ナレッジベース資料(FAQ)


ナレッジベース資料は、よくある質問に対する回答を見つけるためのFAQです。

最近の記事


Why is Scheduled Ionization in Analyst® TF Software 1.8 Not Working with the OptiFlow® Turbo V Ion Source for Nano Flow?

Scheduled ionization in Analyst® TF software 1.8 is not configured to work optimally with the OptiFlow® Turbo V ion source ion source for nano flow. When using the OptiFlow® Turbo V ion source, scheduled ionization is always on, except when the start time in Analyst software is set to zero during pre- and post-run times. This is an issue for the nano spray users, because they will be unable to have the voltage stay on between runs for perpetual spray.

12/06/2021    Academia Omics | Analyst Software

Why Is There No MRMHR Scan Type when Using the Method Wizard for a TripleTOF® LC-MS/MS System?

This article describes the MRMHR workflow for a TripleTOF® LC-MS/MS System using the Method Wizard in Analyst® TF or SCIEX OS Software. MRMHR is not a scan type. It is a description for a set of looped experiments, which can be used for a targeted approach. The looped experiments include a TOF-MS experiment followed by dedicated product ion experiments either in high-resolution or high-sensitivity mode.

Decreasing Run Time when Using the LCMS Reconstruct Algorithm in ProteinPilot™ Software

This article describes how to modify the configuration file for ProteinPilot™ software to decrease the time needed when using the LSMS Reconstruct algorithm, especially when performing large protein ID searches on data sets from a TripleTOF® 6600 LC-MS/MS System.

How Can I Create a Custom Enzyme in BioPharmaView™ 3.x Software?

This article describes how to use a different DataDictionary file to add a custom enzyme to BioPharmaView™ software. The BioPharmaView.Data dictionary file cannot be modified. This will result in a reinstall of the software.

Where Can I Download Skyline Unplugged for a Windows 10 64-bit PC?

Link is provided and installations instructions are described

Can Wiff1 Files Generated by SCIEX OS Software 2.1 from X500 Series Instruments be Searched with ProteinPilot™ Software?

X500 series instruments generate wiff2 file formats, but with the newest version of SCIEX OS Software 2.1, they can also generate a .wiff1 file. Only .wiff1 files can be used to perform a ProteinPilot™ software search.

How Do I Install the Intact Protein Script on the TripleTOF® 5600 and 6600 Systems?

The Intact Protein script can be installed from the Analyst® TF software directory located at: C:\Program Files (x86)\Analyst\Scripts. The ShowInTuneLayout script must be installed and enabled in order to acquire intact proteins.

11/02/2021    Academia Omics | Pharma CRO

What is the Source of the Atomic Weight Information in BPV Flex Software?

BPV Flex software uses the same source of atomic weight information as BioPharmaView™ software. The theoretical value required for the intact workflow uses the average molecular weight; the peptide workflow uses the monoisotopic weight.

Can ProteinPilot™ Software Version 5.0.2 Be Installed on a 2019 Server?

Yes, ProteinPilot™ software 5.0.2 can be run on a Windows 2019 Server. This was not officially tested or mentioned in the release notes, but many users have installed the Windows 10-compatible ProteinPilot software 5.0.2 on the Windows Server 2019 operating system and have run the software successfully in this environment.

Can I Submit mzIdentML Files from ProteinPilot™ Software 5.x to the PRIDE Repository?

This article summarizes the issues with ProteinPilot version 5.0 and mzIdentML created files. Submission of mzIdentML files is still not automated with later versions of ProteinPilot™ software, including version 5.0.x. Complete submissions from ProteinPilot software to PRIDE are not possible, but partial submissions of the mzIdentML are, and this partial submission process is described below.

How Are Peptides Named in BPV Flex Software after in Silico Digestion?

The general rule for naming peptides in BPV Flex software is: the first peptide resulting from a proteolytic cleavage is named T1 for sequences displayed from the N-terminus to the C-terminus; moving toward the C-terminus, the second proteolytic cleaved peptide is named T2, and so forth.

11/01/2021    Academia Omics | Pharma CRO | Software

How to Use the MAM Script in BioPharmaView™ Software 3.0.2 to Transfer Peptide Information to SCIEX OS Software

BioPharmaView™ software 3.0.2 has improved its multiple attributes monitoring (MAM) workflow, and the software now includes a script, MAM-BPV to Analytics Converter, used to create a quantitative processing method for the Analytics mode of SCIEX OS software.

