Table 1.
Top five unique peptide assignments for the three workflows (external CV stepping, internal CV stepping, and SCX prefractionation) (top ETD, bottom CID). Counterpart datasets were interrogated manually for the presence of equivalent precursor ions and fragmentation spectra. Mascot probability scores for the assigned peptides are given
| ETD Top 5 | Internal | External | SCX | Probability |
|---|---|---|---|---|
| External | ||||
| ILGGSVLHLVLALR | Not present | Identified | Not present | 1.27E-06 |
| LKKEDIYAVEIVGGATR | Present | Identified | Not present | 4.50E-07 |
| LLKIPVDTYNNILTVLK | Present | Identified | Not present | 1.66E-07 |
| VPVITGSFVDLSVELK | Present | Identified | Not present | 2.27E-06 |
| VVVDALSGLKGDLAGR | Not present | Identified | Not present | 2.68E-06 |
| Internal | ||||
| AMGIMNSFVNDIFER | Identified | Fragmented | Not present | 2.51E-07 |
| KPLVIIAEDVDGEALSTLVLNR | Identified | Present | Fragmented | 8.79E-06 |
| TALLDAAGVASLLTTAEVVVTEIPKEEK | Identified | Fragmented | Not present | 9.08E-06 |
| TDEFQLHTNVNDGTEFGGSIYQK | Identified | Present | Not present | 8.74E-06 |
| TPAVEGLTEAEEEELRAELTK | Identified | Fragmented | Not present | 1.61E-07 |
| SCX | ||||
| EGQGEGETQEAAAAAAAAR | Present | Present | Identified | 1.80E-10 |
| GVVPLAGTNGETTTQGLDGLSER | Present | Not present | Identified | 5.50E-11 |
| SAAQAAAQTNSNAAGK | Not present | Not present | Identified | 1.19E-09 |
| SSGNSSSSGSGSGSTSAGSSSPGAR | Not present | Not present | Identified | 2.55E-14 |
| TLAPLLASLLSPGSVLVLSAR | Present | Not present | Identified | 7.29E-11 |
| CID Top 5 | Internal | External | SCX | Probability |
| External | ||||
| LIALSIDSVEDHLAWSK | Present | Identified | Present | 9.49E-11 |
| LGANSLLDLVVFGR | Present | Identified | Present | 2.08E-10 |
| TVAGQDAVIVLLGTR | Present | Identified | Present | 4.71E-10 |
| QVLLSAAEAAEVILR | Present | Identified | Not present | 5.42E-10 |
| LTTDFNVIVEALSK | Present | Identified | Present | 5.78E-10 |
| Internal | ||||
| TAFDEAIAELDTLNEDSYKDSTLIMQLLR | Identified | Fragmented | Present | 4.87E-07 |
| VLFPATGYLSIVWK | Identified | Present | Not present | 5.17E-07 |
| GLGTGTLYIAESR | Identified | Fragmented | Not present | 5.89E-07 |
| LALDIEIATYR | Identified | Present | Present | 7.46E-07 |
| TVLIMELINNVAK | Identified | Present | Present | 1.08E-06 |
| SCX | ||||
| PNSEPASLLELFNSIATQGELVR | Not present | Not present | Identified | 1.53E-12 |
| VDNALQSGNSQESVTEQDSK | Not present | Not present | Identified | 3.89E-12 |
| ASASGSGAQVGGPISSGSSASSVTVTR | Not present | Not present | Identified | 2.81E-11 |
| GLAFIQDPDGYWIEILNPNK | Not present | Not present | Identified | 7.00E-11 |
| TQLEELEDELQATEDAK | Not present | Not present | Identified | 1.65E-10 |