BioAnalyst™ Software v1.1 ePack 1 Release Notes
Table of Contents
CD-ROM Contents ......................................................................................................................................... 1
What’s New in This Version .......................................................................................................................... 2
System Requirements ..................................................................................................................................... 2
Installation Instructions .................................................................................................................................. 3
Learning BioAnalyst Software........................................................................................................................ 5
Known Problems and Limitations................................................................................................................... 5
CD-ROM Contents
The BioAnalyst™ Software Release CD-ROM contains a master installation program called Launch.exe
used to install the various BioAnalyst Software components.
The master installer provides the following installation options:
Installation Option
View Release Notes
Install Analyst® QS 1.0
Service Pack 8
Install BioAnalyst Extensions
Install Guided Tour and
Tutorial
Run Guided Tour from CD
Install PepSea Server
Version
--1.7051.0.2
Description
Displays the contents of this document
Installs Service Pack 8 for Analyst QS 1.0
1.1 ePack 1
1.1 ePack 1
Installs the BioAnalyst Software extensions for Analyst QS.
Installs the guided tour, tutorial document, and tutorial data
files to the hard drive.
Plays the multi-media guided tour from the CD.
Installs PepSea server and protein databases to the hard drive
1.1
2.2.17D
In addition to the master installer, the CD also contains the following additional files:
Program
BioAnalyst Guided Tour.exe
BioAnalyst Tutorial.pdf
Version
1.1
1.1 ePack 1
ACRD4ENU.EXE
Applied Biosystems/MDS SCIEX
July 29, 2017
4.0
Description
A multi-media introduction to using BioAnalyst™ Software.
This program requires a sound card.
Self-guided tutorial document describing how to use the
BioAnalyst Software features. Install the Tutorial using the
master installer in order to access the tutorial data files. In
order to view this file, you must have Adobe Acrobat Reader
installed on your computer.
Program for installing Adobe Acrobat Reader. This installer
is located in the AcrobatReader directory of the installation
CD.
Page 1 of 7
What’s New in This Version
The Applied Biosystems/MDS SCIEX BioAnalyst™ Software 1.1 ePack 1 is a suite of high performance
analytical tools for processing biological data from the QSTAR® Pulsar and QSTAR® XL mass
spectrometers. The following changes were made to BioAnalyst Software 1.1 for this release:
Mass Reconstruction

The Bayesian Peptide and LCMS Reconstruct tools now identify masses for peaks with no isotope
or charge evidence; these masses are indicated with evidence “Unresolved”. The charge is
arbitrarily assigned as 2 and can be edited.

An option to deconvolve peaks was added to the Bayesian Protein Reconstruct tool. This feature
greatly improves the determination of masses for samples with overlapping peaks.

Improvements were added to the LCMS Reconstruct tool to make the results less sensitive to range
of the scans selected for the analysis. Detection of long-eluting masses has also been improved.

The calculation of the monoisotopic mass for masses with I (isotopic) and IC (isotopic and charge)
evidence has changed slightly. In previous versions, the centroid of the peak with the lowest m/z
value was simply assumed to be the monoisotopic mass. In the Results Table, the +/- values (the
residuals) for the remaining peaks in the series were calculated from a linear least-squares fit of the
remaining m/z values for an isotope series starting at the reported monoisotopic mass.
In BioAnalyst Software 1.1 ePack 1, the monoisotopic masses for I and IC records are calculated
by doing a linear least-squares fit of all the m/z values, weighted by peak intensity, to determine
both the monoisotopic mass and the residual values. (Because the fit is weighted by intensity, the
residuals will generally not sum to zero.)
Peptide Sequencing

Two new peptide fragment ions b-H3PO4 and y-H3PO4 have been added to the Fragment Ions table
in the Sequencing window. The presence of this fragment is a reliable way to identify the actual
site of phosphorylation for a phosphorylated peptide.
System Requirements
Please see the Analyst® Software QS 1.0 SP8 release notes for the details of the supported hardware
configuration.
Notes

BioAnalyst Software adds only data processing functions but it may be installed on data
acquisition workstations as well as processing stations. Note: some of BioAnalyst Software’s
processing functions are extremely processor intensive and may interfere with data acquisition.

BioAnalyst Software 1.1 ePack 1 has been tested under the Windows® 2000 (version 5.00.2915)
operating system.

