For complete list of released files, please visit the DIA-Umpire GitHub site. Old releases are in the SourceForge site.
Latest user manual: DIA_Umpire_Manual_v1.4_pre.pdf
06/03/2016 (v2.1) Releases
- Reduced memory usage
- Reduced program execution times
- Added checks for missing input files
- No longer dependent on indexmzXML
- <scan> tags offsets are inferred, not parsed from <index> element
- Quant module no longer writes files to the directory of the JAR
- Those files are written to the working directory
- Safe to run multiple instances of Quant concurrently
- Binary compatibility with earlier versions broken
- Old binary files generated no longer work for this version
- SE module unaffected
04/24/2016 (v2.0) DIA-Umpire_v2_0.zip
- Data set level FDR estimation
- Isotope pattern filter added (feature detection)
- Fractional mass filter added (feature detection)
11/20/2015 (v1.4273) DIA-Umpire_v1_4273.zip
- Improved algorithm for feature detection
- Some known bugs fixed
8/16/2015 (v1.4254) DIA-Umpire_v1_4254.zip
- Some known bugs fixed
6/1/2015 (v1.4) DIA-Umpire_v1_4.zip
- New feature – option added to search peptide ions from an input external spectral library. DIA-Umpire currently accepts external libraries in TraML format (normalized retention time is required). Only those peptide ions from the external library will be searched that satisfy the following condition: they were not identified by the initial untargeted database search, or the identification probability was lower than the specified threshold described below.
Please note that this feature is still being tested.
- Feature detection:
- The criteria of defining true features were tuned for Thermo QE and Fusion data to improve feature detection sensitivity.
- Option added to allow features with no other isotope peaks detected. The user needs to specify the minimum isotope number as 1 in the input file (signal extraction parameter): SE.MinNoPeakCluster = 1. For such cases, the program assumes all possible charge states (from StartCharge to EndCharge, as specified in the input file) as different feature entries. Their corresponding pseudo MS/MS spectra are printed in the Q2 tier output file.
- Precursor-fragment grouping:
- Extended the search for fragment peaks to adjacent isolation window if the precursor feature’s m/z is located near the isolation window boundary. The algorithm searches for fragment peaks in the neighboring isolation window that may include the second or the third isotope of the precursor ion.
- Now allow the user to disable deisotoping and adjustment of fragment intensities by setting the following parameters to “false” (signal extraction parameters).
- Targeted extraction
- Internal spectral library is now built using TopN fragments using the fragment selection algorithm described in the DIA-Umpire manuscript (all matched fragments were used in the previous release)
- Use only decoy hits for the target peptide ions that are searched at the targeted re-extraction step. This is done to better estimate the kernel density of the negative distribution in the mixture modeling step (previously all decoys including those corresponding to the already identified ions were used)
- Fragment peak filtering is now also applied during targeted re-extraction search step
- RT search window is estimated by considering the variation of predicted RTs versus observed RTs in a local RT region (3 * sd : 99%)
- Sub-scores updated
- Compatibility updates -
- PepXML parser updated to parse probabilities reported by Percolator
- Performance updates -
- Replace custom sorted arrays by KD tree to improve performance of searching peaks / peak clusters given m/z and retention time ranges.
- Update Java Serialization library – FST from v2.05 to v2.24
1/17/2015: First release version (v1.284) DIA-Umpire_v1_284.zip
- Memory footprint reduced for quantification module
- Improved sensitivity of feature detection for shorter eluting signals
- Modification tags changed
- Bugs fixed
- Spectral similarity score for targeted re-extraction has been replaced by dot-product score
- Mixture modeling for targeted re-extraction has been changed from Gaussian-mixture to the semi-parametric mixture model as previously described in Choi et al. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling, Journal of Proteome Research, 2007
1/17/2015: The version at the time the manuscript was accepted (v1.25) DIA-Umpire_v1_25.zip
- Java 7 or higher: Java SE Runtime Environment 7.