The Proteoform Spectral Matches (PrSMs) page reports all of the PrSMs identified in the experiment.
When Delta M Mode is enabled, two additional columns are available on the PrSMs tab: Delta M Residue and Delta M Fragment(s). The Delta M Residue column shows where the Delta M mass has been placed on the proteoform to produce the highest number of additional matching fragment ions. Each additional fragment ion found by Delta M is displayed in the Delta M Fragment(s) column. The delta masses also display in the ProSightPD fragment map with an orange square around the potential residue where the delta mass was localized.
To further investigate each result, you can launch the ProSight Lite and the TDValidator Lite applications from the PrSMs table.
Column | Description |
---|---|
Confidence | Visual representation of confidence (High Confidence = green, Medium = Yellow, Low = Red). You can define these thresholds. |
Detected Ion Count | The number of fragment ions found in the fragment ion spectra. |
Identifying Node | Search node used to identify this PrSM. |
Annotated Sequence | The proteoforms backbone sequence and PTMs. |
Modifications | List of modifications found on each proteoform. |
# Proteins | The number of proteins each proteoform maps back to. |
Protein Accessions | Parent protein accession. |
Charge | Charge state isolated for fragmentation of the proteoform. |
m/z [Da] | Observed mass. |
Mass [Da] | Monoisotopic observed Mass. |
Theo. Mass [Da] | Theoretical mass based on matched proteoform from the database. |
ΔMass [ppm] | Observed theoretical mass error in parts per million. |
ΔMass [Da] | Observed-theoretical mass error in Daltons. |
Matched Ions | Number of matched fragment ions supporting the PrSM. |
Delta M Residue | Possible location of the delta mass supported by the corresponding Delta M fragments. |
Delta M Fragment(s) | Fragments found using Delta M Mode. |
Proteoform Levels | A new column in the Proteoform result table classifying each result according to the Proteoform levels described by Smith et al. Nature Methods 2019. For more information, see PrSMs page. |
Localized Modifications | Protein PTMs whose site was confidently localized by matched fragments. |
Non-localized Modifications | Protein PTMs whose site was not confidently localized by matched fragments. |
Level | PTMs Localized | PTMs Identified | Sequence Defined | Gene Identified |
---|---|---|---|---|
1 | Yes | Yes | Yes | Yes |
2A | No | Yes | Yes | Yes |
2B | Yes | No | Yes | Yes |
2C | Yes | Yes | No | Yes |
2D | Yes | Yes | Yes | No |
3 | Two are certain and two are ambiguous | |||
4 | One is certain and three are ambiguous | |||
5 | All are ambiguous |