Known Bugs in ProteinProspector Programs
Current Bug Listing at UCSF
V 3.2.1 3/1999
- MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on
your browser preferences to get MS-Isotope to run without displaying the graph.
V 3.2.0 2/1999
- MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on
your browser preferences to get MS-Isotope to run without displaying the graph.
- 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.
V 3.1.1ie 8/1998
- MS-Product doesn't allow multiply charged ions.
- MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- The MS-Fit detailed report fails to report the m/z submitted if any of the data is multiply charged.
- MS-Comp doesn't work if Combination Type is set to Elemental.
- MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
- MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on
your browser preferences to get MS-Isotope to run without displaying the graph.
- 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 *.sp files for
multiple and excluded species filters to work correctly.
V 3.1.1njs 8/1998
- Forward links in results pages don't work with the Internet Explorer browser version 3.
- MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
- MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
- MS-Product doesn't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- The MS-Fit detailed report fails to report the m/z submitted if any of the data is multiply charged.
- MS-Comp doesn't work if Combination Type is set to Elemental.
- MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
- MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on
your browser preferences to get MS-Isotope to run without displaying the graph.
- 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 *.sp files for
multiple and excluded species filters to work correctly.
V 3.1.1 7/1998
- MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
- MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
- MS-Product doesn't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- The MS-Fit detailed report fails to report the m/z submitted if any of the data is multiply charged.
- MS-Comp doesn't work if Combination Type is set to Elemental.
- MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
- MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on
your browser preferences to get MS-Isotope to run without displaying the graph.
- 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 *.sp files for
multiple and excluded species filters to work correctly.
V 3.1 4/1998
- DNA and open reading frame results don't line up with the headers in the MS-Tag output.
- MS-Isotope crashes if the monoisotopic peak abundance is too low.
- MS-Isotope crashes or hangs if the elemental or peptide formula contains phosphorus.
- pI calculation in error under certain conditions.
- MS-Isotope JAVA applet only prints with versions of Netscape Navigator after v4.08 (Netscape Communicator 4.5).
- MS-Product doesn't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- MS-Comp doesn't work if Combination Type is set to Elemental.
- MS-Tag sometimes gives false positives with the CNBr digest in which the parent ion doesn't match.
- MS-Isotope JAVA applet causes Netscape 4 to crash on MACs. You can disable Java on
your browser preferences to get MS-Isotope to run without displaying the graph.
- 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 *.sp files for
multiple and excluded species filters to work correctly.
V 3.0.4 4/1998
- The list of sequences resulting from an MS-Tag unknome search cannot easily
be supplied to MS-Edman for a homology search.
- MS-Digest and MS-Product don't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- 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.
V 3.0.3 4/1998
- The list of sequences resulting from an MS-Tag unknome search cannot easily
be supplied to MS-Edman for a homology search.
- MS-Digest and MS-Product don't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Faulty species alias lists cause database search programs to crash rather than generate error.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- 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.
V 3.0.2 3/1998
- The list of sequences resulting from an MS-Tag unknome search cannot easily
be supplied to MS-Edman for a homology search.
- MS-Digest and MS-Product don't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Faulty species alias lists cause database search programs to crash rather than generate error.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- 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.
V 3.0 7/1997
- Bug in MS-Tag where automated immonium ion assignment alters multiply charged ion assignments.
- Cosmetic bug in MS-Fit multiply charged output. Charges displayed above table in Detailed Results, instead of as subscripts on input masses.
- The list of sequences resulting from an MS-Tag unknome search cannot easily
be supplied to MS-Edman for a homology search.
- MS-Digest and MS-Product don't allow multiply charged ions.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Complement strand DNA translation incorrect, frames 4,5,6 are incorrect.
- Faulty species alias lists cause database search programs to crash rather than generate error.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
- 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.
V 2.0 2/1997
- MS-Tag allow errors mode does not match star ions unless at least one
N-terminal ion type AND at least one C-terminal ion type are
designated.
- Unix version of MS-Digest does not work from html input form. Changing the line
!--Unix version--
FORM METHOD="POST" ACTION="../cgi-bin/msdigest"
to
FORM METHOD="GET" ACTION="../cgi-bin/msdigest"
Will allow MS-Digest to work, however, user supplied protein sequences are tolerated
only up to length ~200.
- All Programs are unable to extract species information from the comment line
of ~15% of NCBInr database entries (mostly originating in PIR). These entries are assigned a
species name of UNREADABLE. The protein name is assigned as the complete
Fasta comment line.
- Complement strand DNA translation incorrect, frames 4,5,6 are incorrect.
- Phosphorylated amino acids s, t and y don't work in MS-Digest user protein.
V 1.1 8/1996
- MS-Tag allow errors mode does not match star ions unless at least one
N-terminal ion type AND at least one C-terminal ion type are
designated.
- MS-Product incorrectly calculates c ions, off by 2 Hydrogens.
- Non-uniform input variable names across htm files for all programs hinders
automated input bypassing of html forms.
- HTML output for all programs contains no line breaks, thus hindering
automated output parsing of search results.
- Global error handling display, repeats footer line.
- When searching the NCBInr database all programs, matches are made to proteins with MW
outside the MW cutoffs. This is caused by combining sequences from multiple entries
to make a single protein, and originates from inability to extract species information
from the comment line of ~15% of entries (mostly originating in PIR).
V 1.0 6/1996
- MS-Tag allow errors mode does not match star ions unless at least one
N-terminal ion type AND at least one C-terminal ion type are
designated.
- MS-Tag incorrectly labels star
ion types in allow errors mode with position number from the wrong end of sequence.
- MS-Digest retrieval by accession number fails frequently.
- MS-Product incorrectly calculates c ions, off by 2 Hydrogens.
- HTML output for all programs contains no line breaks, thus hindering
automated output parsing of search results.