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CHANGELOG.md

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1.10.27 - 2024-05-29

  • Require Java 11+
  • Calculate intensity and MaxLFQ intensity for MS1 labelling-based quantification
  • Fully support MSstatsPTM
  • Generate site reports even when there is no PTMProphet site localization information
  • Add DiLeu-12 in the isobaric labeling list
  • Support both PeptideProphet Probability and Probability column names
  • Add --msstats tag
  • Set the default value of 'minions' (minimum number of ions) to 1 (MaxLFQ normalization options)
  • Minor improvements in the MBR mixture modeling module
  • Significantly improved the speed of loading Thermo raw files
  • Various bug fixes and improvements

1.10.12 - 2023-12-19

  • Add support for multiple ranks per scan
  • Add support for isobaric labelling. Add several new flags for isobaric labelling quantification.
  • Significantly improve the ddaPASEF .d loading speed
  • Propagate modification localization info to LFQ MSstats files
  • Add --perform-ms1quant and --site-reports flag
  • Add combined_site_ before the site report file name
  • Make the MBR ion probability threshold always >= 0.5
  • Do not generate N/C-term modification site report
  • Remove LC-MS file checking
  • Various bug fixes and improvements

1.9.8 - 2023-05-31

  • Add MBR support for the MS1-based label quantification
  • Support fractionated data for the MS1-based label quantification
  • Add apex RT, CV, and IM columns to combined_ion.tsv file
  • Add match type column to some tsv files
  • For FAIMS data, ion = peptide + charge + cv
  • Print the number of transferred ions to console
  • Big improvement on the LDA and mixture distribution modeling
  • Overhaul the indexing of PSM, ion, peptide, and protein
  • Improve the min scans filtering criteria
  • Improve the isotope distribution filtering criteria for MBR
  • Various bug fixes and improvements

1.8.10 - 2023-01-12

  • Fix a crash when the first scan number is a big value
  • Various minor bug fixes and improvements

1.8.9 - 2022-12-03

  • Require Java 9+
  • Write compensation voltage to ion.tsv
  • Add --modlist parameter to take a list of mod masses to reduce the discrepancy issue
  • Set the default value of --mbrtoprun to 10
  • Change the default value of --minexp to 1
  • Change the default values of --tp and --minfreq to 0
  • Change the total intensity from the average of non-zero values back to summation of all isotopic intensities
  • Do not write entries from the contaminant proteins to the reprint reports
  • Print an error message when there are more than one run in an experiment for label quantification
  • Various minor bug fixes and improvements

1.8.0 - 2022-05-27

  • Require Java 9+
  • Generate combined_ion_label_quant.tsv, combined_modified_peptide_label_quant.tsv, and combined_protein_label_quant.tsv
  • MSstats.tsv supports label quant
  • No longer require pepXML files
  • Various minor bug fixes and improvements

1.7.17 - 2021-11-16

  • Improve the logic of picking input spectral files from the folder
  • Change an error message to warning
  • Various minor bug fixes and improvements

1.7.16 - 2021-10-30

  • Generate combined_ion.tsv, combined_modified_peptide.tsv, and combined_peptide.tsv
  • Generate modification site reports
  • Add locprob flag to control modification probability threshold (require running PTMProphet beforehand)
  • Retire proteinquant flag. Add maxlfq flag.
  • Make MSstats.csv support label quant (e.g., SILAC). If there are mixture of light and heavy in on peptide, using NA for the intensity
  • Always write top-N intensity to protein report. Write MaxLFQ intensity when maxlfq=1
  • Always use minions=1 for top-N intensity
  • Support using quantindex file as input
  • Check the integrity of quantindex file before reading it
  • Improve the total intensity calculation
  • Increase the allowed gap of modification mass correction to 4 Da to support the PTM-Shepherd's glycan list
  • Improve the total intensity calculation by taking the average of non-zero values to remove the effect due to different isotope counts
  • Upgrade some libraries
  • Various minor bug fixes and improvements

1.7.5 - 2021-07-22

  • 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.

1.5.5 - 2021-03-02

  • Add high-field asymmetric waveform ion mobility spectrometry (FAIMS) support.
  • Remove log10(KL_negative_1), log10(KL_negative_2), log10(intensity) diff, correlation between runs, matched run percentage scores to make the LDA modeling more robust.
  • Improve mixture distribution modeling.
  • Add minscans parameter.
  • Improve peak tracing with resampling and Savitzky–Golay smoothing.
  • Substract background noise from the intensity.
  • Improve the normalization to be more robust.
  • Generate protein_label_quant.tsv.
  • Use log-ratio median to normalize peptide and protein log-ratios in label quantification.
  • Always use minions = 1 for the top-N protein intensity calculation algorithm (proteinquant = 1).
  • Using the log-ratios within [-log2(1.5), log2(1.5)] to perform normalization in label quant.
  • Suppress a warning due to a bug in Philosopher.
  • Various bug fixes and improvements.

1.4.6 - 2020-11-09

  • Don't stop when there is a protein with no PSM. When protein FDR threshold is 1, there may be proteins with no PSM passing 1% PSM FDR.
  • Change O's mass to 255.15829.
  • Remove a randomness from the algorithm.

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.