New features and improvements - New features and improvements - Oribitrap Hybrid Series ICSW 5.1 Release Notes - Orbitrap Excedion Series - Orbitrap Exploris MX MS - Orbitrap Hybrid Series - Orbitrap Exploris 120 MS - Orbitrap Exploris 240 MS - Orbitrap Exploris 480 MS - Oribitrap Hybrid Series ICSW 5.1 Release Notes - New features and improvements - Thermo Scientific Orbitrap Hybrid Series 5.1 Instrument Control Software Release Notes - Orbitrap Excedion Series - Orbitrap Exploris MX MS - Orbitrap Hybrid Series - Orbitrap Exploris 120 MS - Orbitrap Exploris 240 MS - Orbitrap Exploris 480 MS - topic

New features

—

—

Tune and Method Editor support new Orbitrap Exploris EFOX mass detector.

Improvements

842157

—

Inject Filtering: The instrument allows wider inject filtering for reduced fragmentation of intact proteins.

832170

—

OptaMax Plus: Vaporizer Temperature of 650 °C for the OptaMax Plus is available

851002

—

Mild trapping available on Exploris MX in Application Mode Small Molecule

Defect fixes

245291

2 - High

Chromeleon: Exploris Series ePanel shows disconnected but the instrument can still be controlled in Thermo MS Tuning, calibrations do not show in audit trail

332442

3 - Medium

Exploris GC: Self Calibration is turned on per default after upgrade from 4.1 to 4.2 (first time)

802783

3 - Medium

UI: ME: eDR: View Type: Quan View: Switch button is still visible

822716

2 - High

TNG Tune: 2nd graph discloses quadrupole plots that should only be shown with elevated rights

828499

3 - Medium

UI: ME: Activation Type - Compound specific settings - can be editable for not relevant rows

835457

3 - Medium

UI: ME: eDR m/z window tolerates first mass higher than 2500 for both eDR Window Types

835849

3 - Medium

UI: ME: Adaptive RT: not uploading a rtbin file with FAIMS if previously FAIMS voltage is not set to On

835858

3 - Medium

UI: ME: Adaptive RT alignment must be compatible with Negative polarity for MS2 scans

836578

3 - Medium

FAIMS: IC source cannot be run when FAIMS is installed on OE480 or Orbitrap Excedion Pro w/o ETD (SW error is thrown)

824387

3 - Medium

EThcD: Tune Spectrum View Scan filter displays obsolete values in free running mode

827917

2 - High

During the execution of sequences in Xcalibur, the following message may punctually be reported in warning popup: "Run preparation stopped with an error: GettingPreparedAgent receives Exception in waiting for the MS: The mass spectrometer doesn't assume the expected state."

844250

2 - High

Define Scan in Exploris MS tuning tab glitches to different settings in Chromeleon Console

856391

2 - High

Orbitrap Hybrid Series: MS sequences interrupting due to MS response timeout (partial fix)

New features

396616

—

Orbitrap Excedion Pro - Method Editor: Adaptive RT Full Scan experiment enables Dynamic Time Scheduling for subsequent Targeted MS2 Scans, and also Data Dependent Scans using a Targeted Mass Inclusion Filter, without the need for spiking internal standards.

424869

—

Orbitrap Excedion Pro - Method Editor: Enhanced Dynamic Range (eDR) is available as new Full Scan property

351254

—

Orbitrap Excedion Pro - Method Editor: Pre-Accumulation for MS2 Scans is available as new Global Setting, and enables an additional Resolution 3750.

156646

—

Orbitrap Excedion Pro - Method Editor: Targeted Loss Trigger allows for triggering a dependent scan only when a specified loss ion is detected

746804

—

Orbitrap Excedion Pro BioPharma Edition provides an Extended Mass Range up to 12k Da for all supported scan types. Tune Calibration pane provides a new Calibration Type 'Extended Mass (AHFP)'.

785637

—

Orbitrap Excedion Pro supports the new Optamax Plus ion source

634919

—

Orbitrap Excedion Pro: Activation Types ETD and EThcD enable ETD (Electron Transfer Dissociation) to be optionally combined with supplemental HCD Activation (EThcD). The IC Source Calibration and Check are extended by ETD procedures.

775273

—

Orbitrap Excedion Pro: Hybrid-DIA - Adaptive RT tMS2 workflow supports DIA acquisition combined with Adaptive RT Dynamic Time Scheduling in one method.

155331

—

System Calibration: The System Calibration duration is shortened by an improved Inject Filter Isolation Calibration

Improvements

746032

—

FAIMS: PDF Reports contain additional Embedded System Information about the FAIMS configuration

776123

—

Method execution displays scan type in the RAW file scan header

789709

—

Tune: The "Smart burn-in of ICS" provides higher robustness and early stopping criteria, and replaces the "Short burn-in of ICS" procedure

Defect fixes

751317

3 - Medium

FAIMS: MS disconnection issues after running sequences in User Defined FAIMS Mode

337356

3 - Medium

Method Editor: Chromeleon does not apply method settings from System Templates when "keep current source settings" is selected

760961

3 - Medium

Method Editor: Targeted Mass Filter - Set Maximum Injection Time per Compound: The custom set value must be transferred to the Mass List table

769342

3 - Medium

Method Editor: Targeted Mass Filter with an empty Mass List Table may crash the Method Editor / is not functional when trying to clear or create a new method.

