1.11.11 - 2025-06-30

1.11.9 - 2025-05-03

Require Java 11+
Support the timsTOF ddaPASEF isobaric-labeling quant
Add TMT 35-plex support
Add the chemical formula support to the isotopic label quant with the --formula parameter
Significantly improve the quantification accuracy and precision
Significantly optimize the memory footprint for indexing
Refactor the index writer to make it faster
Write the peak resolution and noise to the psm.tsv for the isobaric labelling
Write apex RT and IM, fwhm RT and IM, and traced scans to ion.tsv and combined_ion.tsv
Write detailed RT and IM information to psm, ion, and combined ion tables
Write traced scans, apex scan number, and parent scan number to PSM tables
Write peptide start, end, prev AA and next AA to label quant tables
Add “Intensity “ prefix to the TMT channel intensity column names
Various bug fixes and improvements

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

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

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

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

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

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.

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.

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.

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.

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

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