Table 1.
Curated list of proteins annotated from LC–MS/MS data processed via MaxQuant
| Protein | Gene | Molecular weight (kDa) | Sequence coverage (%) | Unique sequence coverage (%) | Sequence length | PEP score | PEP |
|---|---|---|---|---|---|---|---|
| Caspase-14 | CASP14 | 27.679 | 14.9 | 14.9 | 242 | 22.3 | 4.75e-11 |
| Heat shock protein beta 1 | HSPB1 | 22.782 | 19.0 | 19.0 | 205 | 11.1 | 7.93e-04 |
| Histone H1.2/H1.3/H1.4 | H1-2/H1-3/H1-4 | 21.316 | 16.0 | 16.0 | 212 | 18.2 | 6.50e-07 |
| Calmodulin-like protein 5 | CALML5 | 15.892 | 47.3 | 47.3 | 146 | 79.5 | 2.87e-60 |
| Fatty acid–binding protein 5 | FABP5 | 15.164 | 24.4 | 24.4 | 135 | 24.8 | 1.44e-13 |
| Protein S100-A9 | S100A9 | 13.242 | 24.6 | 24.6 | 114 | 32.8 | 1.49e-25 |
| Histone H2B1 | H2B1 | 13.990 | 16.0 | 16.0 | 125 | 42.8 | 1.77e-13 |
| Protein S100-A7 | S100A7 | 11.471 | 28.7 | 28.7 | 101 | 15.7 | 1.90e-08 |
| Histone H4 | H4c1 | 11.367 | 26.2 | 26.2 | 103 | 12.0 | 9.65e-05 |
| Dermicidin | DCD | 11.284 | 16.4 | 16.4 | 110 | 13.7 | 2.05e-06 |
| Cystatin-A | CSTA | 11.006 | 39.8 | 39.8 | 98 | 36.7 | 1.99e-21 |
| Protein S100-A8 | S100A8 | 10.834 | 45.2 | 45.2 | 93 | 42.7 | 2.10e-23 |
| Ubiquitin-60S ribosomal protein L40 | 7.132 | 49.2 | 49.2 | 63 | 109.3 | 4.52e-102 |
Proteins with <2 unique peptides and >30 kDa were filtered out. Six proteins found in MALDI-TOF MS protein profiles are shaded in bold. Q values for all annotations (not shown) were found to be 0. MS/MS spectra for peptides used by MaxQuant for annotation are found in supplemental Figs. S9–S21. The PEP score is defined in MaxQuant as derived from peptide posterior error probabilities (PEPs), which have been described by Käll et al. (96). The PEP score calculated in MaxQuant is inversely related to the protein group PEPs and should be treated as a thresholded value. More detailed identification data can be found in supplementary File 2. Furthermore, a brief discussion of other microproteins of interest in the context of ovarian cancer can be found in the supplemental data.