sequences in the ‘whole_seq’ data frame. It calculates the start and end positions of the matched sequences and returns data frame with information about the matching positions.
# Match peptide sequence with provided sequence and calculate positions
whole_seq <- data.frame(
Epitope = c("Boco", "Boco"),
Chain = c("HC", "LC"),
Region_Sequence = c("QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGEISPFGGRTNYNEKFKSRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARERPLYASDLWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKCCVECPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPSSIEKTISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK",
"DIQMTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQRYSLWRTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC"
)
)
matching_result <- match_and_calculate_positions(
converted_data_peaks,
'Sequence',
whole_seq,
match_columns = NULL,
sequence_length = c(10, 30),
column_keep = c(
"PTM_mass",
"PTM_position",
"reps",
"Area",
"Donor",
"PTM_type"
)
)
head(matching_result)## Sequence PTM_mass PTM_position reps Area Donor PTM_type Epitope
## 2 AKVQWKVDNALQSGN <NA> <NA> 1 1093.797 D1 <NA> Boco
## 3 AKVQWKVDNALQSG <NA> <NA> 1 <NA> D1 <NA> Boco
## 4 AKVQWKVDNALQSGNS <NA> <NA> 1 32295.91 D1 <NA> Boco
## 5 AKVQWKVDNALQSGNS <NA> <NA> 1 32295.91 D1 <NA> Boco
## 6 AKVQWKVDNALQSGNS <NA> <NA> 1 32295.91 D1 <NA> Boco
## 7 AKVQWKVDNALQSGNS <NA> <NA> 1 32295.91 D1 <NA> Boco
## Chain Start_Position End_Position
## 2 LC 144 158
## 3 LC 144 157
## 4 LC 144 159
## 5 LC 144 159
## 6 LC 144 159
## 7 LC 144 159Quantify matched peptide sequences
This function takes peptide matching result and quantifies the matched peptide sequences based on the provided quantification method. If the quantification method is ‘PSM’, the function calculates the number of matched peptide sequences in each positions of the provided whole sequence. If the quantification method is ‘Area’, the function select the max value in area column of identical peptide sequences and calculates the sum of the areas of the matched peptide sequences in each positions of the provided whole sequence.
# Quantify matched peptide sequences by PSM
matching_columns = c("Chain", "Epitope")
distinct_columns = c("Donor")
data_with_psm <- peptide_quantification(
whole_seq,
matching_result,
matching_columns,
distinct_columns,
quantify_method = "PSM",
with_PTM = TRUE,
reps = TRUE
)
region <- data.frame(
Epitope = c("Boco", "Boco", "Boco", "Boco", "Boco", "Boco"),
Chain = c("HC", "HC", "HC", "HC", "LC", "LC"),
Region = c("VH", "CH1", "CH2", "CH3", "VL", "CL"),
Region_start = c(1,119,229,338,1,108),
Region_end = c(118,228,337,444,107,214)
)
result_with_psm <- data.frame()
for (i in 1:nrow(region)) {
chain <- region$Chain[i]
region_start <- region$Region_start[i]
region_end <- region$Region_end[i]
region_name <- region$Region[i]
temp <- data_with_psm[data_with_psm$Chain == chain &
data_with_psm$Position >= region_start &
data_with_psm$Position <= region_end, ]
temp$Region <- region_name
result_with_psm <- rbind(result_with_psm, temp)
}
head(result_with_psm)## Character Position Chain Epitope PSM Donor PTM PTM_type Region
## 1 Q 1 HC Boco 0 D1 FALSE <NA> VH
## 2 V 2 HC Boco 0 D1 FALSE <NA> VH
## 3 Q 3 HC Boco 0 D1 FALSE <NA> VH
## 4 L 4 HC Boco 0 D1 FALSE <NA> VH
## 5 V 5 HC Boco 0 D1 FALSE <NA> VH
## 6 Q 6 HC Boco 0 D1 FALSE <NA> VHPlotting peptide in whole provided sequence
This function takes the quantified peptide data frame and plots the matched peptide sequences in the provided whole sequence. The function returns a ggplot object with the matched peptide sequences plotted in the provided whole sequence.
# Plotting peptide in whole provided sequence
domain <- data.frame(
domain_type = c("CDR H1", "CDR H2", "CDR H3", "CDR L1", "CDR L2", "CDR L3"),
Region = c("VH", "VH", "VH", "VL", "VL", "VL"),
Epitope = c("Boco", "Boco", "Boco", "Boco", "Boco", "Boco"),
domain_start = c(26, 50, 97, 24, 50, 89),
domain_end = c(35, 66, 107, 34, 56, 97)
)
x_axis_vars <- c("Region")
y_axis_vars <- c("Donor")
column_order <- list(
Donor = "D1,D2,D3,D4,D5,D6,D7,D8",
Region = "VH,CH1,CH2,CH3,VL,CL"
)
domain_color <- c(
"CDR H1" = "#F8766D",
"CDR H2" = "#B79F00",
"CDR H3" = "#00BA38",
"CDR L1" = "#00BFC4",
"CDR L2" = "#619CFF",
"CDR L3" = "#F564E3"
)
PTM_color <- c(
"Ox" = "red",
"Deamid" = "cyan",
"Cam" = "blue",
"Acetyl" = "magenta"
)
label_value = list(Donor = "D1")
p_psm <- create_peptide_plot(
result_with_psm,
y_axis_vars,
x_axis_vars,
y_expand = c(0.2, 0.2),
x_expand = c(0.5, 0.5),
theme_options = list(legend.box = "horizontal"),
labs_options = list(title = "PSM Plot", x = "Position", fill = "PSM"),
color_fill_column = 'PSM',
fill_gradient_options = list(limits = c(0, 160)), # Set the limits for the color scale
label_size = 1.9,
add_domain = TRUE,
domain = domain,
domain_start_column = "domain_start",
domain_end_column = "domain_end",
domain_type_column = "domain_type",
domain_color = domain_color,
PTM = TRUE,
PTM_type_column = "PTM_type",
PTM_color = PTM_color,
add_label = TRUE,
label_column = "Character",
label_value = label_value,
column_order = column_order
)
print(p_psm)