Learning BioAnalyst Software

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

Version

---

1.7051.0.2

Description

Displays the contents of this document

Installs Service Pack 8 for Analyst QS 1.0

Install BioAnalyst Extensions 1.1 ePack 1 Installs the BioAnalyst Software extensions for Analyst QS .

Install Guided Tour and 1.1 ePack 1 Installs the guided tour, tutorial document, and tutorial data

Tutorial

Run Guided Tour from CD

Install PepSea Server

1.1

2.2.17D files to the hard drive.

Plays the multi-media guided tour from the CD.

Installs PepSea server and protein databases to the hard drive

In addition to the master installer, the CD also contains the following additional files:

Program

BioAnalyst Guided Tour.exe

Version

1.1

Description

A multi-media introduction to using BioAnalyst™ Software.

This program requires a sound card.

BioAnalyst Tutorial.pdf

ACRD4ENU.EXE

1.1 ePack 1 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.

4.0 Program for installing Adobe Acrobat Reader. This installer is located in the AcrobatReader directory of the installation

CD.

Applied Biosystems/MDS SCIEX

April 12, 2020 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-H

3

PO

4

and y-H

3

PO

4

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.



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 license@isb-sib.ch

.

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.)



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.



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: support@sciex.com

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 C

11

H… sorting before C

2

H….

 Cut and paste commands are not available in the Data Dictionary.



 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.



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



Learning BioAnalyst Software

CD-ROM Contents

What’s New in This Version

System Requirements

Installation Instructions