Table 1 Counts of PSMs, unique peptides, and proteins for unfiltered, 1% FDR, and 5% FDR datasets

Unfiltered

2,527,135

44,4225.241

0.176

32,755

3544

Modified

608,357

19,0915.030

0.314

25,362

3478

Unmodified

1,918,778

253,310.212

0.132

7393

66

1% FDR

1,473,636

14,736.377

0.010

19,265

2121

Modified

198,277

3,224.088

0.016

8369

1690

Unmodified

1,275,359

11,512.288

0.009

10,896

431

5% FDR

1,980,884

99,044.212

0.050

22,776

2445

Modified

362,291

31,912.966

0.088

13,299

2188

Unmodified

1,618,593

67,131.246

0.041

9477

257