288280

3 - Medium

Method Editor: Template methods cannot be saved after saving a number of methods previously

692608

3 - Medium

Method Transfer: Erroneous Importing of Orbitrap Exploris 120 methods without AcquireX that were created with ICSW versions smaller than 3.0

826756

2 - High

Method Editor: Last mass for AIF isolation is too low (m/z 40-2500) for intact protein mode

New features

440406

BioPharma: Intact Protein mode supports Full Profile mode

235125

Method Editor: Targeted Mass Filter supports maximum Injection Time as a table value for ddMS2 Scans

153450

Orbitrap Exploris 480 - TurboTMT: TMTpro reagents are expanded to 32-plex

Improvements

374516

Divert Valve: MS Valve turns to defined Waste Position in case of an MS instrument Error to protect the ion source from being flooded

455020

Exploris GC 240: "GCHigherResolution" license enables additional Resolutions 270 k and 300 k

458128

Exploris GC: Tune: Optimization tab provides new CI reagent gas flow optimization procedure

603775

Method Editor: Targeted Mass Exclusion filter is now enhanced by a toggle "Exclude isotopic cluster"

469661

Sequence acquisition stops when the instrument turns to "Source is open / Standby" mode

614368

System Calibration: New Calibration Type IC Source is now selectable separately

621042

System Calibration: Updated checkpoint settings are now permanently saved after each successful calibration step

306611

Tune: Alert Console emits an Error if UHV gauge is defective

Defect fixes

367365

Chromeleon: Method Editor does not size correctly in Chromeleon 7.3.2

749427

Chromeleon: Unable to create instrument methods with Chromeleon 7.3.2 MUc

757353

Exploris GC: Tune Optics are not loaded correctly

721841

FAIMS: MS disconnection issues after running sequences in User Defined FAIMS Mode

327877

Method Editor: Incorrect validation of hidden property "Scan Priority"

593860

Method Editor: Method execution of Decision Trees with Charge State dependent outcomes fails

378777

Method Execution Scan-to-Scan EASY-IC: In parts of the LC/MS run, the instrument does not detect the fluoranthene signal

753295

RAW file: Scan filter displays wrong average Collision Energies (CE) when doing multiplexed MS2 scans with stepped CEs

New features

330867

Exploris GC: User-defined Lock Mass Correction Mode “RunStart” at the beginning of the data acquisition.

344696

Method Editor - Scan Properties: “Custom AGC Targets” display “Absolute AGC Values”.

349492

Method Editor - Scan Properties: “Use EASY-IC” is extended to Lock Mass Correction Mode “Timed”.

344714

Method Execution: extended the Maximum Injection Time Mode “Dynamic” to ddMS2 Scans.

344698

Tune and Method Editor OT Exploris 120 and MX: added Resolution settings 22500, 45000, 90000.

Improvements

321592

Exploris GC: Method Editor - Scan Properties: Product Ion Scan provides Product Ion Window Modes “Center Mass” and “m/z Range”.

326688

Exploris GC: Tune - Calibration: Manual Calibration table is separated by polarities.

455932

Exploris GC: Tune - Optimization: Leak Check has improved scan settings to eliminate m/z 42.

250676

Method Editor - Global MS Settings: “User-defined Lock Mass Injection” transitions to a Scan Property.

346290

Method Editor - Global MS Settings: Renamed “Internal Mass Calibration” to “Lock Mass Correction”.

340473

Method Execution: Instrument preserves the ion source properties defined in the instrument method after method execution has finished.

428795

OT Exploris 240: ddMS2/tMS2 scans allow for broader isolation windows up to 2000 m/z .

338482

OT Exploris MX: Tune Diagnostics - Define Scan functions are extended to Orbitrap Exploris MX to access all MALDI related functionalities.

297528

Tune - Alert Window emits a warning when starting Calibration/Check procedures while syringe pump is off.

277441

Tune Diagnostics - Tools allow for setting a PrOSA Limit value to exclude extreme PrOSA Scaling factors.

158424

Tune Preferences: Hotlink function is now limited to the Ion Source properties.

347290

Tune Preferences: The One-Point-Self-Calibration options are extended by a Calendar View.

358862

Tune: System Calibration stores all calibration values before the ICS Calibration, independent from the ICS HV Calibration outcome.

Defect fixes

381480

API: Using Handshake degrades instrument scan rate.

458619

Chromeleon - Exploris GC: Method Editor Throws TNG Errors in CM

360686

Chromeleon Studio is showing very slow performance, and sporadically no MS Device instrument.