Internet Explorer™ v5.0 or later is required for database searching with the PepSea™ server. If
you wish to use Pro BLAST, you will need Internet Explorer™ v6.0 or higher.
Disk Space Requirements

BioAnalyst Software requires 630 MB of free disk space (approximately 17 MB of this is for the
BioAnalyst Software and the balance is for the PepSea™ server and associated database files). If
installed to the hard drive, the multi-media guided tour and tutorial require an additional 200 MB
of disk space.
Applied Biosystems/MDS SCIEX
July 29, 2017
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About Using Swiss-Prot
A copy of the Swiss-Prot database, as a SIF file, is included with the program. SWISS-PROT is copyright.
It is produced through collaboration between the Swiss Institute of Bioinformatics and the EMBL
Outstation - the European Bioinformatics Institute. There are no restrictions on its use by non-profit
institutions as long as its content is in no way modified. Usage by and for commercial entities requires a
license agreement. For information about the licensing scheme see: http://www.isb-sib.ch/announce/ or
send an email to [email protected].
Installation Instructions
Before installing this software, you must have administrator privileges for the computer you wish to install
on. Contact your IT group if you are unsure of your access rights.
Note: If you are a new user and have never installed BioAnalyst™ Software, go to page 4 and follow those
instructions.
If BioAnalyst Software 1.1 is Already Installed:
Step 1. Log on to the local system with administrator privileges.
You must have administrator privileges on your local workstation in order to perform the installation.
Step 2. Open the BioAnalyst Software 1.1 ePack 1 installer.
Insert the BioAnalyst Software CD into your computer. The Installation Browser should appear
automatically. If this does not occur, then choose ‘Run’ from the Start button. In the ‘Open’ field, type
D:\launch.exe (where D: is your CD-ROM drive letter). Proceed with the installation by clicking the
appropriate buttons.
Step 3. If needed, install Analyst Software QS 1.0 Service Pack 8.
Click the ‘Install Analyst QS 1.0 SP 8’ button in the BioAnalyst 1.1 ePack 1 Installation Browser and
follow the on-screen directions.
Step 4. Install BioAnalyst Software.
Click the ‘Install BioAnalyst Extensions’ button and follow the on-screen directions.
Step 5. If needed, install PepSea Server.
Note: If you have previously installed PepSea Server, you may still want to run the installer included on the
CD since newer versions of the NR and Swiss-Prot databases are supplied with this release.
To install, click the ‘Install PepSea Server’ button and follow the on-screen directions.
Step 6. If desired, install the tutorial.
The Interactive Tutorial has been updated with information about the ‘Deconvolve peaks’ option for the
Bayesian Protein Reconstruct Tool and a sample data file has been included on the CD. To install the
Interactive Tutorial to the hard drive, click the ‘Install Tutorial and Sample Files’ button and follow the
onscreen directions. A shortcut to the Tutorial document will appear on the Analyst QS Software Start menu
after installation.
The CD also contains the BioAnalyst Tutorial, as a PDF, if you do not wish to install the tutorial to the hard
drive. (To read this you must have Adobe© Acrobat Reader© installed.)
Applied Biosystems/MDS SCIEX
July 29, 2017
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For New Users:
Step 1. Log on to the local system with administrator privileges.
You must have administrator privileges on your local workstation in order to perform the installation.
Step 2. Install Analyst Software QS 1.0.
See the Release Notes supplied with that program for installation instructions.
Step 3. Open the BioAnalyst Software 1.1 ePack 1 installer.
Insert the BioAnalyst™ Software CD into your computer. The Installation Browser should appear
automatically. If this does not occur, then choose ‘Run’ from the Start button. In the ‘Open’ field, type
D:\launch.exe (where D: is your CD-ROM drive letter). Proceed with the installation by clicking the
appropriate buttons.
Step 4. Install Analyst Software QS 1.0 Service Pack 8.
Click the ‘Install Analyst QS 1.0 SP 8’ button in the BioAnalyst 1.1 ePack 1 Installation Browser and
follow the on-screen directions.
Step 5. Remove the BioAnalyst Software 1.1 ePack 1 installation CD.
Step 6. Insert the BioAnalyst Software 1.1 installation CD.
As in Step 3 above, the Installation Browser should appear automatically.
Step 7. Install BioAnalyst Software 1.1.
See the Release Notes supplied with that program for installation instructions.
Step 8. Remove the BioAnalyst Software 1.1 installation CD.
Step 9. Insert the BioAnalyst Software 1.1 ePack 1 installation CD again & install BioAnalyst
Software 1.1 ePack 1.
As in Step 3 above, the Installation Browser should appear automatically. Click the ‘Install BioAnalyst
Extensions’ button and follow the on-screen directions.
Step 10. If needed, install PepSea Server.
Note: If you have previously installed PepSea Server, you may still want to run the installer included on the
CD since newer versions of the NRDB and Swiss-Prot databases are supplied with this release.
To install, click the ‘Install PepSea Server’ button and follow the on-screen directions.
Step 11. Install or run the tutorial(s).
To run the Guided Tour from the CD, click on the ‘Run Multi-media Tutorial from CD’ button.
To install the Guided Tour and or the Interactive Tutorial to the hard drive so that they may be used without
the CD, click the ‘Install Tutorial and Sample Files’ button and follow the onscreen directions. Shortcuts to
the Guided Tour and Tutorial document will appear on the Analyst QS Software Start menu after
installation.
The CD also contains the BioAnalyst Tutorial, as a PDF, if you do not wish to install the tutorial to the hard
drive. (To read this you must have Adobe© Acrobat Reader© installed.)
Step 12. If needed, install Acrobat© Reader©
If you have installed the BioAnalyst Tutorial or wish to view the BioAnalyst Tutorial document or the PDF
versions of the on-line help, Adobe Acrobat Reader must be installed on your computer. If you do not have
Acrobat Reader installed, double-click on ACRD4ENU.EXE located in the AcrobatReader folder of the
installation CD to install it.
Applied Biosystems/MDS SCIEX
July 29, 2017
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Learning BioAnalyst Software
There are three sources of help supplied with your BioAnalyst installation.
BioAnalyst Guided Tour: A multi-media guided tour of BioAnalyst is included on the BioAnalyst CD. This
tour may be run from the installation CD or optionally installed with your software. This tutorial will guide
you through examples of the most common uses of BioAnalyst. You may move through the tutorial at your
own pace in order to gain a high-level understanding of the software and its features. Data files are provided
so you can follow along.
BioAnalyst Tutorial: Also provided is a self-tutorial document that walks you through common analytical
procedures in great detail. Data files are provided so you can follow along.
On-line help: There is extensive on-line help, accessed from the Help menu. The Help allows you to view a
topic from the table of contents, using the index or using the 'Find' command to search for any word in any
of the help files. You have the option to print selected topics.
The on-line help is also provided as PDF files, one for each major program area. These files are located in
the Help folder inside the Analyst folder; typically this will be Program Files\Analyst\Help.
Known Problems and Limitations
Please report any problems, limitations and feature requests via the website at:
http://ab-mds-sciex.custhelp.com/cgi-bin/ab_mds_sciex.cfg/php/enduser/ask.php
or via e-mail at: [email protected]
Installation