How Is the Peptide Score Calculated in BPV Flex™ Software 2.1?

The BPV Flex™ Software 2.1 peptide score indicates the probability that the peaks in a given MS/MS spectrum will match those of the theoretical peptide fragments by random chance. Therefore, the score calculation is derived from observed MS/MS fragments and the corresponding intensities, as well as the number of theoretical MS/MS fragments.

What Value Should Be Used for the XIC Width in My SWATH® Acquisition MicroApp Processing Settings?

One common error when using the SWATH® Acquisition MicroApp 2.0.1 for processing SWATH data is to relate the XIC width setting in the processing software with the mass accuracy of the instrument, and set the XIC width to a value that is too low. XIC extraction widths should be set to 50 to 75 ppm, regardless of the mass accuracy of the acquired data.

Unable to Open SCIEX Cloud ProteinPilot™ Software Searches with the Desktop Version 5.0.2

The version of ProteinPilot™ Software in the SCIEX Cloud is version 5.0.3; therefore, group files created in the SCIEX Cloud cannot be downloaded to a desktop and opened in ProteinPilot Software 5.0.2. To download and read a group file on a desktop installation of ProteinPilot Software, the desktop version must be upgraded to version 5.0.3.

Which Glycan Notation Is Used in the BioPharmaView™ Software?

The glycan notation used in BioPharmaView™ Software is the Oxford style.

Remote Data Access Software Error on MALDI TOF/TOF™ instruments

When setting up ProteinPilot™ Software or the imaging acquisition software for the MALDI TOF/TOF™ Systems, a RDA (Remote Data Access) software error message is received: "TOF/TOF Imaging Acquisition Software. The client components used to communicate with the instrument are newer than those found on the instrument. Please update the Remote Data Access service on the instrument."

11/09/2020    Academia Omics | Pharma CRO

What File Formats Can Be Converted with the Newest Version of ProteoWizard Software?

This newest version of ProteoWizard software, version 3.0.20258-97f41f698, can now convert files to the txt format, as well as the three original file types (MGF, mzML and mzXML). For SCIEX software users, the txt file might be a useful option; however, the quality of the output file from ProteoWizard has not tested.

11/06/2020    Academia Omics

ProteinPilot™ Search Error: Unhandled Exception: Out Of Memory Exception

During a search with ProteinPilot™ Software 5.0, 5.0.1 and 5.0.3, the error "Unhandled Exception: Out Of Memory Exception" appears. This issue is due to the LC/MS reconstruct crashing within the ProteinPilot Software when data sets with a high MS1 scan speed are being processed.

Creating a ProteinPilot Software Winner Proteins Results List as FASTA File

This article describes the steps for creating a FASTA file from a ProteinPilot™ software report of winner proteins.

Differences between iTRAQ® Reagents Application Kit - Protein (4374321) and iTRAQ® Reagent 4Plex or 8Plex Kits

This article describes the different workflows for the iTRAQ® Reagents Application Kit - Protein (4374321) and the iTRAQ Reagents - 4plex or 8plex kits.

10/22/2020    Academia Omics | Pharma CRO | iTRAQ Reagent

Why Won't LipidView™ Software Load My Analyst® Software (.wiff) Data Files?

In order to load Analyst® software data files (.wiff files) into LipidView™ software, either Analyst or Analyst TF software must be installed alongside LipidView.

Locating the Name of a Server or PC Using the Command Prompt Window

This article describes the DOS commands used to access the name of the server or PC.

05/14/2020    Academia Omics | Software

Locating the Name of a Server or PC Using the Command Prompt Window

This article describes the DOS commands used to access the name of the server or PC.

05/14/2020    Academia Omics | Software

Accessing ProteinPilot™ Software Searching in the SCIEX Cloud Workspace

To log into the SCIEX Cloud workspace and access the ProteinPilot™ software searching features with just your CloudConnect license, follow the instructions below.

Missing Columns when Exporting the Protein Summary from ProteinPilot™ Software 5.0.2?

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Is Digital PicoView® Source Windows 10 compatible?

