New features in Mascot Server 2.7

Crosslinked peptides

Pairs of peptides linked by intact crosslinks can now be matched in a Mascot search. The parameters that define how to process the data are contained in a named crosslinking method, which is selected for the search. Search results can be exported to xiView. The following types of links can be identified:

  • intralinks – the linked peptides are from the same protein
  • interlinks – the linked peptides are from two different proteins
  • looplinks – connecting two amino acids within a single peptide
  • monolinks – a linker with one end attached and the other free

This screen shot shows the Peptide View report for a pair of peptides linked using EDC, a carbodiimide crosslinker that links primary amines with carboxyls. More information here.

crosslink match

Protein FDR

Search results for auto-decoy searches now report a Protein false discovery rate estimated using a MAYU type of approach. More information here.

decoy stats

Quantitation Summary for export to R, Perseus, etc.

A CSV Quantitation Summary, in which the rows correspond to proteins and the columns contain expression data for the various samples, can be created for files processed in Mascot Daemon with a quantitation method that specifies any of the following protocols:

  • Average for MS1 intensity-based label-free quantitation
  • Precursor for MS1 quantitation using isotopic labels, e.g. SILAC, 15N metabolic, 18O
  • Reporter for MS2 quantitation using isotopic labels, e.g. iTRAQ, TMT

One of the strengths of the Quantitation Summary is that it uses the same rigorous protein inference as the Mascot Protein Family Summary report. A Sample Map, as shown below, is used to add sample identifiers, and specify whether individual files are fractions or replicates. For isotopic labels, label to sample assignment rotation between technical replicates is supported. More information in the Mascot Daemon 2.7 help.

Daemon Sample Map

Other new features

Fragment charge
If fragment charge is present as a 3rd column in an MS/MS peak list, fragments can be matched as if singly charged, which will usually improve the score.
Better filtering of modifications with complementary deltas in an error tolerant searches
For example, a match that gets a fractionally better score by adding 16 Da at one residue and dropping oxidation of a nearby Met can now be suppressed.
Combined search results in Mascot Daemon
Multiple searches, such as fractions, can be selected in Daemon and a merged summary report opened in a web browser
MGF export outputs spectra in the original order
An option has been added to export the peak list in its original order, rather than sorted by precursor Mr.
Handle non-standard modification names in a spectral library
A new configuration file can be used to map modification names used in a spectral library to their Unimod equivalents.
Improved limits on variable modifications
Better site localisation by introducing separate caps on the number of distinct modifications in a PSM, the number of modified sites in a PSM, and the total number of arrrangements to be tested.
Quantitation code moved to Mascot Parser
The quantitation code in Mascot Distiller and Mascot Server has been moved to the Mascot Parser library, making it available to user programs and scripts.

And, of course, an embarrassing number of bug fixes.