The data cleanSpectra “cleans”
Here’s the opendiff view of a file before (left) and after (right) peaks have been cleaned.
UPDATE: Examples of how cleaning may cut out some ion matches.
Without cleaning:
| peaks | ion matches | precursor mass | sequence |
| 208 | 11 | 1544.112183 | HGTDDGVVWMNWK |
| 324 | 10 | 1544.512207 | HGTDDGVVWMNWK |
| 324 | 10 | 1544.512207 | HGTDDGVVWMNWK |
| 267 | 10 | 1818.752197 | TMTIHNGMFFSTYDR |
| 224 | 10 | 2125.862305 | HQLYIDETVNSNIPTNLR |
| 281 | 11 | 2384.902100 | KGGETSEMYLIQPDSSVKPYR |
| 239 | 9 | 2385.282227 | KGGETSEMYLIQPDSSVKPYR |
With cleaning:
| peaks | ion matches | precursor mass | sequence |
| 100 | 10 | 1544.112183 | HGTDDGVVWMNWK |
| 100 | 9 | 1544.512207 | HGTDDGVVWMNWK |
| 100 | 9 | 1544.512207 | HGTDDGVVWMNWK |
| 100 | 10 | 1818.752197 | TMTIHNGMFFSTYDR |
| 100 | 9 | 2125.862305 | HQLYIDETVNSNIPTNLR |
| 100 | 9 | 2384.902100 | KGGETSEMYLIQPDSSVKPYR |
| 100 | 5 | 2385.282227 | KGGETSEMYLIQPDSSVKPYR |
As we limit to 100 peaks for cleaning, this could be problematic for larger sequences (such as the final KGGETSEMYLIQPDSSVKPYR which drops from 9 matches to 5).