Digital PicoView® Source is a nano ion source from New Objectives that is Windows 10 compatible and can be used with many SCIEX mass spectrometers.

How to Install Skyline Software on an Off-Line Computer

To download Skyline software on a computer that is not connected to the internet, use the Unplugged installer or the Administrator installer:

Where Are the Report Templates for BioPharmaView™ Software Stored?

The file folder locations of the report templates for BioPharmaView™ software are listed in this article.

Can Xcalibur Software 3.x and Eksigent Software 4.3 Operate on Windows 10?

SCIEX's Eksigent software and Thermo Scientific's Xcalibur software have not officially been tested together on a Windows 10 operating system. The Eksignet software can be installed on a Windows 10 PC, but then it cannot be configured with any Xcalibur software versions. However, both software types can be configured together on a system running Windows 7, 64-bit.

03/20/2020    Academia Omics | NanoLC 400

How To Enable the New Intact Protein Quant Feature in SCIEX OS 1.7 Software

The Intact Quant feature in Sciex OS 1.7 software platform enables the quantitative processing of intact proteins without sample prep and allows for the complete and compliant intact reconstruction of protein data sets. To activate this feature, an additional, add-on software license, SCIEX OS IntactQuant 1.7 (part number 5078597), must be installed in the C:\ Program Files\SCIEX\SCIEX OS folder.

03/17/2020    Academia Omics | Pharma CRO | SCIEX OS

What Parameters in ProteoWizard Are Needed when Converting .wiff2 Files to mzXML Files?

The parameter settings, including the PeakPicking value, that are used for converting .wiff2 files to mzXML or mzML files in ProteoWizard, are explained in more detail here.

Does the XCMSPlus Software Use MS/MS Data Matching to Identify Metabolites?

XCMSplus software does not use MS/MS matching to identify features. Instead, this software identifies features based on the precursor m/z.

Causes of the taglet.exe Error in ProteinPilot™ Software

The taglet.exe error in ProteinPilot™ software is due to a wide range of issues including incorrect language settings, installation of the software on the incorrect operating system, and the incorrect addition of modifications — to name a few.

AB SCIEX Data Explorer® Software Issue: Periodic Table and Other Software Features Are Grayed Out

The AB SCIEX Data Explorer® software is an embedded software for data processing on the 4800 MALDI TOF/TOF™ and the TOF/TOF™ 5800 Systems and was recently rebranded; however, the rebranding process caused certain applications menu items to become grayed out (periodic table, isotope calculator, and elemental composition). To resolve this issue, install the patch provided in the link in this article.

11/14/2019    Academia Omics

The Peakfinding Algorithm in SimGlycan® Software Improves Search Results on SCIEX Datasets

The Peak Detection & Picking feature in SimGlycan® software versions 5.9.2 and higher offer an improved peak-picking algorithm that is faster and more efficient at handling data from SCIEX TripleTOF® LC-MS/MS System instruments.

11/12/2019    Academia Omics | SimGlycan Software

Why Use the Enterprise Edition of SimGlycan® Software?

SimGlycan Software (a product of PREMIER Biosoft) predicts glycan and glycopeptide structures from SCIEX mass spectrometer-acquired MS/MS data. Some of the advantages of using the enterprise edition of SimGlycan software include being able to create glycan templates so that novel glycan structures can be added to the database.

11/11/2019    Academia Omics | SimGlycan Software

What is SimGlycan Software?

SimGlycan® software is a comprehensive glycan and glycopeptide drawing and structure analysis software.

Does SimGlycan® Software Use .wiff2 File Formats from X500 Series Instruments?

This article describes the possible file input formats for SimGlycan® software.

Upgrading to Analyst® TF Software 1.8.1: Batch Editor No Longer Displays Autosampler ekspert nanoLC400 as an Option

After upgrading Analyst® TF software 1.8 to version 1.8.1, the Eksigent control software no longer displayed the option to chose the ekspert™ nanoLC 400 autosampler. To resolve this issue, in the Eksigent control software, the autosampler driver for the nanoLC 400 must be unregistered and then re-registered.

Aliquots of Bulk iTRAQ® Reagent Require Cold Storage Under Inert Gas

When aliquoting bulk iTRAQ® reagent, vials must be stored at -20 °C under inert gas.

