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3.0 years ago
rishav513
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Hello everyone, Greetings of the day. I have a problem understanding the MaxQuant output file. This is my proteinGroups.txt file :
Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Fasta headers Proteins Peptides Razor + unique peptides Unique peptides Peptides E1 Peptides E2 Razor + unique peptides E1 Razor + unique peptides E2 Unique peptides E1 Unique peptides E2 Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Experiment E1 Experiment E2 PEP Reporter intensity 0 Reporter intensity not corrected 0 Reporter intensity count 0 Reporter intensity 1 Reporter intensity not corrected 1 Reporter intensity count 1 Reporter intensity 2 Reporter intensity not corrected 2 Reporter intensity count 2 Reporter intensity 3 Reporter intensity not corrected 3 Reporter intensity count 3 Reporter intensity 4 Reporter intensity not corrected 4 Reporter intensity count 4 Reporter intensity 5 Reporter intensity not corrected 5 Reporter intensity count 5 Reporter intensity 6 Reporter intensity not corrected 6 Reporter intensity count 6 Reporter intensity 7 Reporter intensity not corrected 7 Reporter intensity count 7 Reporter intensity 0 E1 Reporter intensity not corrected 0 E1 Reporter intensity count 0 E1 Reporter intensity 1 E1 Reporter intensity not corrected 1 E1 Reporter intensity count 1 E1 Reporter intensity 2 E1 Reporter intensity not corrected 2 E1 Reporter intensity count 2 E1 Reporter intensity 3 E1 Reporter intensity not corrected 3 E1 Reporter intensity count 3 E1 Reporter intensity 4 E1 Reporter intensity not corrected 4 E1 Reporter intensity count 4 E1 Reporter intensity 5 E1 Reporter intensity not corrected 5 E1 Reporter intensity count 5 E1 Reporter intensity 6 E1 Reporter intensity not corrected 6 E1 Reporter intensity count 6 E1 Reporter intensity 7 E1 Reporter intensity not corrected 7 E1 Reporter intensity count 7 E1 Reporter intensity 0 E2 Reporter intensity not corrected 0 E2 Reporter intensity count 0 E2 Reporter intensity 1 E2 Reporter intensity not corrected 1 E2 Reporter intensity count 1 E2 Reporter intensity 2 E2 Reporter intensity not corrected 2 E2 Reporter intensity count 2 E2 Reporter intensity 3 E2 Reporter intensity not corrected 3 E2 Reporter intensity count 3 E2 Reporter intensity 4 E2 Reporter intensity not corrected 4 E2 Reporter intensity count 4 E2 Reporter intensity 5 E2 Reporter intensity not corrected 5 E2 Reporter intensity count 5 E2 Reporter intensity 6 E2 Reporter intensity not corrected 6 E2 Reporter intensity count 6 E2 Reporter intensity 7 E2 Reporter intensity not corrected 7 E2 Reporter intensity count 7 E2 Sequence coverage E1 [%] Sequence coverage E2 [%] Intensity Intensity E1 Intensity E2 Only identified by site Reverse Contaminant id Peptide IDs Peptide is razor Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Oxidation (M) site positions
CON__A2I7N3 CON__REFSEQ:XP_001252647 CON__A2I7N3 CON__REFSEQ:XP_001252647 1 1 1 1 1 1 >A2I7N3 TREMBL:A2I7N3 Q27984 (Bos taurus) SERPINA3-7 >REFSEQ:XP_001252647 (Bos taurus) similar to endopin 2B 2 1 1 1 1 1 1 1 1 1 2.2 2.2 2.2 46.941 417 417 417 2 2 0.0037111 5340.6 5027.3 3 7074.5 7001.1 3 2865 3131.6 3 1126.1 1389.7 3 4692.8 5024.2 3 12627 12109 3 3362.7 3379.2 3 1267.7 1167.7 3 1861.2 1756.9 2 2981.2 2926.8 2 1389.6 1479.9 2 178.15 302.27 2 1546.5 1717.9 2 5619 5375.5 2 1539.7 1543.5 2 295.46 272.15 2 3479.4 3270.5 1 4093.3 4074.3 1 1475.5 1651.7 1 947.98 1087.4 1 3146.4 3306.3 1 7007.6 6734 1 1822.9 1835.7 1 972.24 895.53 1 2.2 2.2 795550000 545230000 250320000 + 0
CON__ENSEMBL:ENSBTAP00000007350 CON__ENSEMBL:ENSBTAP00000007350 16 2 1 >ENSEMBL:ENSBTAP00000007350 (Bos taurus) similar to Complement C4-A precursor 1 16 2 1 16 12 2 1 1 0 7.1 1.3 0.6 192.99 1742 1742 3 2 5.3561E-101 5694.3 5357.6 5 7250.4 7332.9 5 10515 10353 5 4163.5 4599.7 5 4935.5 5096 5 6638.1 6588.5 5 4394.7 4237.9 5 4287.1 3948.8 5 2935.1 2775.3 3 5201.9 5185.7 3 7750.5 7592.2 3 2134.4 2467.5 3 2289.9 2420.8 3 4042 3966.3 3 2242.5 2174.4 3 2064.3 1901.5 3 2759.2 2582.3 2 2048.5 2147.2 2 2765 2760.5 2 2029.1 2132.1 2 2645.5 2675.2 2 2596.2 2622.2 2 2152.2 2063.5 2 2222.7 2047.3 2 7.1 5.9 81056000 46722000 34335000 + 1 31 648 960 1119 1408 1792 1915 1976