390589

Ensure API test programs can load from path different to regular "programs" path.

443793

Exploris GC: Hotlink causes “Resolution” and "Scan Range Mode” cells flashing.

390653

FAIMS: instrument should be in standby while running Tune DV diagnostic procedure.

374578

Method Editor – DIA: error popup message “Object reference not set to an instance of an object” appears when modifying MSX ID values.

455541

Method Execution: EASY-IC on: Scan-to-scan cause interruption in rawdata file.

378777

Method Execution: In parts of the chromatogram the instrument does not detect the fluoranthene signal to correct the masses.

378826

Method Execution: unnecessary Hidden Scans/Polarity Switching in tMS2 Method with Funnel RF Level as Table Value.

437271

Method Transfer is not recognizing the OT Exploris model difference in Chromeleon [CM 7.2.10 MUh].

456234

Tune: sporadic false alerts “Source is open”.

485992

Sporadic missing scan in certain acquisition conditions (e.g., TurboTMT).

Defect fixes

424111

Software upgrade to version > 4.2 SP2 may result in a severe issue with loss of instrument configuration.

415092

After software upgrade from version 4.2 to a newer version, Tune displays obsolete warning alerts ([SSPI Link] – Reconnect during run-time) after firmware has been updated.

Defect fixes

356658

FAIMS Cooling Gas flow jumps to 20 L/min

404260

System Calibration: During Quad DC offset calibration, one point is sometimes too far off

405297

System Calibration: Quad isolation shape m/z 1034 iso 500 is not always detected

403256

System Calibration: Quad RF DDS frequency does not get set always on instrument boot

Defect fixes

377461

System Calibration: C-Trap RF frequency calibration selects a frequency outside the optimum

384047

System Calibration: Orbitrap Exploris GC: C-trap RF Amplitude Min. Calibration failed with SW failure during run time

383676

Tune Status pane: Improved Turbo Pump readback robustness

Defect fixes

356984

Method execution Full Scan DDA with Targeted Mass Filter and Fixed/Stepped Collision Energies (CEs): fixed CEs in the Targeted Mass Filter are erroneously executed as stepped CEs

347689

Method transfer: Cannot open certain older methods with Orbitrap Exploris Series 4.2 ICSW – index out of range error message

351444

Orbitrap Exploris GC: License Error with 60k GCHCD license prevents running methods

356173

Orbitrap Exploris GC: Method Editor: Corrected acquisition delay tooltip in Global Settings

356170

Orbitrap Exploris GC: Method Editor: Factor 10x UI recommendation rule is erroneously applied to all GC System Templates

356174

Orbitrap Exploris GC: Method Editor: Restore Default context menu does not work for parameters under Ion Source Properties

364748

Full Scan acquisition with Mild Trapping option (Small Molecule Application Mode) leads to signal drop in positive mode

New features

153451

AcquireX support is provided for peptide mapping (AcquireX Ab) with Orbitrap Exploris 240 and Orbitrap Exploris 480

221915

Method Editor: New management of tables in DIA scan

168318

Method Editor: New table format is available for SIM scan. SIM with multiple broad scan ranges is provided for Orbitrap Exploris 120, 240 and GC.

153788
286667

Method Editor: Options are provided to select the order with which precursors are selected for data-dependent scans

186364

Method Editor: TMT 18-plex is supported by TurboTMT on Orbitrap Exploris 480

235118

Method Editor: The new option “Auto-Extended” is provided for MS2 Scan Range Mode (Small Molecule Application Mode)

285925

Orbitrap Exploris GC: Method Editor provides a “Run Start Mass Calibration” template in system template

290954

Orbitrap Exploris GC: Tune Calibration pane provides a Manual Calibration panel

284960

Orbitrap Exploris GC: Tune Preferences provides a panel for Self-Calibration Options

235073

Tune and Method Editor: Additional resolution settings are accessible for Orbitrap Exploris 240 and Orbitrap Exploris 480 (11.25k, 22.5k, and 90k)

214828

Tune: Scheduled one-point mass calibration (via Tune Preferences)

Improvements

302210

Diagnostics: FlexMix Spray Optimization (neg+pos) applies Source Gases independent from polarity

310820

FAIMS: Tune Calibration pane enables One-Point Mass and Customized Mass procedures which are compatible with FAIMS attached

208815

Method Editor: User experience is enhanced when changing “Max. number of multiplexed ions”

254731

Method Execution: Spray Voltage stays “On” during the execution of Run Start EASY IC

154537

Orbitrap Exploris GC: Chromeleon: Data Audit Trail exposes 'MS Tune Reports' from Thermo Exploris Series ePanel

Note This improvement is available only on Chromeleon versions ≥ 7.3.2.

