The Proteoform Spectral Matches (PrSMs) page reports all of the PrSMs identified in the experiment.

The annotated sequence showing modifications, LogE,-LogP, are shown for each PrSM. To view additional information about related proteoforms, proteins, and isoforms, select the down arrow next to Show Associated Tables, .

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.

Figure PrSMs page

To further investigate each result, you can launch the ProSight Lite and the TDValidator Lite applications from the PrSMs table.

Table Commonly used columns on the PrSMs page

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.

Table Proteoform Level Classification System

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