The XlinkX/PD Search node identifies the crosslinkers and has the parameters described in the following table.
Parameter | Description |
|---|---|
Protein Database | Specifies the name of the FASTA database to search. |
Enzyme Name | Specifies the reagent used for protein digestion. After you select your enzyme, you can also specify the type of enzymatic cleavage to consider (fully enzymatic, partially enzymatic, limited to C terminal, or limited to N terminal). |
| To add to the list of enzymes, refer to the section on “Defining Chemical Modifications,” in the Proteome Discoverer User Guide. |
Maximum Missed Cleavages
| Specifies the maximum number of missed cleavage sites per peptide to consider during the digest. Range: 0–10; default: 2 |
Maximum Peptides Considered | Specifies the maximum number of peptides searched or scored per spectrum. Range: 1–1000; default: 10 |
Minimum Peptide Length | Specifies a peptide’s minimum sequence length. Range: 1–1000; default: 5 |
Maximum Number Modifications | Specifies the maximum number of modifications on a peptide. Range: 1–1000; default: 4 |
Minimum Peptide Mass | Specifies the minimum peptide mass to consider. Range: 1–(unchecked); default: 300 |
Maximum Peptide Mass | Specifies the maximum peptide mass to consider. Range: 1–(unchecked); default: 7000 |
Minimum score | Specifies the score cutoff to apply in the identification of the single peptides of the crosslinked MS1 precursor in the MS3 and MS2 spectra. Identifications below this threshold are thrown away and are not assembled to crosslinks. Default: 0 |
Maximum score difference | Minimum score difference–the score difference to the second-best peptide in the identification list. Peptides with a score too close to the second-best ID are removed and not assembled to crosslinks. Default: 4 |
Precursor Mass Tolerance | Specifies the mass tolerance used to match the precursor mass to the database. Range: 0.01 ppm–1000 Da; default: 10 ppm |
Fragment Mass Tolerance | Specifies the mass tolerance used to match fragment peaks to the database. Range: 0.0001–2.0 Da; default: 20 ppm |
FTMS Fragment Mass Tolerance | Specifies the mass tolerance used for matching fragment peaks from FTMS scans. Range: 0.0001–2.0 Da; default: 20 ppm |
ITMS Fragment Mass Tolerance | Specifies the mass tolerance used for matching fragment peaks from ITMS scans. Range: 0.0001–2.0 Da; default: 0.5Da |
Allowed Precursor Mass Offset | Specifies the Mass offset (13C–12C) used for matching the precursor mass to the database. Range: 0–3; default: 0 |
Allowed Precursor Signal To Noise | Specifies the minimum signal-to-noise where the precursor monoisotopic mass is accepted as is. Range: 0–1000; default: 10 |
Static Modification | Applies the same specific mass to all occurrences of that named amino acid, as in an exhaustive chemical modification. You define the available modifications in the Chemical Modifications view on the Administration page, which you open by choosing Administration > Maintain Chemical Modifications. |
Static Any N-Term Modification | Specifies the static modification on the N terminus of each peptide involved in the crosslink. |
Static Any C-Term Modification | Specifies the static modification on the C terminus of each peptide involved in the crosslink. |
Static Protein N-Term Modification | Specifies the static modification on a peptide only if the peptide includes the protein N terminus. |
Static Protein C-Term Modification | Specifies the static modification on a peptide only if the peptide includes the protein C terminus. |
Dynamic Modification | Specifies the dynamic modifications. The available modifications are defined in the Chemical Modifications view on the Administration page. Default: None |
Dynamic Any N-Term Modification | Specifies the dynamic modification on the N terminus of each peptide involved in the crosslink. |
Dynamic Any C-Term Modification | Specifies the dynamic modification on the C terminus of each peptide involved in the crosslink. |
Dynamic Protein N-Term Modification | Specifies the dynamic modification on a peptide only if the modification is at the N-terminus, and the peptide includes the protein N terminus. |
Dynamic Protein C-Term Modification | Specifies the dynamic modification on a peptide only if the modification is at the C-terminus, and the peptide includes the protein C terminus. |