318301

Orbitrap Exploris GC: Tune and ion source optimization reports contain a leak check history plot, filament current and emission current plots, and an emission current set value plot

327864

Tune and Method Editor: Optimized default ESI/HESI gas flow settings for Orbitrap Exploris 120, 240, MX

302209

Tune: Source gas and temperature are set independently from polarity

153260

Tune: Calibration Status panel: reworked the update of Recommended Calibration dates depending on the procedure outcome

308704

Tune: Calibration Status panel: clarified display of Last Successful Calibration to ‘Outdated’ after Venting and Bake-out

302209

Tune: Source gas and temperature are set independently from polarity

152982

Tune: Status pane: Added an exception for the “Temperature change since calibration” monitoring for automatically started bake-outs after venting the instrument

280624

The Orbitrap Exploris Series 4.2 Installer updates the MongoDB from version 4.06 to version 4.0.28.

Note MongoDB needs to be uninstalled manually when downgrading from version 4.2 to an older version. The ISO image contains a MongoDB uninstaller.

Defect fixes

291191

AcquireX: Method Editor needs to mark incompatible Mass List Types in red

203732

Chromeleon: Method Editor menu bar is missing

302180

Method Editor / Instrument Configuration: Settings “Contact Closure” are named the same but refer to different functions (Digital Input/Output)

245745

Method Editor: MSX ID in Mass List Table changes when switching between Quan and Qual Views

221534

MongoDB uses too large memory (>3GB) at background

318660

TurboTMT: Method Editor needs to mark the incompatible MS2 property “Scan Range Mode = Auto” in red

329295

Workstation method editor cannot be launched without Foundation installed (affects Chromeleon Enterprise)

322914

Installation of workstation OES removes previously installed workstation version

297887

System Calibration: Electronics Smart Calibration is checking against the wrong frequency range in interference peak removal procedure

Improvements

270859

FAIMS Pro and Pro Duo: Adjusted fan speed monitoring thresholds

254371

FAIMS Pro and Pro Duo: DV Tune and DV Check procedures operate at a wider DAC range to support FAIMS operation at altitudes > 2000 m

263849

FAIMS Pro and Pro Duo: Improved gas control to conserve cooling gas

218222

Instrument Manuals: PDF documents provide translations of the English Operating Manual and Pre-Installation Requirements Guide in Chinese, French, German (Operating Manual only), Italian, Japanese, and Spanish

229906

Tune System Calibration includes a reworked noise-canceling procedure (Interference Peak Removal) as part of the Electronics Smart Calibrations

154508

Tune System Calibration runs independent from selected Application Modes (Small Molecules, Peptide, Intact Protein)

250289

Tune System Calibration/Check: Improved robustness of the HCD Fragmentation and Trapping Efficiency Check

242936

Tune System Calibration: Further improvements of the Isolation Shape Analysis algorithm to obtain a shorter duration of system calibration procedure

232380

Tune System Calibration: HCD Fragmentation and Trapping Efficiency Check is now also part of the System Calibration

243124

Tune: The About Tune box now shows active licenses for all Orbitrap Exploris mo

156731

Tune: The Status pane (By Function / By Board) displays Turbopump readbacks in the Vacuum System node

152982

Tune: The Status pane (By Function) indicates the ambient temperature change since last calibration in the new Performance node

633

Orbitrap Exploris GC: Apply a yellow warning when a fullscan range is beyond the 15x rule in method editor

622

Orbitrap Exploris GC: Remember the last used polarity to an added new line in the internal lock mass table in method editor

653

Orbitrap Exploris GC: Enable MSMS and all resolutions on the Standalone Workstation

Defect fixes

164799

Chromeleon: The instrument method of extracted raw files now shows the Orbitrap Exploris model as instrument name

245000

Chromeleon: Method Editor shows AcquireX UI Elements when instrument is operated by Chromeleon

153267

Chromeleon: Method Editor: Cannot edit Mass List Tables when maximized as popup window

267594

Method Editor: Added 45000 resolution for DIA Scans

233648

Method Editor (Full Installation): RF Level Conversion is erroneous when importing methods between Orbitrap Exploris 120/240/MX and Orbitrap Exploris 480

258112

Method Editor Ion Source Properties: Gas Mode settings are available when Source Type is NSI

243767

Method Editor: Orbitrap Exploris 120 Mass List Tables: MSX-IDs are changed when saving and reopening the method

263755

Method Editor: tMS2 Scan: Method Download Validation fails with stepped Collision Energy

280344

Method Editor: When “RunStart” is selected in the global MS Settings, scan properties show “Use EASY-IC” parameter

258279

Method Execution: Multiplexing in tMS2 negative mode is not executed when polarity is a table value

261532

Tune Calibration Status: Recommended Calibration Dates need to reset after Venting and Bake-out event

258076

Thermo Foundation Instrument Configuration: The Contact Closure configuration dropdown list labels are now aligned with the Method Editor (Transition close-to-open, Transition open-to-close)

258413

Nanospray Flex Ion Source: Source interlock does not always prohibit acquisition mode

