3.3.1 released Feb 14, 2000

• Fixed problems with Finnigan LC/MS file importing.
• Updated the contact information.
• This is a full version available as FAT binary (which runs natively on both 68K and PPC processors). It does not have an expriation date.

3.3 released Jan 11, 2000

• Fixed a problem with demo registration number verification.
• This is a full version available as FAT binary (which runs natively on both 68K and PPC processors). It does not have an expriation date.

3.2 ß10 released Jan 1, 2000

• Fixed a bug preventing the display of the LC/MS peak data.
• Adjusted buffer sizes so that if results exceed 32K, at least the first portion of the data is displayed.
• Fixed word wrap display problems caused by the GUI modifications in 3.2b9.
• This is a beta version available as FAT binary (which runs natively on both 68K and PPC processors). It does not have an expriation date.

3.2 ß9 released Nov 17, 1998

• Made GUI modifications to circumvent a serious problem with system crashing under MacOS 8.5 (Note that this fix imposes a 32K limit on all text areas, so you may find that you need to clear search output to prevent running out of room.)
• Made improvements to the Finnigan MS/MS reading code.
• Added a tab-delimted option to the digest display for easier exporting to spreadsheets.
• Made improvements to the updating of sequences and digest after altering the crosslink setup.
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC

3.2 ß8 released July 26, 1998

• Modified the sequence window so that if a FASTA formatted sequence is pasted in or opened it will extract the header line and place it in the sequence's notes.
• Fixed a bug in the custom AA dialog that casued a crash when changing the AA set menu selection.
• Seletion of residues involved in internal crosslinks or crosslinked to other sequences which are connected to the first sequence by other crosslinks will now correctly account for the 'flow' into the unselected portion of the first sequence. (The mass may appear to be 18 Da. heavier than expected, but this is due to the hypothetical hydrolyzed bond at the end of the selection.)
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC processors) that will expire at the end of Jan, 1999.

3.2 ß7 released December 5, 1997

• Added the menus for the custom file pickers that were accidentally left out of the 3.2 ß6 release.
• Fixed a bug - which also exists in 3.1.1 - that caused Sciex negative ion files to be displayed as positive when importing.
• Fixed a bug in the Crosslinks dialog which was causing the wrong links to be deleted.
• Fixed bugs in the calculation of crosslinked digest fragments that caused crashing.
• Fixed bugs in how crosslinked sequence groups are saved.
• Redesigned the Potential Modifications dialog to fold in the custom modifications.
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC processors) that will expire at the end of July, 1998.

3.2 ß6 released October 7, 1997

• Fixed a 68K-specific bug in 3.2 ß5 that caused a crash when modifying the amino acid set.
• Added folder pickers to the More Options dialog to allow the user to set the default MS data folder and the default sequence folder.
• The digest fragments can now be displayed in a variable number of decimal places.
• Rearranged the open-ended search window controls in a more logical manner.
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC processors) that will expire at the end of April, 1998.

3.2 ß5 released August 10, 1997

• Fixed some crosslink inconsistancies.
• Revised the way custom amino acids work so that now ANY amino acid can be replaced by a custom amino acid.
• Made speed improvements to PepID and the openended sequence search.
• Added an option to allow PepID or openended searching of FASTA formatted protein databases (such as OWL).
• Added a mass fingerprint search option to the openended sequence search window.
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC processors) that will expire at the end of April, 1998.

3.2 ß4 released April 20, 1997

• The use of cross-correlation in MS/MS PepID analysis was replaced with a much faster intensity-based scoring system (ISCOR) due to patent issues. The ISCOR values will be different from the old XCORR values but the interpretation is qualitatively similar. More details on the new ISCOR method can be found in the documentation.
• Fixed some bugs (post 3.1) in the display of crosslinked digest fragments.
• Sped up the amino acid composition display in the sequence window.
• Fixed a problem (post 3.1) with pasting styled text into the sequence window.
• Fixed a problem where sequences with a space as the first character of the file name did not show up in the window menu. An initial blank is now replaced with an underline.
• Fixed a loophole allowing "foreign" characters in the sequence.
• Made the number of charge-states displayed in the digest window a user-definable parameter which can be set in the digest options dialog.
• Added an option in the MS/MS import dialog to limit the number of ions to the X most intense ions, where X is defined by the user.
• Use of the arrow keys to navigate in the sequence text editor no longer causes a recalculation of the sequence (post 3.1 problem).
• Added a z+2 ion option to the CID fragment ion calculation.
• Adjusted the CID display of the peptide sequence alongside the fragments up one position.
• "Save as Default" buttons in windows and dialogs were relabeled "Save Settings" to make their function clearer.
• "New Sequence" is now hotkeyed to cmd-N.
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC processors) that will expire at the end of August, 1997.
• (Version 3.1.1, also released on April 20, 1997, was a maintenance update to the full version 3.1 which contained the ISCOR change and other bug fixes.)

