CHANGES.txt

v.0.5.0
---
* Added support for MS3-based TMT quantification
* Added additional contaminant matrices for TMT 10-plex and 16-plex
* pyTMT now uses pymzml v.2.5.2 to read mzML files

v.0.4.3
---
* Minor bug fix
* Corrected standalone mass for TMT 16-plex 133C

v.0.4.2
---
* Added function to collapse individual peptide TMT intensities into protein TMT intensities
* Added options to determining parsimony groups in collapsing peptide data into proteins
* Added option to separate proteins into light and heavy groups based on SILAC labels
* Patching standalone percolator

v.0.4.1
---
* Added support for TMT 18-plex
* Added non-negative least square method for contamination correction

v.0.4.0
---
* Pytmt now supports TMT contaminant correction.
* Added support for TMT 16-plex


v.0.3.5
---
* Pytmt now reads the percolator output log file from crux to assign mzML files to Percolator file_idx
* When no log file is present, Pytmt falls back on the old method of ordering mzML files by file names

v.0.2.8
---
* input changed from specifying percolator directory to percolator file path
* added preliminary support for standalone percolator output (psms)