• Hidden parts of the forms or output were displayed whilst they were loading.
• The pre-search parameter which dealt with results from another search had menu items for batchtag and msmatch. These have now been removed.
• Decoy accession numbers are now put in square brackets in Search Compare tab delimited output so they sensibly displayed in Excel. The word "decoy" is put in the gene name column for such entries in such reports.
• Hit numbers are now put in square brackets in Search Compare tab delimited output so they sensibly displayed in Excel.
• Usermod entries in the quan.txt file could not have non-isotopic elements in their delta formula.

• mshome.htm
• html/peakSpotter.htm
• html/wiffread.htm
• html/images/fragtag.gif deleted
• html/images/wznowsma.gif deleted
• html/instruct/allman.htm
• html/instruct/batchtagman.htm
• html/instruct/bridgeman.htm
• html/instruct/compman.htm
• html/instruct/dbstatman.htm
• html/instruct/digestman.htm
• html/instruct/faman.htm
• html/instruct/fitman.htm
• html/instruct/homologyman.htm
• html/instruct/isoman.htm
• html/instruct/nonspecificman.htm
• html/instruct/patternman.htm
• html/instruct/prodman.htm
• html/instruct/seqman.htm
• html/instruct/servadmn.htm
• html/instruct/tagman.htm
• html/js/info.js
• html/misc/bughist.htm
• html/misc/faq.htm
• html/misc/invar.htm
• html/misc/links.htm
• html/misc/publications.htm
• html/misc/revhist.htm

• Quantitation in Search Compare/MS-Display didn't work if there was a mass modification. It now gives an answer. Any answers given should be checked manually.
• FA-Index hung when sorting the accession numbers for the dbEST.human database.
• Fixed the following problems with Search Compare tab delimited multi sample reports:
• Sample number now a column in peptide reports.
• Uniq pep column now available in peptide reports.
• Header not printed if there were no results to report in the first sample.
• Whether the Uniq Pep column is included in the report depends on whether any of the hits had homology hits. However this was previously done on a per fraction basis so the columns could potentially not line up. Now the column is included if any of the fractions have homology hits.

• params/dbest.spl.txt

• mshome.htm
• html/images/unknome.gif deleted
• html/instruct/faman.htm
• html/instruct/servadmn.htm
• html/instruct/tagman.htm
• html/js/info.js
• html/misc/revhist.htm

• Batch-Tag searching sometimes failed on LINUX versions. This was thought to be because some peaks in the centroid file had exactly the same M+H (not m/z) value. Replacing a sort with a stable_sort seemed to get rid of the problem.
• FA-Index hung when sorting the accession numbers for the dbEST.others database.
• The User Protein Sequence option on the Create or Append to User Database form on the FA-Index page had some instructions that needed correcting slightly.
• The User Protein Sequence option on the Create or Append to User Database form on the FA-Index page accepted characters that weren't amino acids (eg numbers).
• Search Compare crashed if the peptide sequences contained numbers. This shouldn't happen but see the bug above.

• mshome.htm
• html/instruct/servadmn.htm
• html/misc/bughist.htm
• html/misc/revhist.htm

• There was a problem with Batch-Tag if Windows was used as the web server with LINUX compute nodes and an mgf file without a .mgf suffix was uploaded.
• Incorrect font used for the error message if an invalid user modification is used.

• params/info.txt
• params/links.txt
• params/mgf.xml
• params/usermod.txt

• mshome.htm
• html/instruct/servadmn.htm
• html/js/info.js
• html/misc/bughist.htm
• html/misc/revhist.htm

• Search Compare protein report Uniq Pep column sometimes had negative numbers if Keep Replicate Peptides was selected. This also meant too many homologous proteins were retained.
• Search Compare Num Unique column gave incorrect values if Keep Replicate Peptides was selected.
• Messages are now printed out during quantitation either every time a peptide is processed from the raw file or every 10 seconds, whichever is the longer time. This was to get around a problem with Apache timing out (which it does after 5 minutes of inactivity) when there was a problem with a slow wiff file. Occasionally wiff files are very slow to process when they are on a network drive. The cause of this presently unknown.
• Link to Batch MSMS Searching manual missing.