11/09/2019    Academia Omics | Pharma CRO | iTRAQ Reagent

Multiple Period Experiments Cannot Be Processed in BioPharmaView™ Software 2.x and 3.x

Data processing for intact proteins and peptide mapping in BioPharmaView™ software versions higher than 2.x do not allow for multiple period experiments.

Calculating the Theoretical Average Mass for an Intact Protein in BioPharmaView™ Software

BioPharmaView™ software uses the isotopic masses published by NIST online at: https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl. Please note that the results generated will be the same throughout all SCIEX software (e.g., PeakView™ and ProteinPilot™ software).

What Is the Organic Solvent Used with iTRAQ® Reagents during Shipment?

All iTRAQ®, aTRAQ™ and mTRAQ® reagents are shipped in acetonitrile from the factory.

Does ProteinPilot™ Software 5.0.2 Support MALDI TOF/TOF™ Systems?

Description of which ProteinPilot™ software versions still support 4800 and 5800 MALDI TOF/TOF™ systems.

Are CloudConnect and SWATH® MicroApps within PeakView® Software Windows 10 Compatible?

The software package, PeakView® 2.2, CloudConnect 1.2 beta and SWATH® 2.0.1 software. is needed to perform the OneOmics workflow and/or SWATH protein data processing and is Windows 7 and Windows 10, 64-bit compatible.

Can Skyline Version 4.2.1 and Higher Process .wiff2 File Formats?

Yes , Skyline version 4.2.1 can process .wiff2 files generated using SCIEX OS software.

List of CE Capillaries with Pre-burned Detection Windows

CE capillaries with pre-burned detection windows are available for purchase; the dimensions and coating information for these products are listed here.

What Causes BioPharmaView™ Software To Stall when Processing Data or Running Batches?

BiopharmaView™ software will stall when processing data when more than one instance of the software is open or if there are some corrupted files in the processing queue folder in the BioPharmaView program files folder.

Changing the Number of Decimals Displayed in Analyst® Software Calibration and Metric Plots

This is a set of instructions for changing the number of decimals displayed in Analyst® software quantitation metric plots and calibration curves. The default number of decimals leaves the significance so low that you can not reproduce the results shown in the results table. A warning is given to let customers know that Regedit is a dangerous utility.

BioPharmaView™ Software 2.x/3.0.x Cannot Open the Data for Subsequent Samples if the Data for the First Sample Is Corrupted

BioPharmaView™ software 2.x/3.0.x cannot open the data for subsequent samples if the data for the first sample is corrupted.

Bio Tool Kit Software License iNeeded for SCIEX OS 1.x and PeakView Software.

The Bio Tool Kit software can be activated within PeakView 2.x and SCIEX OS 1.x software but a separate software license is needed.

What Are the Specifications of the Six-Protein Mixture Supplied with the iTRAQ® Kit?

Specifications of the six-protein mixture (PN 4348363) supplied with the iTRAQ® kit include the accession numbers of the proteins and their mass per tube (in µg and nmol).

01/09/2019    Academia Omics | Pharma CRO | iTRAQ Reagent

What Are the Peptide Sequences in the Six-Peptide Mixture (PN 4465940)?

The six-peptide mixture (part number 4465940) is used for the calibration of mass spectrometers. The kit contains the following six peptides and their mono-isotopic masses: bradykinin (2-9 clip) (904.4681), angiotensin I (1296.6853), glu1-fibrinopeptide (1570.6774), ACTH (1-17 clip) (2093.0867), ACTH (18-39 clip) (2465.1989), and ACTH (7-38 clip) (3657.9294).

Nomencature Used by BiopharmaView™ Software for N-Gylcan Names

BioPharmaView™ software uses predefined N-glycan structures (following the Ludger product names), or software users have the option to build their own custom modifications.

How Do You Export a Library in LibraryView™ 1.0.1 Software?

The export of a library from LibraryView™ 1.0.1 software is described here.

Exporting ProteinPilot™ Software Data to PRIDE (PRoteomics IDEntifications)

Exporting ProteinPilot™ software data to the PRoteomics IDEntifications (PRIDE) database requires the .group files be converted to XML files. ProteomeXchange fully supports both MS/MS proteomics and SRM data submissions. Other types of proteomics data, including ProteinPilot data, is also possible using the partial submission mechanism.