3.2 ß3 released February 10, 1997

• Fixed a bug (post 3.1) which could cause the program to crash when editing or creating custom modifications.
• Fixed some semantics of the seq. notes window to avoid losing unsaved changes when closing a seq. or quitting.
• Generally made text display less likely to cause buffer overflow crashes.
• Fixed a minor bug that caused the numbering of interal fragment ions to be low by one when getting details on a MS/MS Pepid match.
• The sequence window now displays the sequence and selection masses to four decimal places.
• Added CID options to display the peptide above the fragments or alongside the fragments.
• Made several other (hopefully) minor changes.
• This is a beta version (available as either 68K, PowerPC native, or FAT binary - which runs natively on both 68K and PPC processors) that will expire at the end of April, 1997.

3.2 ß2 released January 2, 1997

• Fixed a bug in 3.2 ß1 that caused peptides with N-terminal group names shorter than 6 letters to fail to display the peptide sequence when showing the digest fragments, openended search results, or MS/MS Pepid results.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of April, 1997.

3.2 ß1 released December 1, 1996

• Added an optional display of the elemental composition for the sequence or the sequence selection (Enabled in the More Options... dialog).
• Made the display of the amino acid composition optional (Enabled in the More Options... dialog).
• Existing custom amino acids and termini can now be edited.
• The digest charge-state display can now be configured to calculate negative ion m/z's.
• Added simple functions to the searches menu to calculate m/z's from a MW or MW's from an m/z.
• The sequence speaking routine were adjusted slightly and an option to change the pause length after every third residue was added (Adjusted in the More Options... dialog).
• CID ion prediction now includes the choice to use monoisotopic masses, average masses, or a switch mass. The displayed sequence will also wrap now if it is longer than 15 residues. These changes were made primarily to allow for calculation of MALDI in-source fragment ion masses.
• The reading of tab-delimited text MS/MS files is now buffered to speed up the import time.
• The importing of MacBioSpec sequences was improved so that modified residues/termini are recognized.
• The preferences file has been stabilized so that this version and all future versions will use the file called "Sherpa Preferences".
• Crosslinks within a sequence and between sequences can now be added and saved. The list of crosslink types is fully editable. The crosslinks can be included in the calculation of mass, elemental composition, and digest fractions. (They are currently not taken into account by the openended search, MS/MS interpretation, or by the secondary LC/MS searches such as glycosylation and phosphorylation.) The "Insulin [human]" file in the "Sample Sequences" folder provides an example of crosslinks.
• Custom amino acids, termini, modifications, and crosslinks can now include up to 6 different editable element types.
• Fixed some sequence text handling problems in the sequence window.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of April, 1997.

3.1 released December 1, 1996

• Fixed the c ion calculation so that it is calculating the c ion (Biemann nomenclature) [ C + 2 ion or C" ion (Roepstorff nomenclature)] instead of the C ion (Roepstorff nomenclature).
• Fixed a potential print bug when printing digests.
• Fixed the printing loop so that it displays the title of the document being printed instead of calling every document "unknown".
• Fixed a printing bug with sequences whose lengths were one greater than a multiple of 75.
• Fixed motif length display bug in the user-def. modifications header.
• Fixed a potential looping display bug in the routine that gives user-def. modification specifics in the search header.
• Fixed an occassional sequence window linkage bug.
• Fixed a problem causing an annoying recalculation / display update when switching between sequence windows.
• This is the first full (non time-limited) version of Sherpa (available as either 68K or PowerPC native) .

3.0.10a ß released September 4, 1996

• Fixed a bug in the openended sequence search (which is also the front end of the MS/MS Pepid search) that sometimes was not identifing all posibilities when searching multiple charge states. This was due to it quitting the search when a large mass (from a higher charge state) was too big to be found in the remaining bit of sequence to search, thus a smaller mass (from a lower charge state) might not get a chance to be compared to the whole sequence. This bug existed as far back as version 3.0.8 ß. The correction of this bug is the only difference between version 3.0.10 ß and version 3.0.10a ß.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of December, 1996.

3.0.10 ß released August 1, 1996

• A box displaying the amino acid composition of the sequence or of the sequence selection was added to the sequence window.
• An optional display of the estimated isoelectric point (pI) of the sequence was added to the sequence window. (Enabled in the More Options... dialog).
• An optional display of the estimated molar extinction coefficient at 280nm for the sequence was added to the sequence window. (Enabled in the More Options... dialog).
• An option to display the C18 (0.1% TFA) HPLC index for digest peptides was added to the digest window. (Enabled in the new Digest Display Options dialog accessable from the digest window).
• Fixed a bug in the way that modifications and multi-line sequences in the Pepid results were handled when getting details.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of December, 1996.

