Modification notation - BioPharma Finder Software - Peptide Mapping Analysis User Guide - View Peptide Mapping Analysis results - View the Results tables - Modification notation - Charge State Results table parameters - Process and Review page - BioPharma Finder Software - BioPharma Finder Software

Variable modification

For example, 7:T95–R119 = 2544.30062m(C98+Carbamidomethylation) shows:

• C98 = the modification occurs at the cysteine at position 98 in the full protein sequence 7
• Carbamidomethylation = the modification type

Multiple modifications

For example, 1:F35–K44 = 1248.6139m(K36+Glycation)(~D37–53.0499) shows two modifications:

• A glycation at residue K36
• An unspecified subtraction of 53.0499 amu at residue D37 (approximate location)

Unspecified modification

An unspecified modification is the addition or subtraction of a given mass of unspecified origin.

For example, 1:D1–R24 = 2587.29857m(~V2+57.0261) shows:

• ~V2 = the modification is approximately on the V residue at position 2 in the full protein sequence 1
• +57.0261 = the addition of the mass of 57.0261

The Enable Mass Search for Unspecified Modifications option must be selected in the processing method (Parameters > Identification > Advanced Search) for the application to perform these identifications.

Dimer

For example, 1:D1–R24 = 2587.29857m[2x] shows the application identified the peptide as a dimer (2x).

Nonspecific

For example, 1:S10–R24 = 1588.78791m[nonspecific] shows that the identified peptide was produced from an unexpected cleavage for the specified protease.

Adducts

For example, 1:V83–K108 = 2844.34288m(Na+) shows that the peptide is a Na⁺ adduct.

The application detects adducts when an identified mass is higher than the expected precursor mass by a specific amount, for example, ~22 amu higher for a Na⁺ adduct, based on the given charge state.

The application search for many possible adducts, including Na⁺, 2Na⁺, Ca⁺², and Fe⁺³.

Gas phase modifications

Gas phase modifications occur during the gas phase ionization process in the mass spectrometer. Gas phase modifications are distinct from post-translational modifications that occur before the MS experiment.

These modifications may include oxidation, partial fragmentation of the peptide from the b or y ion side, or the loss of H₂O, NH₃, or glycans.

1. Gas phase oxidations: GasPhaseOxidation, GasPhaseDoubleOxidation
2. For example, 1:S179–K188 = 1067.55326m(GasPhaseOxidation) shows that the application identified a peptide (S179–K188) with a mass consistent with oxidation during the ionization process in the mass spectrometer.
2. Gas phase losses: GasPhase–Y Ion, GasPhase–B Ion, GasPhaseH2OLoss, GasPhaseNH3Loss, GasPhase–GlcNAc
3. For example, 1:K243–R296 = 1156.5149m(N292+A2G0F)(GasPhase–GlcNAc) shows that the application identified a peptide (K243–R296) with a mass consistent with the loss of GlcNAc (A2G0F glycan) during the ionization process in the mass spectrometer.

Disulfide/trisulfide bonds

For example, 1:D1–R24/1:V83–K108 = 5315.583m[1ss] shows that there is a disulfide bond (1ss) between peptides D1–R24 and V83–K108.

Furthermore, 1:C6–K13/G126–L129 = 1280.6039m[1ss](+Trisulfide) shows that there is a trisulfide bond (1ss+Trisulfide) between peptides 1:C6–K13 and G126–L129.

The Perform Disulfide Bond Search option must be selected in the processing method (Parameters > Identification) for the application to perform these identifications.

Glycan

For example, A2G1F or M5 shows the association of a glycan with the peptide.

The Glycosylation option must be enabled in the processing method (Parameters > Identification > Advanced Search) for the application to perform these identifications.

Partial gas phase GlcNAc losses (denoted GasPhase–GlcNAc) are also possible. See “Gas phase modifications” above.

Sequence variant

A sequence variant occurs when a given amino acid residue is replaced with a different amino acid residue within a peptide.

The Search for Amino Acid Substitutions option (Single base or All) must be selected in the processing method (Parameters > Identification > Advanced Search) for the application to perform these identifications.

When the Search for Amino Acid Substitutions option is selected, an additional “Sequence Variant” column appears in the Results table which lists the specific amino acid variant that was found.

For example, 2:G1250–K150 = 2488.2996m(V149R) shows that the application detected that the V residue at position 149 was replaced with R. The Sequence Variant column displays “V149R”.

Deletion

A deletion (residual loss) is the loss of a single amino acid residue within a given sequence identification.

The Enable Residue Deletion option must be selected in the processing method (Parameters > Identification > Advanced Search) for the application to perform these identifications.

The “Site” column in the Results table displays the deleted amino acid residue.

For example, 2:A46–K60 = 1950.9516m(Y50+Deletion) shows that the application detected that residue Y50 was deleted from the identified peptide A46–K60. The Site column displays “Y50”.