11/09/2018    Academia Omics | Software

Difference between Rapid and Thorough Searches in ProteinPilot™ Software

The rapid search and a thorough search settings in ProteinPilot™ software determine which parts of the search algorithm will be invoked and effectively how deep the sample will be searched to find the right answers.

How to adjust, save and export the table settings in an Analyst Quantitation Table

Instructions how to modify (choose and adjust the visible columns, change the significant figures and notation), save and export an Analyst Quantitation Table.

Using the 25 Micron ESI Electrode with the DuoSpray™ Source?

A 25 micron ESI electrode can be used with the IonDrive™ Turbo V source and the DuoSpray™ source.

iTRAQ® Reagents: Can Samples Labeled with Both the 4-Plex and 8-Plex Kits Be Mixed?

The iTRAQ® Reagents chemistry for 4plex versus 8plex kits is described.SCIEX does not recommend mixing samples labeled with the reagents from the two separate iTRAQ® kits, 4plex and 8plex, due to the differences in the reagent chemistry.

10/16/2018    Academia Omics | Pharma CRO | iTRAQ Reagent

Compatibility of ProteinPilot Software 4.5 Beta with Microsoft Office 2016

ProteinPilot software 4.5 beta is not compatible with Microsoft Office 2016.

Which Amino Acids in the PepCalMix Are Labeled?

The PepCal Mix (P/N 5045759) contains 20 heavy-labeled peptides, with the heavy isotopes incorporated in the amino acids, K and R.

Keeping a Nano LC/MS System Running after Sample Acquisition Is Completed

To keep a nano LC/MS system running after sample acquisition has completed, the LC/MS can be configured two different ways, assuming the Nano Eksigent 400 system is used.

Plate Template Used for Tissue Imaging on MALDI TOF/TOF Instruments?

To use the Mass Spectrometry Imaging Starter Kit design by LaserBio Labs™, your tissue needs to be mounted onto a blank LC MALDI plate. This blank MALDI plate fits a 123 mm x 81 mm plate holder. A starter template is provided here to create a customized plate for MALDI data acquisition.

10/08/2018    Academia Omics

What Are the Options in Data Explorer Software To Improve Spectral Quality?

This document lists a couple of options on how to improve spectral quality using Data Explorer software 4.11

07/09/2018    Academia Omics

Where Can I Find Instructions for the Protein Preparation Kit?

Protein preparation instructions can be found on the SCIEX website at https://sciex.com/Documents/tech%20notes/Protein-Preparation-Kit-Protocol.pdf or https://sciex.com/products/standards-and-reagents/automated-protein-digestion-solution.

Exporting .T2D Files in Batch Mode from the Raw Data Spotset

To export .T2D files in batch mode from the raw data spot set on a MALDI plate, locate the Remote Data Access software in the program files and install the T2DExporter.

06/04/2018    Academia Omics | Pharma CRO

Setting Up MRM Transitions if Q1 Mass Is Identical to that of a Second Compound

To set up a MRM transitions where the Q1 mass for one compound is identical to a second compound in Analyst® software, change the Q1 mass of the second compound by 0.1 -0.05 Da. After making this adjustment, the software will accept the duplicate mass for Q1.

Optimal CE Voltages for Peptide Analysis on TripleTOF® Systems

The collision energy (CE) and the collision energy spread (CES) values needed for peptide analysis (during protein IDA identification and SWATH® acquisition) can be optimized using Information in the rolling CE setting embedded in the Analyst® TF software.

Archiving and Purging MALDI TOF/TOF™ Data and Creating Database Backups

Described herein is a general procedure on how to archive/purge data from a MALDI TOF/TOF™ system, as well as how to back up data.

05/31/2018    Academia Omics | Pharma CRO

What Are the Reasons for Hybrid Electrodes Probe Blockage?

Common issue reported with hybrid electrodes probes.

05/15/2018    Academia Omics | Mass Spectrometers

Error in SWATH MicroApps: Window Widths below 4 Da Are Not Supported

This error will appear if the SWATH configuration file is not edited to allow for window widths below 4 Da.

05/15/2018    Academia Omics

Protocols for Protein Precipitation in Samples before Using iTRAQ® Kits

To prepare samples prior to iTRAQ® reagent labeling, use the following protocols.