625

Orbitrap Exploris GC: Correct “Collision Energy Type” in MS2 Scan type in Tune

627

Orbitrap Exploris GC: Correct “HCD collision energy” tooltips in Method Editor

632

Orbitrap Exploris GC: Correct “Negative Quad Isolation Check” error message

636

Orbitrap Exploris GC: Add “Ion Source Optimization Report” Header to the optimization report in Tune

637

Orbitrap Exploris GC: Default “Hot link” is unchecked in Tune Preferences

640

Orbitrap Exploris GC: Change default mass and mass range under Optimization in Tune

661

Orbitrap Exploris GC: Correct “Injection Flatapole DC and Inter Flatapole Lens” names that associate to the corresponding procedures in Tune

208147

Orbitrap Exploris GC: Plot Chromatogram is not active when the system is on

250789

Orbitrap Exploris GC: User saved “Favorites” settings in Tune are not loaded if MS2 scan is defined with normalized collision energy

265908

Tune Diagnostics: Removed “ICD Calibration (No Ions Required)” from Partial Calibration tree

153053

Tune Plots: All plots need to clear when going to the next sub procedure

154440

Tune Plots: Context menu “Copy to Clipboard” needs to be functional outside the graph plot area

276236

TNG Tune: Set Value Positive Ion Spray Voltage shows value “0” instead of actual set value when running sequences

Defect fixes

252969

System Calibration: eFT calibration may fail due to wrong fit

253113

Orbitrap Exploris MX System Check: Negative HCD Fragmentation and Trapping Efficiency Check may fail on too low m/z 1506 intensity

New features

188489

Tune: Customized Mass Calibration and Check run the Mass Calibration with User-definable mass lists.

190826

Tune: Calibration pane provides a One-Point Mass Calibration procedure using fluoranthene.

152876

Tune: Fore Vacuum supervision: The user needs to be informed if transfer tube is clogged.

153034

Method Editor: Global Settings - Internal Mass Calibration provides various internal calibration modes (RunStart, Scan-to-Scan, Timed).

154268

Method Editor: Global Settings - Internal Mass Calibration offers Lock Mass Injection functionality for user-defined lock masses.

153449

Raw file spectra provide access to extended peak data supported by FreeStyle 1.8 and higher

Improvements

235608

Tune and Method Editor Precursor m/z: Quadrupole Isolation Range checking needs to consider the first mass of the quadrupole isolation window.

236947

Tune and Method Editor Scan Range checking needs to restrict Full Scan ranges to the Factor 15 rule (Orbitrap Exploris 120, 240, 480, and MX).

214822

Tune Diagnostics: rearranged the Tools tree for improved access to the toggles and settings separated by category: Calibration, Define Scan, Application Mode, Method Setup, Peripherals.

193411

Tune System Calibration: Faster, more robust Isolation Shape Analysis algorithm results in shorter duration of system calibration procedure.

557

Tune: Mass Calibration Due Time is active in Diagnostics Pane also for Orbitrap Exploris GC.

629

Orbitrap Exploris GC Tune: Move “Quadrupole Isolation Check” and “Quadrupole Calibration” to Diagnostics Pane.

604

Orbitrap Exploris GC Tune: improvements in the Quad Iso Calibration procedure.

195617

Chromeleon: ePanel Thermo MS Tuning: Instrument Audit Trail logs information about Tune events.

225995

FAIMS Pro Duo: a firmware update mitigates 'overcooling' of the FAIMS electrodes.

214725

Software Manuals / Online help: New website https://www.analyteguru.com/ succeeds deprecated PlanetOrbitrap.com.

156632

Thermo Foundation Instrument Configuration: Ion Source: When toggle “Enable Sweep Gas for NSI Source” is disabled, the sweep gas will disappear from the Tune and Method Editor user interface, and inactivate the sweep gas flow.

243744

Method Editor: Full Scan: added a recommendation to set the first mass to values ≤2500 m/z.

203331

Method Editor: Targeted Mass Filter: Property 'Collision Energy Mode' is removed and HCD Collision Energy (% or V) allows access to 1 (fixed), and 2, 3, 4, 5 (stepped) set values.

211730

Method Editor: Targeted Scans: Property 'Collision Energy Mode' is removed and HCD Collision Energy (% or V) allows access to 1 (fixed), and 2, 3, 4, 5 (stepped) set values.

559

Orbitrap Exploris GC Method Editor: Add property “Isolation offset” to SIM scan.

217910

Method Execution: EASY-IC applies the same lock mass correction behavior for ddMS2 scans as with User Defined Lock masses.

213667

Orbitrap Exploris 120 provides access to precursor m/z isolations up to m/z 2500 in ddMS2/tMS2 and SIM scan types.

Defect fixes

204120

Tune Diagnostic procedure for ICS Burn-in and HV Current Calibration unexpectedly requires FlexMix infusion.

533

Orbitrap Exploris GC Tune: Limited the mass range in plot chromatogram and monitor mass accuracy tables.

555

Orbitrap Exploris GC: Reorder repeller and source offset values recorded in raw files under Optics table of Instrument Method section.