• params/acclinks.txt
• params/dbest.spl.txt
• params/disc_hist.par.txt deleted
• params/elements.txt
• params/expectation.txt
• params/immonium.txt deleted
• params/indicies.txt
• params/info.txt
• params/itraq.txt
• params/itraq8.txt
• params/mat_score.txt
• params/novo_graph.par.txt deleted
• params/quan.txt
• params/unimod.txt
• params/usermod.txt
• params/batchtag/default.xml

• mshome.htm
• html/instruct/homologyman.htm
• html/instruct/servadmn.htm
• html/js/info.js
• html/misc/revhist.htm

• Batch-Tag searches that were aborted before they started weren't being properly cleaned up until the daemon tried to start them.
• There were missing columns in Search Compare tab delimited reports if the previous and next amino acid were reported and more than one search were compared.
• Search Compare comparisons peptide reports of quantitation data sometimes crashed.
• The parameter max_btag_searches, defined in params/info.txt, had a default value of zero rather than one.
• If Batch-Tag/MS-Tag mass modification searches were done with constant modifications set then the mass modification was reported relative to the constant modification rather than the unmodified amino acid. This also caused problems if the match was viewed in MS-Product

• If the Batch-Tag Service on the Windows version was installed using btag_daemon rather than btag_daemon.exe on the command line it was installed with the wrong name.
• If a Batch-Tag search fails for any reason the user isn't informed about the reason.
• If a Search Compare report shows no results the search parameters aren't printed.
• If a the Default search page is used on an existing project then the instrument is always set to ESI-Q-TOF.

• Search Compare reports which took longer than 5 minutes to generate activated an Apache timeout. This has been solved by printing progress messages.
• Performance problem with network drives due to flushing the output buffers too much when writing out Batch-Tag results files.
• An error message is now printed if unknown elements are used in MS-Isotope.
• There was a problem if both variable and constant N or C terminal modifications were used at the same time (eg iTRAQ N-terminus and Acetyl N-terminus).
• There was a confusing error message given if command line arguments weren't properly specified (eg when running FA-Index from the command line).
• There were some problems with CNBr searches.

• Neutral loss modifications couldn't be combined with other modifications.
• The Batch Tag daemon isn't started the first time it is used.
• There was no check to see if the same modification is set as a constant and a variable modification.
• Carbamidomethyl C was set as both a constant and default modification on the default Batch-Tag form.
• In MS-Product matched masses weren't shown in red in the immonium ion and theoretical spectrum tables.
• If the precursor charge was reset in MS-Tag from File the new charge wasn't passed through to MS-Product.
• The root user was able to create projects.
• Quantitation ratios were not being calculated for peptide where the modification name had a dash character (eg. Gln->pyro-Glu).
• Quantitation ratios were not being calculated for cases where one of the peaks had no data in the area where the peak was expected.
• A lot of memory was being used up in the quantitation ratio calculate by using deque instead of vector. This appears to be a bug in the Visual C++ compiler.
• The maximum MSMS peak setting on Search Compare wasn't being passed through to MS-Product and MS-Tag from File.
• Some printing problems have been resolved.
• Peptide hits with expectation values below the expectation value limit were being rejected as there was another peptide with an expectation value above the limit but with a better disciminant score. This generally occurs when both hits are correct due to coeluting peptides.
• Problem with discriminant scoring for the ESI-FT-ICR-CID instrument.

• batchtag/default.xml, deleted variable mod Carbamidomethyl C.
• disc_score.txt
• disc_score2.txt
• instrument.txt
• elements.txt - Hg added.
• instrument.txt
• usermod.txt - Carboxy (W), Cation:N(1)H(4) (Neutral Loss), Delta:H(2)C(3) (K), Delta:H(4)C(3)O(1) (CHK), Delta:H(4)C(6) (K), Delta:H(6)C(6)O(1) (K), Delta:H(8)C(6)O(2) (K), Dioxidation (W), GluGlnIleGlyGly (K), HNE (CHKPRT), HNE+Delta:H(2) (CHKPRT), HNE-Delta:H(2)O (CHKPRT), Label:13C(6)15N(2)+GluGlnIleGlyGly (K) added.