05/01/2018    Academia Omics | Pharma CRO | iTRAQ Reagent

ProteinPilot™ 5.x Software: Incorrect Result Output for Instrument Names in the Group File

ProteinPilot™ software uses the incorrect mass spectrometer name in its group file output file. When a TripleTOF® 5600 system was selected, the group file contains the name QSTAR® Elite instead for system information. This causes the wrong results to be output; if the incorrect instrument name is used, then the incorrect tolerance settings are applied.

ProteinPilot Software Datafile Cannot be Searched because two files are acquired under same file name

Searching for ProteinPilot software files using Windows Explorer cannot be done because there are two files acquired under the same file name. This is a long known issue for all ProteinPilot versions that only one file per file name can be searched using ProteinPilot software.

BioPharmaview™ Software: Simultaneous Analysis of Disulfide Bridges and Cysteine Modification Not Possible

Disulfide bond mapping in BioPharmaView™ software is described in the user guide. However, creating a disulfide bridge table in addition to analyzing cysteine modifications simultaneously is not described and cannot be done.

MarkerView™ 1.2.1 and 1.3 software and PeakView® 2.2 software can import T2D files generated on the TOF/TOF™ series of instruments.

02/26/2018    Academia Omics | MarkerView Software

How Many Vials of Each iTRAQ® Reagent Are in the Multiplex Kit?

Each iTRAQ reagent multiplex kit (PN 4352135) contains 5 vials of of the following iTRAQ reagent labels: 114, 115, 116, and 117.

02/26/2018    Academia Omics | Pharma CRO | iTRAQ Reagent

Separating Concatenated .wiff Files in Analyst® Software

To separate concatenated .wiff file sets, a script called Make Subset File is used. This script might have limitations for Analyst® and Analyst TF software because it depends on the experiments in the file (i.e., the script does not work for IDA methods). The script is found on the Analyst TF software CD in the folder \Extras\Scripts\Make Subset File.

Which Calibration Standards Can Be Used for Intact Protein Analysis on TripleTOF® and X500 Systemss?

An APCI calibrant solution for the SCIEX X500B System and a mAb standard from Waters were compared. Results show that the mass to charge ratio for the calibrant solutions remain constant regardless of the charge state. Secondly, for readings over 500 m/z, the calibration is highly linear for the X500B system.

12/14/2017    Academia Omics | Pharma CRO | QTOF Systems

Tips and Tricks for Cation-Exchange Chromatography for the iTRAQ® Protocol

The manual injection procedure for the iTRAQ® protocol requires a 22-gauge syringe with a 2-inch needle (purchased separately). This article lists some tips and tricks on how to set up the syringe when using cation-exchange columns for samples treated with the iTRAQ reagent.

12/08/2017    Academia Omics | Pharma CRO | iTRAQ Reagent

Where can I download MaxQuant software?

MaxQuant software is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets. It supports all main labeling techniques like SILAC, di-methyl, TMT and iTRAQ, as well as label-free quantification.

12/01/2017    Academia Omics | Software

Where Can I Find a Column Part Number from Eksigent?

The provided link lists all micro and nano columns including nano chip columns.

How Does the Score in the Peptide Sequencing Section of BioPharmaView™ Software 2.1 Work?

Each peptide is displayed in a table after processing the peptide digest in BioPharmaView™ software. A score is given to each peptide after it is compared to the theoretical proteolytic digest.

Reasons for Data File Processing Failure with the Data Converter Version 1.3 Beta

What are the potential issues listed which can cause the SCIEX MS data converter version 1.3 beta to not work correctly?

11/22/2017    Academia Omics | Pharma CRO | Software

What Default URL Is Used for Configuring the Mascot Server with ProteinPilot™ Software?

Configuring the Mascot server from the ProteinPilot™ software requires the default URL to be used.

What Is Skyline Software and What Data Types Does It Work With?

This article includes a general description of the features of Skyline software and the possible data formats from SCIEX instruments that work with Skyline.

Acetic Acid Is Needed To Prepare the PepCalMix Peptides in the SWATH® Acquisition Performance Kit

This article describes the experimental issues when formic acid is used to prepare the PepCalMix for the SWATH® Acquisition Performance Kit instead of 5% acetic acid.

Where Can I Download Skyline Software ?

This article includes the link to a free download of Skyline software.

