TMT-Integrator 4.0.2

• Add an exception when checking repeated reference tags

TMT-Integrator 4.0.1

• Revise the error message to point out which columns having the repeated reference tags
• Fix the issue of truncated peptides

TMT-Integrator 4.0

• add a new function for the matches between protein IDs and fasta headers
• add a new parameter, prefix, for indicating decoy sequences
• fix the rounding issue
• add a new parameter, log2transformed (default: true). Users can choose whether to export ratio and abundance reports in the log2 scale or not.

TMT-Integrator 3.4

• Use lower letters for modified sites (in addition to phosphorylation)
• Allow custom protein header formats as defined in Philosopher (please see https://github.com/Nesvilab/philosopher/wiki/How-to-Prepare-a-Protein-Database for more details)

TMT-Integrator 3.2.1

• enable EBI reference proteomic databases

TMT-Integrator 3.1.0

• export multiple/single site reports for different PTMs.
• bug fixing and other improvements

TMT-Integrator 3.0.0

• Add a check point to check parameters and PSM tables prior further process
  1. Reference intensity is used for abundance calculation if the MS1 intensity is absence.
  2. No gene report is exported if the gene is absence, and the protein ID will be used for other tables.
• An additional multi-mass report (i.e., groupby=5) is generated for N- and O-glycosylation data sets.
• Simplify mod tags in the mod_tag parameter, i.e., mod_tag: N-glyco/O-glyco for glycosylation
• Use assigned modification column to filter PSMs (instead of modified peptide column)
• Shorten filename
• Truncate modification mass to four digits
• Use Protein ID, instead of Protein
• add protein ID in peptide/site-level reports
• change column name (Proteins to Protein)
• bug fixing and other improvements

TMT-Integrator 2.4.0

• Fix an issue of using virtual reference
• Fix an issue of mod_tag

TMT-Integrator 2.1.15

• Allow the reference in different TMT channels
• Fix a bug of virtual channel

TMT-Integrator 1.1.10

• add a new filtering criteria: minimum allowed number of enzymatic termini (min_ntt)