pyVseq 0.6.1

• Handle plotting fragment ions for very large (>50 amino acids) sequences.

pyVseq v0.6.0

• Much faster reading of large MS data files
• MS data file index is only built if not already present
• Text encoding fixes
• New parameter: diagnostic_ions, default value 3 (Diagnostic ions to use per fragmentation series, from this ion to the end of each sequence)
• New parameter: intensity_percent_threshold, default value 0.01 (Remove peaks from MS2 spectra whose intensity is below this % of the maximum intensity)
• New parameter: keep_n, default value 15 (Keep the first n spectra sorted by sum of diagnostic ions intensity)

pyVseq v0.5.3

• Log MSdata file name
• Replace deprecated method for PDF creation

pyVseq v0.5.2

Vseq Viewer:

• Fix PTM pinpointing in y-series.
• Fix default config file path.
• Create output directory if it does not exist.
• Report sum of intensity of matched ions.
• If a "test_dm" column is present in the input file, it will override the experimental Δmass values.

MSFReader:

• Now extracts Δmass information.
• New argument: Decoy label ('-l', '--label', default="DECOY').
• New argument: Write combined table ('-a', '--all').

pyVseq v0.5.1

• Both Vseq and VseqExplorer are now faster.
• Fix positions of fixed modifications when a peptide contains more than two.

pyVseq v0.5.0

VseqExplorer:

• Accept mzML files as input.
• The infile argument now accepts wildcards (*) in the input path.
• Support for running with qsub job scheduler.
• Output directory now contains all generated files including logs.
• Nested directories will be generated as required by the output path argument.

Vseq:

• Added -n, --integrate parameter that will run ScanIntegrator.
• Experimental: Will attempt to shorten output paths that go over the Windows path length limitation.

Tools:

• MSFreader: More versions of ProteomeDiscoverer MSF files can be parsed.
• ScanIntegrator: Now a standalone tool that can be used from command line, or within Vseq.
  • Read config file (Vseq.ini).
  • Calculate variance, alpha, chi2 and p-value for fit.
  • Add int_matchwidth parameter (± Bins to match experimental and theoretical isotopic envelopes).
  • Skip input file if there are no scans to search.

pyVseq v0.4.2

• Update scan integration to work with new format.
• Create summary table with hyperscore, v-score, e-score and deltamass for all entries.
• Warn of duplicate entries in input table.

pyVseq v0.4.1

• Progress bars now update properly with every completed task.
• Added documentation (work in progress).
• Bug fixes.

pyVseq v0.4.0

• Add hyperscore to SCAN INFO table. Hyperscore is now available as a candidate sorting option.
• Replace minimum vscore parameter with vscore threshold parameter. The threshold is now applied to the criterion chosen to sort candidates by (ions_matched, e_score, product, v_score or hyperscore).
• Save error tracebacks to log file.
• Bug fixes.

pyVseq v0.3.1

• Faster mzML processing
• Faster matched ions calculations