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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