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Table 2 Number of peptides identified at 1% FDR from 20 MS/MS datasets generated by [27]

From: Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy

Sample ID Max quant MS-GF+ Percolator PLATO
2014-03-04-mel3p1 2533 2967 3748 3898
2014-03-04-mel3p2 2770 3341 4467 4412
2014-03-06-mel3p1 2441 2704 3632 3681
2014-03-06-mel3p2 2594 3140 4271 4157
2014-03-04-mel4p1 2634 3108 3929 4073
2014-03-04-mel4p2 1765 3073 4004 3757
2014-03-06-mel4p1 2401 2824 3526 3682
2014-03-06-mel4p2 1745 2694 3856 3954
2014-03-05-mel5p1 3010 2517 3742 3923
2014-03-05-mel5p2 3342 2561 4023 4127
2014-03-06-mel5p1 2934 2643 3929 4059
2014-03-06-mel5p2 3060 2592 4070 4014
2014-03-05-mel8p1 3375 3057 4006 4297
2014-03-05-mel8p2 3764 2976 4511 4556
2014-03-06-mel8p1 3331 3023 4375 4454
2014-03-06-mel8p2 4139 3444 4801 4839
2014-03-04-mel12p1 1948 1601 2724 2870
2014-03-04-mel12p2 2013 1408 2855 3121
2014-03-06-mel12p1 2004 1301 3028 3005
2014-03-06-mel12p2 2628 1601 2942 3356
  1. MHC-bound peptides were eluted from melanoma samples collected from five different patients (identified as mel3, mel4, mel5, mel8, and mel12), with two biological replicates (p1/p2) per patient, each analyzed on two independent MS/MS runs (identified by the date in the sample ID). For each MS/MS dataset, the largest number of identified peptides is typeset in italics