153327

Chromeleon: AcquireX UI Elements show in Method Editor when instrument is operated by Chromeleon.

233966

FAIMS and tSIM ddMS2 - Method Execution: MS2 scans are collected at the same CV, regardless of the CV used as a table value in the master SIM scan.

245244

FAIMS: Tune Ion Source pane: Sweep Gas is set when using “Get Default” function.

153573

Thermo Foundation Instrument Configuration: Behavior of “Enable Sweep Gas for NSI” differs from Tribrid Series Instrument Control Software.

235015

Method Editor: 45000 resolution is missing for Full MS and SIM.

153360

Method Editor: Ion Source Properties: UI validation formula for gas flows is incorrect.

243792

Method Editor: Mass List Tables: Within the same User-defined MSX ID group, different HCD Collision Energies and Adducts are restricted erroneously.

243763

Method Editor: Mass List Tables: Collision Energies (CE) are not imported when CE types (Absolute, Normalized) are different.

218273

Method Editor: tSIM + MSX methods with adjacent mass ranges are correctly validated but not executed.

237786

Method Execution: EASY-IC does not correct masses in ddMS2 scans.

New features

153032

FAIMS Pro Duo Interface: Tune and Method Editor support Highflow LC/MS applications using HESI/APCI sources

152894

Tune: Calibration pane user interface is aligned with Tribrid Series 3.4

186434

Orbitrap Exploris 120 Method Editor provides more options: up to five experiments per method, Microscans, Multiplexing of up to 20 targets, Custom AGC Target

174361

Method Editor provides an Isotope Exclusion Filter to choose assigned or unassigned isotopes for triggering data dependent scans

Improvements

190370

FAIMS Pro Duo: improved AGC performance when method applies different Compensation Voltages (CV)

199341

FAIMS Pro Duo: High resolution mode definition: inner electrode temperature increased from 70 °C to 80 °C

156627

Data acquisition: Intensity display correction for very low precursor isolation widths

155669

Tune: System Calibration: improved resume function from the last valid checkpoint if procedure has failed

194014

Tune: System Calibration: improved Injection Filter Low-m/z RF Calibration to enhance ion transmission for m/z values < m/z 150 on some systems

209230

Tune: Calibration option 'Skip Spray Stability Evaluation for Mass Calibration' moved to the Diagnostics pane

189067

Tune and Method Editor support MALDI and DART sources for Orbitrap Exploris 120, 240, 480

202700

Tune: improved readability of PDF Reports for calibration, check, and diagnostics procedures

174997

Method Editor: Targeted MS2 scans and Targeted SIM scans support Polarity as a table value also when multiplexing in tSIM and tMS2 experiments

153453

Method Editor: Targeted MS2 scans support Fixed and Stepped Collision Energies as a table value also in multiplexing tMS2 experiments

166860

Method Editor: Targeted Mass Filter supports Stepped Collision Energy

187465

Method Editor: RunStart EASY-IC scans are moved to the “Prepare for Run”-time and consider more than the very last lock mass correction for a more reliable lock mass correction at the beginning of the data acquisition

155244

Method Editor: Mass List Table UI recommendations are aligned with Tribrid Series 3.4

175638

Orbitrap Exploris 480 Method Editor: Dynamic Exclusion Filter supports prefiltering data dependent scans with multiple branches

Defect fixes

201250

Data Acquisition: Missing masses in Full MS when first mass is set > m/z 2500

202960

FAIMS Pro Duo: DV Tune procedure gives temporary false error alert

177971

Tune: Calibration: System always switches to Low Pressure after procedure run if in Intact Protein mode regardless of prior pressure

204120

Tune: Diagnostic procedure for ICS Burn-in and HV Current Calibration unexpectedly requires FlexMix infusion

152898

Tune: Error message for HESI vaporizer readback is incorrect on certain instruments due to wrong delta value

153397

Tune: System Calibration: When calibration fails, Recommended Date info gets lost and Performance Status shows an Error

183927

Handshake: When recording a RAW file triggered by handshake mode, one extra scan is added into RAW file

190496

Method Editor Summary: Error when printing (complex) instrument methods

198382

Method Editor: DIA method does not start because calculated window lies outside precursor mass range when Window Placement Option is active

207283

Method Execution Orbitrap Exploris 480: Cycle time is longer than defined in the method when multiple ddMS2 branches use scan priority

546

Orbitrap Exploris GC - Tune: Leak Check fails when Scans to Average is turned on in Tune.

540

Orbitrap Exploris GC - Tune: Incorrect Theoretical Masses for Negative Ions are shown in Customize Calibration within Tune.

541

Orbitrap Exploris GC - Tune: Users cannot run a normal mass calibration after a custom calibration. Customize Calibration runs even if it is not selected.

186

Orbitrap Exploris GC - Tune: Selecting “Abort” does not stop all selected Ion Source Optimizations.