If you cancel part way through installation of BioAnalyst® Software 1.1 EP1, the remaining
BioAnalyst Software 1.1 may not operate correctly and/or attempting to install the ePack again
may fail. This is because the Cancel command in the installer does not always work correctly after
a certain point in the installation process. If this happens, you must remove and reinstall
BioAnalyst Software 1.1.
General

The File menu options and their keyboard equivalents for Cut, Copy, Paste, and Undo do not work.
Use the corresponding right-click menu commands to replace this missing functionality.

Unique cleavage chemistries, such as the formation of homoserine or homoserine lactone by CnBr
cleavage after methionine, are not supported. Pay careful attention to the masses of peptides
computed in the Protein Sequence window formed by such cleavage events.

The minimum sizes of the Protein Sequence, Search Database and Sequencing Windows are too
large to allow their complete viewing on an 800x600 resolution monitor. It is advised that you set
your screen resolution to 1024x768.

Analyzing data acquired from a Q TRAP™ System with BioAnalyst 1.1 ePack 1 is not
recommended.
Data Dictionary

The sorting order in the Data Dictionary is strictly alphabetical so you may be surprised to find
chemical formula C11H… sorting before C2H….

Cut and paste commands are not available in the Data Dictionary.
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July 29, 2017
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
Do not define cysteine or methionine modifications with a space before the name. The Search
Database window will set the default Cysteine and Methionine modifications incorrectly if a
modification has a space before the name in the Data Dictionary.
Mass Reconstruction

The Bayesian Peptide, Peak Scoring and Manual Reconstruct tools currently return only
centroided mass distributions so the peak shapes are not preserved in the mass graph and will
appear as very sharp triangular peaks. The peak shapes of analysis records from the other
reconstruction tools are retained and therefore preserve the peak shapes of their constituent mass
distributions are correct in the mass graph.

The Bayesian Protein tool is very processor intensive so it is not advisable to apply it to entire
TICs, as it may take many hours to complete. Use the LCMS Reconstruct tool instead. Setting the
Iteration parameter to a lower value in the Bayesian Protein tool may improve performance.

