A sample is a protein or a mixture of proteins digested by an endoprotease.
The peptides are measured using a spectrometer.
The spectrometer output is a peak list.
Each peak is a pair (mass, intensity).
Ideally each peak should represent a peptide in the sample. This is not the case
because some peaks are not present, some are noise, besides chemical or physical modifications
can occur on peptides changing their masses.
Often proteins are isolated using 2D gels, this gives an idea of the pI and Mw of the unknown proteins.
If known, you can specify Mw and pI for your sample.
Upload a file:
You can upload the PMF data directly from a file on your computer.
Masses do not need to be sorted.
Supported formats are:
pkm format, produced by the Voyager software of Perseptive Biosystems or the GRAMS software
Example:
OP=0 Center X Peak Y Left X Right X Time X Mass Difference Name STD.Misc Height Left Y Right Y %Height,Width,%Area,%Quan,H/A 833.319 2189 833.260 833.378 0.016 0 0 C 0.? 0 762 762 854.843 5078 854.769 854.917 0.001 0 0 C 0.? 0 3453 3453 863.419 5108 863.064 863.775 0.001 0 0 C 0.? 0 3567 3567 872.402 12519 872.347 872.456 0.002 0 0 C 0.? 0 11417 11417 874.395 6730 874.331 874.460 0.002 0 0 C 0.? 0 3559 3559 887.786 5903 887.540 888.031 0.003 0 0 C 0.? 0 4131 4131 898.475 3329 898.416 898.534 0.006 0 0 C 0.? 0 1377 1377 904.366 7432 904.199 904.533 0.001 0 0 C 0.? 0 5596 5596 955.300 2598 955.229 955.371 0.011 0 0 C 0.? 0 1089 1089
All lines before the line ending with ‘H/A’ are ignored.
After that, every other line is interpreted, the first column as the mass value,
the second column as the peak intensity.
dta format, produced by Sequest
Example:
this line is a comment line 899.546 1498 910.471 9718 920.45 2858 966.572 3228 1066.544 3342 1081.669 0 1130.681 0 1158.593 0 1166.623 0 1179.601 1204 1192.566 1660 1209.583 930 1213.544 1162
The first line is a comment line.
For each subsequent line, the first column is interpreted as the mass value,
the second column as the peak intensity.
If the intensity is null, the line is ignored.
pkt format, produced by the Data Explorer software of Applied Biosystems
Example:
81 1480.70557 1480.53 1481.13 1 17676 100.00 78777.88 215.64 15651.54 0.00 64 1439.72058 1439.55 1440.14 1 15787 89.32 69269.72 190.02 14596.77 168439.80 80 1479.70349 1479.45 1480.16 1 15097 85.41 71367.88 183.53 14046.04 187889.00 6 927.40973 927.27 927.64 1 14592 82.55 60508.18 177.22 12293.43 111441.10 66 1440.72168 1440.53 1441.05 1 14270 80.73 63693.18 172.73 14845.78 0.00 119 1639.84241 1639.58 1640.30 1 13500 76.38 70965.65 163.87 14066.58 191023.41 120 1640.83862 1640.66 1641.33 1 13055 73.86 64899.15 158.87 14484.64 0.00 7 928.41229 928.27 928.66 1 9375 53.04 37568.11 112.70 12488.59 0.00 155 1881.81982 1881.43 1882.32 1 8170 46.22 38734.46 98.14 17109.73 0.00 153 1880.81995 1880.61 1881.11 1 8145 46.08 33871.89 95.28 15818.97 118650.67 83 1481.70532 1481.55 1481.92 1 8032 45.44 33069.30 97.74 15581.68 0.00 122 1641.84314 1641.69 1642.38 1 7889 44.63 34656.24 94.40 15879.55 0.00 68 1441.73120 1441.54 1442.17 1 5531 31.29 28062.78 65.77 13122.96 0.00 40 1305.63635 1305.43 1306.08 1 4977 28.16 22964.59 60.26 14204.21 39906.37 8 929.42041 929.21 929.79 1 4791 27.10 22765.49 58.35 12668.57 0.00 156 1882.83765 1882.62 1883.15 1 4535 25.66 26779.96 54.26 11810.26 0.00 199 2248.82861 2248.42 2249.23 1 4304 24.35 20417.10 52.13 16448.57 0.00 48 1419.60510 1419.35 1420.05 1 3773 21.35 20049.58 45.92 12723.64 38017.72 235 2613.02393 2612.76 2613.53 1 3476 19.66 21082.94 41.36 16568.03 0.00The second column of each line is the mass value, the sixth column is the peak intensity.
Mass list format
Example:
//this line is a comment line //this line is another comment line 899.546 910.471 920.45 966.572 1066.544 1081.669 1130.681 1158.593 1166.623 1179.601 1192.566 1209.583 1213.544
You can begin the file by as many comment lines as you like (none is accepted too).
A comment line begins with //.
Each value of the file is interpreted as a mass.
Mass and intensity format
Example:
//this line is a comment line //this line is another comment line 899.546 1498 910.471 9718 920.45 2858 966.572 3228 1066.544 3342 1081.669 1144 1130.681 1232 1158.593 1424 1166.623 910 1179.601 1204 1192.566 1660 1209.583 930 1213.544 1162 1262.672 739 1277.699 1259 1314.772 810
You can begin the file by as many comment lines as you like (none is accepted too).
A comment line begins with //.
Each subsequent line should consist of 2 columns.
The first column is interpreted as the mass value and the second as the peak intensity.
The end of the line shouldn't contain other information.
Aldente format
Example:
Sample sString "Sample_name" fPi 9.00 iMw 70000 iNbPeak 7 Peak fMass 868.606000 fIntensity 3958.000000 Peak fMass 877.086000 fIntensity 1850.000000 Peak fMass 893.044000 fIntensity 1559.000000 Peak fMass 898.537000 fIntensity 1362.000000 Peak fMass 900.519000 fIntensity 3121.000000 Peak fMass 936.583000 fIntensity 2537.000000 Peak fMass 939.438000 fIntensity 1660.000000