• mshome.htm
• default.htm
• index.htm
• missing.htm
• html/pform.css
• html/instruct/allman.htm
• html/instruct/batchtagman.htm
• html/instruct/bridgeman.htm
• html/instruct/compman.htm
• html/instruct/dbstatman.htm
• html/instruct/digestman.htm
• html/instruct/faman.htm
• html/instruct/fitman.htm
• html/instruct/homologyman.htm
• html/instruct/isoman.htm
• html/instruct/nonspecificman.htm
• html/instruct/patternman.htm
• html/instruct/prodman.htm
• html/instruct/seqman.htm
• html/instruct/servadmn.htm
• html/instruct/tagman.htm
• html/java/SpectrumGraph.jar
• html/js/info.js
• html/misc/bughist.htm
• html/misc/dipep.htm
• html/misc/faq.htm
• html/misc/invar.htm
• html/misc/links.htm
• html/misc/mutation.htm
• html/misc/publications.htm
• html/misc/revhist.htm
• html/misc/trypsin.htm

• html/print.css

• Quantitation doesn't work on high resolution data.
• Some very intensive searches can run out of memory (eg No enzyme combined with mass modifications) can fail especially if the first protein in the list is a heavy one.
• Average mass searches in MS-Fit don't work properly.

• There was a problem processing multiple spectra with programs using MS data, such as MS-Fit and MS-Bridge.
• There were sometimes problems when one of the peaks of a quantitation pair was so weak that the peak fitting failed. If the first guess of the intensity divided by the noise standard deviation is less than the signal to noise threshold or there are no samples in this area of the spectrum an intensity of zero is now assumed.
• Error now printed if sample can't be extracted from a wiff file.
• Error now printed if spectrum can't be extracted from a wiff file.
• The code that deleted old temporary files didn't work properly in October. This led to temporary files not being deleted.
• Uniprot comment lines weren't correctly written out when using the Create or Append to user database feature in FA-Index.
• Font colour wasn't correctly specified in coverage maps, the abort search button and the coloured background used for multiply charge ions in MS-Product.
• The amino acid N was erroneously listed as a protonation site for some instruments.
• An error message is now printed if a time comparison report of two different projects is attempted.
• The parent ion tolerance units can't be changed after a project has been calibrated.
• Signal to noise ratio calculations wrong for TOFTOF iTRAQ data.
• If an R image fails to draw for some reason the rest of the report is now generated.
• The Search Compare links to MS-Product reports from mzXML results don't work.
• Batch Tag no enzyme searches sometimes fail if the N-terminus is heavy (eg 8 plex iTRAQ).
• There were sometimes problems doing quantitation on calibrated data.
• Batch Tag/Search Compare don't work with DNA or EST databases.
• MS-Digest doesn't work with Protein converted DNA databases.
• It is possible to create a project with the same name using Batch-Tag and Batch-Tag Web. These projects interfere with each other.
• In a multi-sample report the fractions are sorted alphabetically rather than numerically.
• Search Compare can run out of memory when processing very large searches.
• There are problems if the m/z values in an mgf file aren't sorted into m/z order.
• In MS-Bridge hits which only contained a single unlinked peptide and which contained the link amino acid weren't displayed.
• The Hide HTML links tick box didn't work in MS-Bridge and MS-NonSpecific.