What Is the Full Amino Acid Sequence of BETA-GALACTOSIDASE in the LC/MS Peptide Calibration Kit?

The full amino acid sequence for beta-galactosidase is provided in the FASTA file format. The kit (part number 4465938) contains one vial of beta galactosidase digest (625 pmol/vial).

How Is a Hardware Profile Created in Simulation Mode with an Eksigent 4.x and Analyst TF Software?

Description of the steps to place the Eksigent software in the AAO system of the Analyst® software and how to run it in simulation mode.

How Is the SWATH® Acquisition Variable Window Calculator Excel Sheet Used?

This article includes step-by-step instructions on how to calculate variable windows for your SWATH® acquisition experiment and how to generate the input and output list.

What is the IP Address Used by the Uniprot Server to Submit a ProteinPilot™ Software 5.x Search?

This article describes the website links that are being used to submit a ProteinPilot™ software (v 5.x) search.

ProteinPilot™ Software 5.0: What Are the Criteria for Including a Peptide in the Feature Tab?

The general filters for peptides are listed here. These are applied through the feature tab in ProteinPilot™ software.

Is ProteinPilot™ Software 5.0.1 Compatible with Windows 10?

Is ProteinPilot™ Software 5.0.1 compatible with Windows10? No, it works only with Windows 7, Service Pack 1, 64-bit.

How Are SWATH™ Acquisition Files Recalibrated?

The procedure for recalibrating a SWATH™ acquisition file is outlined here.

How Can an Ion Library Group File Generated by ProteinPilot™ Software Be Uploaded to BaseSpace?

The procedure for uploading a group file generated by ProteinPilot™ software is described here. The group file is used as an ion library in BaseSpace and is uploaded using the CloudConnect MicroApp within PeakView® software.

08/03/2017    Academia Omics | PeakView Software

What Is the Function of the Collision Gas (CAD) on QTRAP® System Instruments?

The various functions of the CAD gas are described for the QTRAP® System instruments and the different scan types.

What Is a Fraglet.exe Error when Running ProteinPilot™ Software 5.0?

A "Fraglet-exe-Error" can have many causes within the ProteinPilot™ software. In some cases, this error is caused when installing ProteinPilot on an incompatible operating system.

Intact protein script for TripleTOF™ instruments

This knowledge article summarizes when to use the intact protein script in

How Are the Method Parameters Chosen for Autocalibration Samples in the X500 Series?

Method parameters for autocalibrations submitted in SCIEX OS batches are automatically chosen from the sample after the autocalibration.

How do I store iTRAQ® labeled peptides?

Store iTRAQ® reagent labeled peptides at -20 or -80 degrees Celsius. Avoid having the peptides undergo multiple freeze/thaw cycles. iTRAQ-labeled peptides can degrade over time.

04/07/2017    Academia Omics | Pharma CRO | iTRAQ Reagent

MALDI TOFTOF: Can I calibrate using a linear mode acquisition method in batch mode?

When calibrating a linear mode acquisition method in batch mode the software reports that a reflector mode acquisition method is required in order to use the batch mode.

03/24/2017    Academia Omics | Pharma CRO

Why doesn't a TrEMBL FASTA file work for a ProteinPilot search?

This is a known issue, and the TrEMBL database is not recommended for use with ProteinPilot software. The TrEMBL database is automatically annotated and not reviewed and could contain redundancies in terms of protein sequences, protein ascension numbers, etc.

How many processing cores will my ProteinPilot Software use?

The number of processing cores used by ProteinPilot Software is defined by the license file and the physical capabilities of the instrument.

How do I search an EST or other nucleotide database

How do I search an EST or other nucleotide database

ProteinPilot error fraglet.exe CHEMICAL EXCEPTION

ProteinPilot error fraglet.exe CHEMICAL EXCEPTION

Can I reverse the flow on my Eksigent Nano Chrom XP C18 column when experiencing high back pressure

Can I reverse the flow on my Eksigent Nano Chrom XP C18 column when experiencing high back pressure

What solutions should be used for the nano 2D LC Eksigent pump seal rinse and the Autosampler wash

What solutions should be used for the nano 2D LC Eksigent pump seal rinse and the Autosampler wash

10/07/2016    Academia Omics | NanoLC

How do I modify the parameter translation file for mass tolerance and threshold for reporting iTRAQ ratios

Mass tolerance and threshold values for reporting iTRAQ ratios can be tuned by editing a configuration file.

