Need help in understanding MaxQuant output files
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17 months ago
rishav513 • 0

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.

Proteomics • 738 views
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