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Table 1 Summary of the numbers of peaks generated by AB3D, MZmine 2, MSight, SuperHirn and OpenMS for standard peptide mixture consisting of BSA peptides with different concentrations (96 amol, 480 amol, 2400 amol, 12 fmol, 60 fmol and 300 fmol) and peptides derived from four standard proteins such as beta galactosidase, phosphorylase b, myoglobin and cytochrome c with the same concentrations, and their replicates (n = 4) using Data set 1

From: A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry

BSA Conc. N AB3D MZmine2 MSight SuperHirn OpenMS
Total TP FP Total TP FP Total TP FP Total TP FP Total TP FP
300 fmol 1 1,482 208 1,274 4,980 240 4,740 1,317 169 1,148 2,009 201 1,808 3,305 240 3,065
2 1,458 205 1,253 4,901 246 4,655 1,155 175 980 1,896 202 1,694 3,393 240 3,153
3 1,452 207 1,245 5,047 235 4,812 1,437 176 1,261 2,007 201 1,806 3,214 239 2,975
4 1,415 214 1,201 4,875 239 4,636 1,333 173 1,160 1,919 205 1,714 3,052 228 2,824
UKP   261    276    195    249    263  
60 fmol 1 1,022 189 833 2,620 193 2,427 1,062 164 898 1,182 167 1,015 1,340 198 1,142
2 1,033 185 848 2,521 185 2,336 1,047 166 881 1,257 173 1,084 1,264 193 1,071
3 975 181 794 2,374 187 2,187 909 152 757 1,160 165 995 1,239 190 1,049
4 950 181 769 2,318 186 2,132 833 154 679 1,187 167 1,020 1,153 185 968
UKP   217    220    177    202    210  
12 fmol 1 752 145 607 1,474 146 1,328 603 128 475 869 130 739 773 150 623
2 742 148 594 1,449 150 1,299 513 121 392 858 140 718 754 147 607
3 695 151 544 1,262 145 1,117 624 128 496 789 128 661 680 148 532
4 673 154 519 1,234 143 1,091 518 122 396 752 130 622 642 141 501
UKP   177    170    134    170    161  
2400 amol 1 655 122 533 1,279 124 1,155 440 98 342 747 107 640 619 118 501
2 653 115 538 1,193 113 1,080 414 93 321 769 107 662 585 118 467
3 598 117 481 1,112 113 999 360 86 274 716 105 611 581 117 464
4 612 118 494 1,080 116 964 368 87 281 689 112 577 553 114 439
UKP   138    135    100    137    128  
480 amol 1 668 101 567 1,237 108 1,129 450 83 367 778 87 691 630 100 530
2 622 94 528 1,191 97 1,094 431 81 350 768 89 679 592 94 498
3 608 100 508 1,094 103 991 388 76 312 731 99 632 569 90 479
4 593 93 500 1,063 93 970 358 71 287 688 94 594 498 93 405
UKP   115    123    88    118    104  
96 amol 1 688 97 591 1,488 102 1,386 433 76 357 730 83 647 673 89 584
2 636 88 548 1,311 92 1,219 408 71 337 717 83 634 658 87 571
3 583 92 491 1,103 89 1,014 379 68 311 703 84 619 584 77 507
4 553 88 465 1,060 87 973 316 64 252 697 85 612 489 76 413
UKP   106    110    79    110    94  
  1. Values in individual rows for each concentration represent the individual number of known peptides of BSA and the four other standard proteins from 4 replicates. Values in UKP rows represent the total numbers of unique known peptides identified from 4 replicates. TP and FP represent true positive and false positive, respectively.