• deleted batchtag/params_big.xml, batchtag/params_nuc.xml, batchtag/params_nucf1.xml, batchtag/params_pa.xml, batchtag/script.xml and batchtag/sprot_default.xml.
• const_mod.txt - iTRAQ8 Lys, Acrolein56 Modified Cysteine and Dimethyl Acrylamide Modified Cysteine added.
• disc_score.txt
• enzyme.txt - CymostrypsinFWYMEDLN added.
• enzyme_comb.txt - Trypsin DE-N, CNBr/Arg-C, CNBr/V8 E, CNBr/Arg-C/V8 E and CNBr/Lys-C/V8 E added.
• homology.txt - Formyl N Terminus added.
• imm.txt - masses in this file adjusted for electron rest mass.
• info.txt.
• instrument.txt - changes to positively charge bearing amino acids, some defunct calibration parameters removed.
• n_terms.txt - Carbamidomthyl changed, Formyl and iTRAQ8 added.
• quan.txt - 'SILAC NC of L and SILAC R' and iTRAQ8 added.
• usermod.txt - Oxidation of M, Carbamidomethylation of MHK, Carmbamylation of SILAC_NC K, Acetyl-met1 of K, Acetyl-met2 of K, Ubiquitination of SILAC K, Ubiquitination of SILAC_NC K, Ubiquitination2 of K, Carbamidomethylation of KHMED, Methylation of E, Dioxidation of M, Oxidation of W, Nedd8_LysC of K, Ubiq_LysC of K, Lysine Formylation and Tyrosine oxidation to 2-aminotyrosine added.

• batchtag/default.xml.
• disc_score2.txt.
• expectation.txt.
• expectation.xml.
• genelinks.txt.
• itraq.txt.
• itraq8.txt.

• mshome.htm
• default.htm
• index.htm
• html/wiffread.htm
• instruct/allman.htm
• instruct/dbstatman.htm
• instruct/faman.htm
• instruct/homologyman.htm
• instruct/instaix.htm
• instruct/instnti.htm
• instruct/instunix.htm
• instruct/servadmn.htm
• js/info.js
• misc/invar.htm
• misc/revhist.htm

• images/folder.gif

• Script init.R split into two files, initargs.R and initgraph.R.
• New R scripts expectationDensity.R, peptideDensity.R, scatterSurvival.R and quan.R.
• Modified R script msmsErrorScatter.R.

• Modified Perl script mssearch.pl.

• Sequence and charge displayed at the top of the page.
• Small form allowing the sequence to be resubmitted with a modified sequence, a different fragment ion tolerance, more peaks or a modified maximum fragment charge. This is useful for helping to locate the position of post translational modifications.
• Parts of report are now contained in expandable blocks.
• Font smaller in report.
• Error plot slightly smaller

• Min digest fragment length option didn't work properly on MS-Digest/MS-Bridge.
• For some instruments (eg Q-STAR) MS-Bridge/MS-NonSpecific/MS-Seq/MS-Tag didn't allow pasted peak lists with a small number of peaks as there was a mimimum number of peaks specified for different instruments. Now the peak filtering options have been disabled for pasted peak lists for both MS and MSMS data.
• Maximum hits default in Batch-Tag and MS-Tag changed from 20000 to 2000000. The old value sometimes caused problems with Batch-Tag searches.
• The code that deleted old temporary files didn't work properly in July. This caused a problem with MS-Product as for this reason it wasn't able to display the error graph.

• elements.txt - lithium added.
• instrument.txt - high energy ion types removed from TOFTOF settings.
• species.txt - added GLYCINE MAX and HUMAN ADENOVIRUS 5.
• usermod.txt - added Tyrosine oxidation, DiMethylation of R, Methylation of H, Formaldehyde adduct and Hydroxymethyl.

• mshome.htm
• revhist.htm

• msmsErrorScatter.R
• init.R

• There is now a link to Peak Spotter from the home Prospector page.
• Most of database queries changed over to SELECT queries so there is no need to change the database installation now. Also it is moderately faster.
• MSMS and PSD spectra now identified as MSMS.
• All JOB_RUN_ITEMS are processed not just ones with an ACQUISITION flag.
• Diagnostics tick box to help resolve problems. PEAK_LIST_ID is listed in the diagnostics.
• Correct calibration equation used for all MSMS spectra.
• Precursor mass no longer used to resolve MS/MSMS.
• Correct instrument serial number written to calibration file.
• Run numbers should be correct.
• Spot set templates are no longer listed in the spot set list.
• Raw data is only written out if the acquisition status is 10.