10/07/2016    Academia Omics | iTRAQ Reagent

Can ethanol be substituted for isopropanol when performing iTRAQ protocol for 4Plex and 8Plex

Can ethanol be substituted for isopropanol when performing iTRAQ protocol for 4Plex and 8Plex

10/07/2016    Academia Omics | iTRAQ Reagent

Can the Eksigent Nano III ion source fittings withstand the back pressure when using a UPLC

Can the Eksigent Nano III ion source fittings withstand the back pressure when using a UPLC

10/07/2016    Academia Omics | NanoLC 400

Ekspert™ 400 LC system – Change the mobile phase

How to change mobile phase on Ekspert™ 400 LC system

10/07/2016    Academia Omics | Pharma CRO | NanoLC 400

Late elution of peaks on Eksigent nano Tempo Classic

Late elution of peaks on Eksigent nano Tempo Classic

10/07/2016    Academia Omics | NanoLC 400

Why are the peaks centroided in ProteinPilot Group files

Why are the peaks centroided in ProteinPilot Group files

How do I reset values or changes made in the ParameterTranslation file or ProteinPilotDataDictionary file in ProteinPilot

It may be required to reset the values within these files if they have been manually adjusted incorrectly.

Can I convert t2d files to mzxml file using 4700 data

Can I convert t2d files to mzxml file using 4700 data

10/07/2016    Academia Omics

Can I use the Proteinpilot SW with 4700 data

Can I use the Proteinpilot SW with 4700 data

fraglet.exe not wellformed invalid token at line 1 and position 33112not wellformed invalid token at line 3 and position 71

ProteinPilot gives the error fraglet.exe not wellformed invalid token at line 1 and position 33112not wellformed invalid token at line 3 and position 71

Ekspert 400 AS3 Error Message ERROR SAMPLE-NEEDLE VIALBOTTOM ACTIVATED

Ekspert 400 AS3 Error Message ERROR SAMPLE-NEEDLE VIALBOTTOM ACTIVATED

09/04/2016    Academia Omics | NanoLC 400

Troubleshooting Amplifier Reset

An Amplifier Reset alert simply means that the pump has emptied and refilled. As the pump has a finite volume then this refilling is expected if running for a long time or at a high flow rate. Note that an Amplifier Reset is an Alert not an Error. If an Amplifier Reset occurs the pump will refill and continue to pump at the programmed rate. An Amplifier Reset will not cause the sample batch or queue to stop. If an Alert message appears indicating that an Amplifier Reset has occurred the first step is to determine if this is a natural reset or not. In the following section are steps described how to determine the cause of an amplifier reset.

09/04/2016    Academia Omics

Ekspert 400 AS3 Error Message Pump volume is not sufficient to run LC method without a restroke.

Ekspert 400 AS3 Error Message Pump volume is not sufficient to run LC method without a restroke

09/04/2016    Academia Omics

How to install ProteinPilot 4.5b and upgrade from ProteinPilot 4.0 to ProteinPilot 4.5b

This procedure describes the removal and install of ProteinPilotTM software 4.5b in great detail.

Can I use the Eksigent 3.12.1 software on a Win7 64 bit PC

Instructions on how to configure Windows 7 for use with the Eksigent 3.12.1 software.

07/08/2016    Academia Omics | NanoLC 400

MarkerView 1.2.1 error Could not get method information for A1_MS_1.t2d when trying to download data

MarkerView 1.2.1 error Could not get method information for A1_MS_1.t2d when trying to download data

07/08/2016    Academia Omics | MarkerView Software

Does the Mascot.dll script work with Analyst 1.6 on a win 7 PC

Defines the issues and workarounds required to use the script.

07/08/2016    Academia Omics | Software

TripleTOF® System Vacuum Interface Routine Cleaning

How to clean the vacuum interface of the TripleTOF instruments

MarkerView Microsoft Office 2013 This method or property is not available because this command is not available for reading.

When Markerview 1.2.1 is used in conjunction with Microsoft Office 2013 report generation fails with the message This method or property is not available because this command is not available for reading.

10/01/2015    Academia Omics | MarkerView Software