New features

152951

FAIMS Pro: Data acquisition optimizes FAIMS CV post-switching delay time when using multiple CV Voltages per experiment

153796

FAIMS Pro: Total Carrier Gas Flow succeeds FAIMS User Gas to enable lower flow rates for improved nano spray (NSI) stability

153696

FAIMS Pro: Instrument configuration supports user-defined IP addresses for FAIMS

152892

Tune Diagnostics provides restructured procedures separated by category (Partial Calibration, Optional Calibration) and polarity (Positive, Negative)

152877

Tune Diagnostics provides Low m/z Spectral Mass Accuracy Calibration and Check to obtain high mass accuracy also in the low mass range

154453

Tune Diagnostics provides a tool to change the Mass Calibration Due Time

153319

Tune supports Collaborator interfaces via license

153450

Method Editor supports TMTpro Reagent (TMT-16-plex) for Orbitrap Exploris 480

163618

Method Editor supports variable collision energies in a Mass List Table for multiplexing experiments

Improvements

153497

Tune: Instrument Status pane displays vacuum pressures in a separate heading “Vacuum System”

152895

Tune: System Calibration and Check stop the syringe pump when procedure has finished to save consumption of FlexMix

152998

Tune: System Calibration: Calibration Solution Pre-Check forces the ion transfer tube to 320 °C for optimal spectral quality of FlexMix

152997

Tune: System Calibration includes an Interference Peak Removal procedure (only run after Venting and Bake-out)

152996

Tune: System Calibration provides an improved Quadrupole Main and End Segment DC Calibration

185621

System Calibration Negative: Improved robustness of ICS Active HV Current calibration subprocedure so that the procedure runs successfully after the first attempt

152994

Tune: System Check checks HCD Fragmentation/Trapping in both ion polarities

152978

Tune Diagnostics provide Tooltips for the whole diagnostics procedure tree

152897

Tune Diagnostics provide High Mass Range Calibrations (AHFP) also for Negative polarity when using Application Mode 'Intact Protein'

153051

Tune Diagnostics provides an improved Quadrupole Maintenance Check procedure

152983

Tune Diagnostics provides an improved Transfer Tube Maintenance Check procedure

154542

Tune Diagnostics procedure “Disable AGC” disables PrOSA when AGC mode = fixed

155647

Help Files: Method Editor provides an Online Help

155646

Help Files: Tune provides an Online Help

164760

AcquireX: Improved robustness for running experiments with Mass List Tables >5000 entries

152995

BioPharma: Improved eFT phase calibration to improve mass accuracy for High Mass Range applications

173884

tSIM Isolation Offset: the user can define an isolation offset for the isolation windows. The parameter is accessible as table value

152874

Method Editor: user needs to access updated System Templates as applies with the upcoming release OES 3.0

152875

Method Editor: Global MS Settings provide optimized default values per selected Application Mode (Small Molecule, Peptide, Intact Protein)

152979

Data Acquisition: RAW files include signal instability warnings in the Error Log

Defect fixes

152969

Chromeleon: User cannot open Method Editor Workstation Standalone from client computer

153344

Data Acquisition: Instrument still scanning in Standby and Off mode

183927

Data Acquisition: When recording a RAW file triggered by handshake mode, one extra scan is added into RAW file

153308

EASY-IC: In Polarity Switching experiments, ICS AGC is not done for each polarity separately

166232

Method Editor: DIA peak lists do not give original values when Mass Defect is set back to 1.0005 m/z

180523

Method Editor: Could not run Quan View DIA methods when Precursor Mass Range exceeded last mass m/z 524

166862

Method Editor: DIA scan Window Placement Optimization not properly applied for non-zero Window Overlap value

153270

Method Editor: Incorrect RF Lens Value Shown when Importing Methods between Orbitrap Exploris models

152940

Method Editor: Targeted Mass Filter does not support Fixed Collision Energy as table value (SureQuant)

170714

Method Execution: Dynamic exclusion filter: Mass tolerance mode “m/z” not working

153420

Method Validation: Mismatch of Ion Source type configuration during sequence submission

153577

Tune: System Calibration: Not all 'after venting procedures' run after venting - and 'after venting procedures' run although no venting took place

162574

Tune: Ion Source pane calls wrong default (H)ESI settings when 'Current LC Flow' = 500 μL/min

Improvements

9783

Orbitrap Exploris 120 Method Editor: Extend Data Dependent MS2 Method to create TopN experiments with N=1,2,3,4 in DDA

9781

Orbitrap Exploris 120 Method Editor: Provide System Templates for TopN experiments with N=1,2,3,4