Invoking a database search from the Results Table, when PepSea™ server is not running, does not
result in an error message, nor is the Database Search window created. Launch the PepSea server
to correct this problem.

The ‘Delete Pane’ command does not work for a Data List pane made from a mass graph or text
data file.

The values for m/z, Area and +/- in the subtable for Mass (avg.) may be truncated when you print
a Results Table. If you hide a few columns, via the ‘Select Columns…’ right-click menu, and then
print, the values are not truncated.
Protein Sequence Window

When reading protein descriptions from Swiss-Prot format sequence files only the first 70
characters from the DE line(s)are displayed.
Database Searching

Due to slight differences in the way BioAnalyst™ Software and PepSea compute average
molecular weights of peptides you may observe tiny mass differences between the masses returned
from Peptide Molecular Weight searches and what BioAnalyst Software would calculate from the
sequences found.

Nothing prevents the local host computer from being set in the “Use a different computer” field in
the Search DB Defaults. This setting causes the searches to fail. If searches are to be done on the
local host, select the “Use this computer” setting.

Attempting to add multiple databases with PepSea™ Administrator without invoking the ‘Write
List’ command between each entry will cause PepSea Administrator to crash.

Using ‘X’ as a wildcard for PepSea™ searches of DNA databases (such as EST) is not allowed.

Changing settings in the Search Database Defaults window only takes effect in new Search
Database windows.

Using more than 10 residues for amino acid searches of DNA databases, such as EST, is not
allowed. If you enter more than 10 residues, the program will give a message telling you there may
be undefined amino acids (B, J, O, U or X)

If you try to run a search without a database present, you will get an error message “IDispatch error
#49.”

If database searches are done on a remote system, PepSea server will remain running on the remote
server. PepSea must be closed using the task manager on the remote system.

The PepSea server cannot handle a digest agent where the cut site is BEFORE a specified AA (e.g.
AspN). When doing searches such as this an assertion message is displayed in yellow over the
system tray. Results from peptide molecular weight searches using such digest agents are incorrect.
Applied Biosystems/MDS SCIEX
July 29, 2017
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To work around this, define the complement of the digest agent rule (e.g. for AspN, “Cut at: /D”
is the same as:
“Cut at: A/,B/,C/,D/,E/,F/,G/,H/,I/,J/,K/,L/,M/,N/,O/,P/,Q/,R/,S/,T/,U/,V/,W/,X/,Y/,Z/
But not at: /A,/B,/C,/E,/F,/G,/H,/I,/J,/K,/L,/M,/N,/O,/P,/Q,/R,/S,/T,/U,/V,/W,/X,/Y,/Z”.)

You may have problems searching if BioAnalyst Software is set to Single User mode and a
different user attempts to search. The program will display a message concerning the PepSea
license and, following that, another message about the Data Dictionary. This is due to Windows®
2000 security settings. Add the new user to the PowerUsers group instead of just the Users group
and the search will work correctly.

You may receive an assertion error (it will appear in red text in the lower right corner of your
screen) if you select the Full Lookup command for a sequence match from a DNA SIF file. Ignore
the error; the Full Lookup returns the correct sequence.
Sequencing

Sometimes double-clicking a sequence tag in the sequence tag list in order to move it into the
hypertag field will cause one of the flanking masses to change by 0.0001 Da.

If you’re interested in finding only simple internal ions (those which have not lost NH 3 or CO, etc)
then you must select at least one of the other internal ion types in order to activate the ‘Find
Internal Ions’ button.

The sequencing window never uses or reports average masses.

‘Label Immonium Ions’ will label all theoretical immonium ions on the spectrum, regardless of
whether or not a peak is present.

Immonium ions in the fragment ions results can be counted as a match even though the cell has an
entry of n/a.

The ‘From spectrum’ option in Manual Sequencing does not use any custom amino acids from the
Data Dictionary. All other types of sequencing do use these amino acids, if assigned a one-letter
code.

Sequencing results from data saved to a text file, and especially data that was centroided before
being saved to text, should be examined carefully. The de novo sequencing algorithm is not
optimized for text data files.

Changing information in the Data Dictionary for modifications in use in a sequencing window,
doesn’t always update the sequencing window correctly. Close any sequencing windows before
making changes to the Data Dictionary.
Peptide Mapping

Mapping with non-specific cleavages and many modifications can take several hours or more. The
Mapping Strategy topic in the on-line help describes a strategy for mapping that will minimize
processing time and generate fewer false positives.
Copyright 2000-2003 by Applied Biosystems / MDS Sciex
Applied Biosystems/MDS SCIEX
July 29, 2017
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