3.0.9 ß released June 5, 1996

• The user can now create and store their own custom modifications which can be considered in the open-ended & pepid searches.
• Fixed a bug in the open-ended search (which is also the front end of the pepid MS/MS search) where it was not considering all modification possibilities.
• Added more modification options to the open-ended/pepid searches.
• Added more fragment ion types (including high energy fragments) to the CID fragment ion prediction function. (Which ion types are displayed is set in the "CID..." dialog.)
• Added buttons to most windows & dialogs to allow the user to save the current settings as the default or to set the window's settings to the program default values. This allows more localized control of the preferences as opposed to using the "Save Preferences" menu option which saves the the settings of all windows & dialogs at once.
• Added more elements to be used in creating custom termini or amino acids.
• Added a save warning option (set in the More Options... dialog) to ask if the user wants to save a sequence if it is being closed or the program is being quit and the sequence has unsaved changes.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of August, 1996.

• Faster open-ended and pepID searches. The speed gain increases significantly with the mass being searched.
• Added a single amino acid substitution option for both the open-ended and pepID searches. It allows one residue per peptide to be mutated to any other residue. (This option is not additive with other modifications and should generally be used sparingly and with its two consensus termini contraint option to avoid huge numbers of possibilities.)
• Added a full sequence display option for the theoretical digest peptides displayed in the digest window. Open-ended and pepID search results are also now displayed in this format which wraps the sequence in twenty-five residue blocks.
• Fixed open-ended search sorting bug.
• Fixed a rare but potentially lethal bug in LC/MS importing.
• Improved the application's performance in situations where it is running low on memory
• Added support for importing MS/MS data from tabbed text files. This means that MS/MS files in any format not currently supported natively can be imported by saving the raw data in a text only format where each line of the file is an m/z value followed by a tab and then its corresponding intensity.
• Added support for importing Sciex API 100/300 MS data files.
• Activated the phosphorylation search's indicator ion confirmation option.
• Fixed a problem which caused program crashing on systems without an FPU.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of August, 1996.

• Improved printing routines including special formatting for printing sequences and digests. Print paramters are now saved with documents.
• Revamped the Peptide Match ratings. There are now just two categories: "probable peptide matches" (matches made to ion groups) and "possible peptide matches" (matches made to single ions). Experimental observations did not show a significant difference in reliability between matches of categories 1 and 2 in the old system.
• Fixed a flag bug in the ion grouper which could cause mistakes by the unidentified ion and file comparison routines.
• Removed sorting bug in common unidentified ion output.
• Fixed a bug in the open-ended search where more than 2 termini were sometimes reported when using the modification options.
• Relaxed the N&O-linked rating categories in the glycosylation search.
• Made several other minor changes and fixed including new icons.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of June, 1996.

• Added a routine to remove fractional mass MW groups (e.g. if it finds a MW group with charge states +2, +3, +4 it wont report the +2 and +4 ions as a +1, +2 pair at half the mass.)
• Fixed potentially lethal probem in the MS/MS PepID cross-correlation.
• Fixed potential memory overflow problem in the display of MW groups, glycosylation results, and phosphorylation results.
• Added option to sort MW group output by scan or by mass.
• Fixed glycosylation step linkage problem for MW groups.
• Added a smoothing option to the LC/MS import dialog.
• Fixed a problem where LC/MS files were not being closed properly.
• Fixed cursor placement bug when pasting in the sequence editor.
• Fixed bug in updating of the digest type in the digest window.
• Made several other minor cosmetic/behavior changes.
• Fixed problem where Sherpa was unable to see certain Finnigan files. Added file type 'BINA' to the file type '????' (unknown) as an acceptable file type for Finnigan MS files. (Retrieving files by FTP using Telnet sets the file type to 'BINA' while using Fetch to FTP them leaves the file type as '????'.) If the file is not set to one of these two types it will not be viewable in the import dialogs.
• This is a beta version (available as either 68K or PowerPC native) that will expire at the end of Feb, 1996.

• Fixed CNBr fragment bug
• Fixed MW Grouper bug / streamlined the MW Grouper
• Fixed MW Grouper sorting bug
• Added a % of MW error tolerance option to the MW Grouper dialog.
• Added cross-correlation scoring option for PepID based on Eng et al. 1994.
• Redesigned the new custom AA/termini dialog:
  • Added arrow controls
  • Added an 15N option
  • Added a menu of the 20 std. AA's which can be used as a starting point
  • Added an instantaneous composition display
• Worked out the Finnigan format so Finnigan ESI LC/MS and MS/MS files can be read. However, this version is still truly beta in this regard.
• Centroided data is now treated differently than profile data.
• Added a user override mode to the LC/MS and MS/MS import dialogs to allow the user to change the positive ion/negative ion and profile/centroid flags.
• Fixed bugs in the Phosphorylation searches/ made improvements in the Phosphorylation searches.
• This is a beta version that will expire at the end of Feb, 1996.

• Initial public release in Aug., 1995. All previous versions were internal.