SHIFTS v0.5.1

Fix a bug that would cause some missing Global and Local FDR values even if these FDRs were applied to all PSMs.

SHIFTS v0.5.0

Changes to PeakFDRer:

• Removed parameter peak_outlier_value. Peak FDR is now only calculated applied to PSMs that have been assigned to a peak. Orphan PSMs will contain missing values for Peak FDR and will not be affected by the Peak FDR filter.

• Added parameter localFDR_to_orphans_only (default value = false). If set to true, PeakFDRer will calculate and apply the local FDR threshold to orphan PSMs only. PSMs assigned to a peak will not be used nor affected by this filter.

• Added parameter globalFDR_to_orphans_only (default value = false). If set to true, PeakFDRer will calculate and apply global FDR threshold to orphan PSMs only. PSMs assigned to a peak will not be used nor affected by this filter.

SHIFTS v0.4.4

• Configuration file: Default value of peak_outlier_value is now 0

SHIFTS v0.4.3

• Change the name of PeakSelector folder. Move the program to root folder

Full Changelog: v0.4.2...v0.4.3

SHIFTS v0.4.2

The last changes for SHIFTS, a battery of programs for high-throughput PTM (Post Translational Modifications) processing.

Full Changelog: v0.4.1...v0.4.2

SHIFTS v0.4.1

PeakModeller: Fix error when creating log file

SHIFTS v0.4.0

• SHIFTSadapter, DuplicateRemover, DMcalibrator, PeakModeller: The infile argument now accepts wildcards (*) in the input path.
• PeakSelector: The number of decimal places in the apex list can now be controlled with the decimal_places parameter.

SHIFTS v0.3.2

• Remove recom_mod_peptide_column param
• Bug fixes

SHIFTS v0.3.1

RECOMfilterer

• New corr_xcorr parameter to calculate corrected xcorr.
• Decoy prefixes can now be any length.
• Add RECOMfiltered MH and sequence to output.

PeakAssignator

• New recom_mod_peptide_column parameter (Name of column containing Recom sequence with deltamass in XXX[DM]XXX or XXXXXX_DM format).
• Assigned sequence now takes into account Recom mod. position if applicable.

PeakFDRer

• Separating PeakFDRer output according to the batch table is now optional.
• experiment_table command line option is now called batch.
• New BatchSeparator module.

SHIFTS-4 v0.3.0

• PeakModeller is significantly faster
• Decoy and Target score thresholds removed from RECOMfilterer
• PeakFDRer will warn about scans that don't belong to any group in the Experiments Table