• Corrected some problems with electron rest mass corrections in the MS-Product fragment ion list.
• Fixed a problem with quantitation where sometimes the raw data was truncated before the end of the high mass profile.
• Fixed a problem with the public server whereby report headers weren't included in MS-Tag from File.
• Links to files in the prospector temp directory sometimes had \ rather than / in the address. Eg: /prospector/4.21.3/temp\Apr_13_2006\graph1.txt
• Incorrect year in copyright notices in results pages.
• Peptides # in database column in Search Compare peptide report gave incorrect values when different modifications to the same peptide were alternative possibilities in the stored hits for a given spectrum.

• info.txt - new parameter for R installation binary and relocated parameter directory.
• usermod.txt - SILAC L modifications

• mshome.htm
• revhist.htm

• mssearch.pl - version number now just in one place.

• New R scripts msmsErrorScatter.R and init.R in cgi-bin

• Measured Light/Heavy Intensity Ratio
• Measured Light/Heavy Area Ratio
• Actual Heavy/Light Intensity Ratio
• Actual Heavy/Light Area Ratio

• If the results name has a certain characters in it (one example is the + character). Then the link to Full Search Compare Options from the Batch-Tag results page doesn't produce the Search Compare form.
• If the Search Compare remove (accession number) tick box is ticked then the links to the single protein peptide reports from the protein report don't give a report for a single protein.
• Accession number limited searches of large databases (eg Uniprot) where the search gets split up into a lot of different sections can fail or run very slowly because of a memory leak.
• Quantitation reports in Search Compare involving lots of wiff files sometimes don't work.
• There are problems with quantitation and the MS-Display program if user modifications contain a dash (-) character.
• The <nobr> directive has been removed for cells containing quantitation ratios.

• acclinks.txt - new Swiss Prot accession number link
• enzyme_com.txt
• homology.txt
• instrument.txt
• n_terms.txt
• usermod.txt

• mshome.htm

http://server_name/prospector/4.21.1/html/peakSpotter.htm

• RT with and without fraction being taken into account (so you can see if a peptide occurs in different fragments).
• m/z
• M+H so you can look for common contamonant peaks for example.
• Charge then M+H.
• Centroid intensity (only relevant for the LCQ).
• Peptide score.
• Discriminant score.

• Fixed an bug with multi-sample peptide reports with MS data links.
• Fixes the heavy use of memory for searches with a lot of modifications/No Enzyme. Some searches of this type will now run a lot faster.
• Protein names in the peptide report are now "wrapped" if they are too long.
• Fixed some bugs in the intinsic ratio quantitation calculations.
• Lan's quantitation usermods added.

• dbstat_hist.par.txt

• homology.txt - changed rules for acetylation
• instrument.txt - added new intact loss ion types
• quan.txt
  • previous line 4 (contains a string for the modification along with the amino acid) now no longer required.
  • previous line 5, new line 4 - more than one amino acid can be specified here.

• mshome.htm
• peakSpotter.htm

• TOFTOF database needs new Oracle procedure.

• Some of the strings used to identify the scans to sum together for Q-STAR iTRAQ quantitiation were being incorrectly written out to the results file. Eg:

  1998,:2009,3

  rather than

  1998,2:2009,3

• The software can now correctly handle the situation of having no peaks in a spectrum in an mgf file.
• The name field option on the FA-Index page mistakenly had the same CGI name as the database field. The correct name is now included.
• Histogram of peptide m/z errors now only counts peptides from homologous proteins once.
• Fixed error whereby Start AA and End AA contained random characters in time report if there is no peptide hit for a given spectrum.
• The spectrum applet has been amended so it leaves less blank space at the top of the graph.
• An error is printed if there is insufficient information in an mgf file to allow extraction of the raw data from a wiff file. This can happen if an mgf file created by an old version of the Mascot.dll is used.