CON__ENSEMBL:ENSBTAP00000023402 CON__ENSEMBL:ENSBTAP00000023402 1 1 1 >ENSEMBL:ENSBTAP00000023402 (Bos taurus) 46 kDa protein 1 1 1 1 1 0 1 0 1 0 5.1 5.1 5.1 46.017 411 411 1 0.0051386 1063.7 997.54 1 1007.1 1024.9 1 801.43 827.43 1 669.3 697.32 1 841.07 858.3 1 972.9 970.54 1 670.27 647.33 1 1286.4 1184.9 1 1063.7 997.54 1 1007.1 1024.9 1 801.43 827.43 1 669.3 697.32 1 841.07 858.3 1 972.9 970.54 1 670.27 647.33 1 1286.4 1184.9 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5.1 0 49381000 49381000 0 + 2 974 True 1042 3948 6555 6555 0 106
CON__ENSEMBL:ENSBTAP00000024146 CON__ENSEMBL:ENSBTAP00000024146 10 3 3 >ENSEMBL:ENSBTAP00000024146 (Bos taurus) similar to alpha-2-macroglobulin isoform 1 1 10 3 3 10 9 3 2 3 2 5.9 2 2 164.34 1477 1477 4 3 3.2619E-259 4017.2 3853.1 5 12920 12452 5 8503.8 8767 5 2661.5 3055.6 5 3485.2 3684.9 5 6664.9 6616.6 5 5206.4 4991.9 5 2770 2551.4 5 956.04 938.56 2 5371.6 5126.1 2 3439.6 3537.3 2 525.55 701.86 2 879.93 934.9 2 1880.5 1841.5 2 1076.3 1042.2 2 870.56 801.88 2 3061.2 2914.5 3 7548.2 7325.9 3 5064.2 5229.7 3 2136 2353.7 3 2605.3 2750 3 4784.4 4775.1 3 4130.1 3949.7 3 1899.4 1749.6 3 5.9 5.1 37098000 8015300 29083000 + 3 226 543 573 666 1294 1838 2123 2314
CON__ENSEMBL:ENSBTAP00000031900 CON__ENSEMBL:ENSBTAP00000031900 11 2 2 >ENSEMBL:ENSBTAP00000031900 (Bos taurus) 121 kDa protein 1 11 2 2 10 10 1 2 1 2 8.7 3.2 3.2 121.45 1064 1064 2 2 3.7422E-138 3358 3255.1 4 14459 13937 4 13789 13775 4 2591 3220 4 2724.7 2839.4 4 3794.1 3781.7 4 2839.5 2729.4 4 2940.9 2708.9 4 1148.3 1078.6 2 1262.4 1271.3 2 963.69 999.17 2 855.69 888.4 2 1069.1 1099.4 2 1404.7 1402.5 2 1064.5 1023.2 2 1218.5 1122.3 2 2209.6 2176.6 2 13197 12666 2 12825 12776 2 1735.3 2331.6 2 1655.5 1740 2 2389.4 2379.2 2 1775.1 1706.3 2 1722.4 1586.5 2 8.5 8.7 18460000 4966500 13493000 + 4 500 580 1818 2272 2274 2320 2321 2550
H-INV:HIT000031075 CON__ENSEMBL:ENSP00000377550 REFSEQ:NP_002265 CON__P13646-1 TREMBL:C9JA77 CON__Q6IFX2 H-INV:HIT000031075 CON__ENSEMBL:ENSP00000377550 REFSEQ:NP_002265 CON__P13646-1 TREMBL:C9JA77 7 7 7 6 6 3 1 1 1 1 1 1 0 0 0 0 0 0 >IPI:IPI00009866.7|SWISS-PROT:P13646-1|TREMBL:A1A4E9 A8K2H9 B4DL17|ENSEMBL:ENSP00000246635|REFSEQ:NP_705694|H-INV:HIT000031075|VEGA:OTTHUMP00000164632 Tax_Id=9606 Gene_Symbol=KRT13 Isoform 1 of Keratin type I cytoskeletal 13 >ENSEMBL:ENSP00000377550 Tax_I 6 7 1 0 5 5 1 1 0 0 10.5 2.6 0 49.588 458 458 420 420 458 355 452 1 1 1.4034E-29 328.1 308.06 1 349.88 353.88 1 313.41 320.69 1 259.17 268.81 1 293.61 298.24 1 285.5 293.81 1 331.26 315.24 1 262.04 241.36 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 328.1 308.06 1 349.88 353.88 1 313.41 320.69
CON__P00761 ENSEMBL:ENSP00000394114 REFSEQ:NP_001070731 ENSEMBL:ENSP00000387702 ENSEMBL:ENSP00000337113 REFSEQ:NP_001193718 TREMBL:A6XGL3 Q53ZF3 Q53ZV8 Q7Z445 Q7Z5P3 Q7Z5Y9 CON__P00761 7 1 1 1 1 1 1 7 1 1 1 1 1 1 6 0 0 0 0 0 0 >P00761 SWISS-PROT:P00761|TRYP_PIG Trypsin - Sus scrofa (Pig). 7 7 7 6 7 5 7 5 6 5 39 39 35.5 24.409 231 231 586 567 563 562 532 237 22 21 7.3643E-138 35321 33074 37 28122 29197 37 32457 32787 37 28732 29429 37 26150 26998 37 30069 30154 37 23334 22421 36 38737 35681 37 18466 17347 19 20676 20794 19 15606 16164 19 12884 13304 19 12761 13278 19 17830 17663 19 11442 11077 19 23389 21544 19 16855 15727 18 7446 8402.9 18
I need to understand, what is Reporter intensity in this file and how to proceed for differential expression analysis with this file as in Bioconductor packages like DEP, there is talk about LFQ.intensity that is not available in this file, so, I need to understand how to proceed with this file. I am new to proteomics analysis and I am totally depressed now. Any help would be appreciated.
