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CHANGELOG.md

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1.7.5 - 2020-07-22

  • Require Philosopher 4.0.0+.
  • Support library and lib keywords in the experiment names to recognize library runs. Library runs will always be used as donor runs.
  • Support prmPASEF.
  • Disable MBR when there is only one run.
  • Change the default value of mbrtoprun to 100000.
  • Add filelist flag to bypass command length limitation in Windows.
  • Various minor bug fixes and improvements.

1.4.4 - 2020-09-29

  • Supporting SILAC and other isotopic labeled data.
  • Print more information about match-between-runs.
  • Add --writeindex to write index to disk for further usage.
  • Add --spectraldir option to take spectral files' directories as input.
  • Add --excludemods option to exclude certain modifications in protein quantification.
  • Add --minexps option.
  • Change the default value of --proteinquant to 2.
  • Change the default value of --mbrmincorr to 0 and use > for it.
  • Change the default values of --proteinfdr and --peptidefdr to 1.
  • Change the default value of --requantify to 1.
  • Change the default value of --mbrtoprun to 10.
  • Changing --proteinquant to 1 and --minexps to 1 if there are less than 3 experiments.
  • Implement a module writing combined_protein.tsv from scratch.
  • If the experiment names do not have _, using <exp>_<expIdx> instead.
  • Upgrade timsTOF data reading API to 2.7.0.
  • Various bug fix and optimization.

1.3.0 - 2020-06-05

  1. Implement the MaxLFQ protein intensity calculation algorithm. Add --proteinquant 1/2 to control the used algorithm.
  2. Add a Pearson correlation coefficient to measure the similarity of light and heavy RT-intensity profile in label quantification.
  3. Add more info to label quantification output.
  4. Change > minFreq to >= minFreq
  5. Various bug fixes and improvements.

1.2.0 - 2020-05-21

  1. Support non-timsTOF (e.g., Orbitrap) data.
  2. Support match-between-runs.
  3. Support match-between-runs' ion, peptide, and protein level false discovery rate control.
  4. Support isotope labeling based quantification. (beta)

1.1.0- 2020-05-15

  1. Add new parameters.
  2. Make the quantification more accurate.
  3. Various bug fix and optimization.

1.0.0 - 2020-04-24

  1. The first version after renaming IMQuant to IonQuant.