• Deisotoping added to the instrument file for LTQ on the public server.
• Random characters are sometimes printed at the end of error messages. This was because the message sent with the error message wasn't null terminated.
• There was a problem dealing with mgf files with less spectra than processors.
• An error message is now printed if there are no spectra in the data file.
• A couple of changes have been made to stop the program halting or hanging if a Gaussian can't be fitted to a discriminant score distribution.
• MS links only available if there is MS data in the centroid files.

• The amino acid N was erroneously listed as a protonation site for some instruments.
• DB-Stat sometimes runs out of memory when used against a very large database. This problem was caused by the histogram feature introduced in 4.0.7.
• Mass tolerances in programs such as MS-Fit, MS-Bridge and MS-NonSpecific were handled incorrectly for multiply charged peaks.
• In MS-Bridge hits which only contained a single unlinked peptide and which contained the link amino acid weren't displayed.
• The Hide HTML links tick box didn't work in MS-Bridge and MS-NonSpecific.

• MS-Homology crashes if a mass is specified in a sequence and no amino acid combination correspond to it.
• The electron mass isn't currently subtracted when calculating the exact mass which could lead to a significant discrepancy at low mass (around 5 ppm at 100 amu).
• CNBr peptides incorrectly handled by MS-Product.

• The delete DNA database option in FA-Index doesn't delete all the DNA database files.
• MS-Homology fails to calculate the correct score if two or more of the sequences entered have different lengths and match the same bit of database sequence with the same number of errors. Only the shorter matching sequence is now retained.
• y type ions are off by 2 Da in MS-Comp.
• A HTML break code is printed at the top of the report if XML output is chosen. This problem doesn't occur if the results are saved to a file.

• MS-Fit and MS-Tag batch searches have a write text file option which doesn't do anything.
• MS-Fit and MS-Tag crash if no data is entered.
• MS-Seq composition exclude option doesn't work.
• Command line FA-Index instructions confusing.
• The first fragment ion peak is not passed to MS-Product when a peptide sequence link is from the MS-Tag results.
• The NCBI ftp site used for most of the databases has now changed.

• The user defined amino acids u, v, w and x don't have their masses correctly initialised.

• Sometimes MS-Product doesn't display product ions when accessed via a link due to there being no specified instrument parameter. This problem is apparent, for example, when going from MS-Tag to MS-Digest and then to MS-Product.
• Link to MS-NonSpecific from home page incorrectly specified.
• MS-Fit, MS-Bridge, MS-NonSpecific can't deal with average mass.
• In the MS-Fit results hits containing two cysteines are reported twice.
• MS-Product calculate the internal ions masses incorrectly if the N-terminus is modified.
• MS-NonSpecific hits reported incorrectly. The peptides all have an extra amino acid at the end.
• Links to MS-Tag Unknome still available.

• In Netscape 4.7 and older browsers the links to other programs sometimes don't work because spaces in the URLs aren't escaped.
• Detailed report flag not passed on when doing mixture searches from MS-Fit.

• Multiple charges don't work in MS-Digest.
• Multiply charged peaks aren't found in MS-Tag.
• Mixed digests don't work.
• User protein field needs to be cleared before MS-Digest works.
• MS-Fit homology search doesn't work.
• HPLC Index incorrectly reported in MS-Digest XML output.
• Some programs don't work with older versions of Netscape/Internet Explorer.
• Pdefault and Ddefault database prefixes incorrectly named in the manual (they were called PDefault and DDefault).
• Empty protein/DNA entry not possible in a database.
• Sometimes names/accession numbers/species aren't reported for Pdefault and Ddefault type databases.
• W-ion masses calculated incorrectly.

• No fragment ions are reported in MS-Product if you click on a peptide sequence link in MS-Digest.
• Tolerance incorrectly handled for multiply charged data if mmu tolerance units is used.
• Accession number link in results pages doesn't work for Ludwignr database.
• Some NCBInr entries are reported as having UNREADABLE species which are in fact reference entries with more than one comment line. Such entries sometimes have more than one species.
• Only Da tolerance works if the data is negatively charged. A work around is to define tolerances as negative numbers for negatively charged data.
• MS-Tag save hits to file doesn't work properly.
• H3PO4 and SOCH4 losses are not reported in MS-Product if the instrument specific default ion types tick box is selected.
• MS-Digest should print an error message if invalid amino acids are used in a user protein (eg, if the user uses lower case letter by mistake).

