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Table 2 Summary of the numbers of peaks generated by AB3D, MZmine 2, MSight, SuperHirn and OpenMS for the real biological data (data set 2)

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

Fraction. N AB3D MZmine2 MSight SuperHirn OpenMS
Total TP FP Total TP FP Total TP FP Total TP FP Total TP FP
FK1 1 496 197 299 529 155 374 328 147 181 760 105 655 500 195 305
2 498 193 305 469 148 321 365 172 193 739 112 627 447 190 257
3 490 211 279 503 150 353 379 178 201 808 127 681 484 205 279
UKP   279    231    234    209    258  
FK2 1 1,049 426 623 1,117 344 773 779 392 387 1,416 254 1,162 917 390 527
2 1,074 433 641 1,087 337 750 743 386 357 1,517 248 1,269 813 352 461
3 1,416 515 901 1,454 404 1,050 767 429 338 2,036 333 1,703 1,284 440 844
UKP   651    547    547    496    551  
FK3 1 613 330 283 651 275 376 686 323 363 763 184 579 528 310 218
2 725 344 381 757 280 477 675 310 365 975 194 781 636 349 287
3 657 372 285 897 373 524 754 298 456 1,064 236 828 604 344 260
UKP   489    468    481    366    453  
FK4 2 1,476 446 1,030 1,465 335 1,130 1,317 430 887 1,969 266 1,703 1,064 355 709
3 1,452 576 876 1,705 509 1,196 1,574 533 1,041 2,064 361 1,703 1,213 506 707
UKP   681    597    650    474    566  
FK5 1 1,709 423 1,286 1,674 329 1,345 526 251 275 2,128 237 1,891 643 229 414
2 2,038 425 1,613 2,231 349 1,882 721 305 416 2,988 259 2,729 834 274 560
3 2,031 572 1,459 2,432 509 1,923 1,696 489 1,207 3,126 340 2,786 1,186 401 785
UKP   768    687    636    553    516  
  1. Values in individual rows for each fraction represent the individual numbers of identified peptides from 3 replicates. In fraction 4, results for two replicates were presented because there was one missing replicate. Values in UKP rows represent the total numbers of unique known peptides identified from 2-3 replicates. TP and FP represent true positive and false positive, respectively.