• MS-Comp doesn't work if the full amino acid composition of the ion is specified.
• DB-Stat crashes if the pre-searches select no entries.
• If a selected accession number is not present in the database the program either prints an incorrect error message or crashes.
• If the instrument specific default ion types are selected in MS-Product or MS-Tag then the default lists of amino acids which are defined in instrument.txt for MSMS fragmentation are not initialised properly.
• If the pre-searches select no entries it is still possible for the search programs to get a hit.
• The name and species pre-searches don't work properly it one of the names/species contains spaces.
• When a subsequent MS-Fit search is invoked from the MS-Fit results page to find mixture components an obselete name is used to describe the data format. This is not known to cause any problems at present.
• The coverage count in MS-Fit is out by 1 if the last amino acid in the protein is included in one of the hits.

• There is a limit to the size of the database that can be used of around 2 GBytes.
• The hit information line in MS-Fit containing the percentage of hits, size, PI and protein name now makes up the first line of the detailed result table. Netscape and IE display the results fine but when they are copied from IE into Word the first column of the table is formatted to the width of the information line. This pushes everything else together resulting in a messy table that has to be reformatted by hand.
• The column header is MH+ in MS-Digest when the data in multiply charged.
• Every 50th peak in MS-Digest doesn't get reported.
• If there is only a single base on the last line of an entry in a DNA database then frames 5 and 6 come out the same. This only affects a small proportion of the entries.
• The protein sequence is erroneously appended to the name for a few NCBI entries (eg. Accession no:464430).
• MS-Tag crashes if there are more than 400 internal ions in a potential hit. This only affects very high mass peptides.
• The Genpept accession number link doesn't work.
• The Owl accession number link doesn't work.
• MS-Tag in homology mode sometimes fails to find hits that it should find if the number (or %) of unmatched ions is too low.
• The lowest mass peptide is not reported in MS-Digest. This isn't normally a problem as masses below 500 Da aren't displayed by default.

• IUPAC ambiguity codes not supported in DNA to protein conversions.
• mmu tolerance calculations incorrect.
• The programs crash if the msparams/colors.txt file is missing.
• MS-Fit MOWSE scores can be incorrectly ranked if the score overflows what can be stored in a 4 byte integer number.
• The format of the OWL database has changed. This means that most of the time the link from accession number in the reports doesn't work.
• After the MS-Pattern list of sequences option has found a hit in a protein it only starts looking for new hits at the end of the peptide it has just found whereas it should start looking at the next amino acid.
• Pepsin enzyme rules incorrect.
• Some SwissProt entries don't have accession numbers. This causes problems with the UNIX versions of Prospector.
• The delta mass column in the MS-Pattern and MS-Tag reports can span 2 lines when viewed on Internet Explorer.
• Next 20 entries button on the FA-Index Database Summary Report doesn't work if seqdb directory or msparams directory has been relocated.

• There are sometimes problems with inputs of lists of text strings (eg. list of sequences in MS-Edman) if the cursor does not end up at the start of the line underneath the last text string. There are problems both when the cursor ends up directly at the end of the last text string (with no carriage return) and when there are lines after the last text string containing only space or tab characters.
• Setting the ion types in MS-Comp to include anything except MH+, y or b+H2O and the combination type to elemental caused the peptide mass and mass error columns in the report to show incorrect results.
• There are sometimes problems with inputs of lists of text strings (eg. list of sequences in MS-Edman) if the cursor does not end up at the start of the line underneath the last text string. There are problems both when the cursor ends up directly at the end of the last text string (with no carriage return) and when there are lines after the last text string containing only space or tab characters.
• Excluded species entries have to be placed after multiple species entries in the species.txt file for multiple and excluded species filters to work correctly.