Defect fixes

9667

BioPharma: Application Mode "Intact Protein" uses unsafe Extended Trapping 1 eV

9849

EASY-IC: ICS Prechecks should give dedicated error for extreme mass deviation

9683

EASY-IC: Issues with ICS ion intensities after prolonged idle time

9817

RunStart EASY-IC: Miscorrection when polarity switching is active

9844

System Calibration: C-Trap RF Frequency Calibration should avoid 3.2 MHz

Improvements

9409

Limit maximum C-Trap RF for increased robustness

9261

BioPharma: Provide AHFP calibration in TNG Tune Diagnostics

Defect fixes

9228

BioPharma Orbitrap Exploris 240: Loss of signal at maximum S-lens RF amplitude during intact mAb LC-MS analysis

9498

DIA: Method transfer from Orbitrap Exploris Series ≤ 1.1 SP1 to Orbitrap Exploris Series 2.0 does not consider the new AGC Target Normalized Base 1e5

9267

Diagnostics: Quadrupole Maintenance Test switches rod configuration but does not apply rod-specific calibration set

9524

FAIMS communication LED remains off when ion source is removed and reconnected

9242

FAIMS DV Tune and Check are not always shown in Tune Diagnostics pane

9461

FAIMS: In-source CID together with FAIMS results in a defect raw file

9464

Method Execution: In-source CID is not applied for data-dependent scans

9341

System Calibration: Checkpoint “Inject Filter (IF) Calibration” separates IF Isolation Calibration and Check, trapping users with poor IF calibrations

9470

UI: Method Editor crashes when deleting Targeted Mass Exclusion Filter from the method

9283

UI: Tune: Ion Source tab: “Get Defaults” ion source values for “Current LC flow” does not work

New features

4846

AcquireX: Orbitrap Exploris 240 and 480 support AcquireX workflows for Application Mode “Small molecule”

765

iAPI provides access to real-time control of Orbitrap Exploris 480

7514

Method Editor provides access to latest System Templates updates directly via the Thermo Fisher Cloud

8144

Method Editor: Application Mode ‘Small Molecule’ provides optionally access to Mild Trapping settings to reduce MS1 fragmentation of labile compounds

7513

Method Editor: Ion Source pane provides access to time-dependent ion source gas flows

5121

Method Editor: RunStart EASY-IC allows for internal mass calibration only at the beginning of the data acquisition

7512

Method Editor: tMS2 and DIA scans use isochronous injection times for multiplexing experiments

322

Method transfer: Method Editor is able to open and save methods from all Orbitrap Exploris Series instruments

7953

Tune Calibration pane: System Calibration provides improved help text in gray box, Alert Window and Calibration Reports

8174

Chromeleon: Orbitrap Exploris Series 2.0 shall run under Chromeleon 7.2.10

8173

Chromeleon: Orbitrap Exploris Series 2.0 shall run under Chromeleon 7.3

Improvements

5012

EASY-IC: Method Execution and Tune operate IC Source in idle mode when EASY-IC is not use

8090

EASY-IC: Thermo Foundation Instrument Configuration provides the possibility to switch off the IC Source

7545

FAIMS Pro provides same optimized CV values aligned with Tribrid Series and TSQ Series instruments

7121

Method Editor: DIA Scan AGC target is aligned with Tribrid Series - Normalized Base (100%) is equal to 1e5

8542

Method Editor: Mass List Tables: MRFA is default compound aligned with Tribrid Series

8816

Method Editor: Mass List Tables: Pop-up Warning 'Columns don't match' has improved messages when importing Exactive Series Global Lists

7119

Method Editor: Targeted MS2 Scans: 'Dynamic RT' provides a Retention Time Standards Table for Pierce PRTC Mixture (Orbitrap Exploris 240 and Orbitrap Exploris 480 models)

7410

Scan Filter: Methods using Internal Mass Calibration hide “lock” to improve generating XICs from the same scan filter

8001

Tune Calibration pane: Recommended Date of a mass calibration updates after successful system calibration

643

Tune: Ion Source pane provides improved default Ion Source Parameters

Defect fixes

7919

Installer: Uninstallation report of Orbitrap Exploris Series 1.1 shows content of installation

7840

Instrument stays in Off mode after Data System Computer Reset

6605

Method Editor: Audit trail shows wrong number of data dependent scans

8747

Method Execution: Too much precursor ion intensity is remaining when using stepped (N)CE

8555

RAW file Scan Header: Precursor Fit Filter: 'Error in isotopic envelope fit' is not recorded

4972

RAW files: Instrument Method settings do not reflect Method Editor Summary content

8489

Tune cannot start because TNGConfig.xmb file gets corrupted sporadically

6095

Tune Diagnostics pane shows FAIMS procedures although FAIMS is not attached with the instrument

8869

Tune: Application Mode 'Intact Protein': Trapping voltage of Continuous acquisition is misaligned with Instrument Method acquisition

Improvements

8053

Instrument Configuration: Check box “Enable Minimum Gas Flow Requirement for Ion Source” replaces the previous text field.

8348

System Calibration: Improved Bent Flatapole RF calibration.

8162

System Calibration: Improved Quad Transm./Rod Config Calibration.

8115

System Calibration: Removed checkpoint after quadrupole isolation calibration.

Defect fixes

8128

Alerts Console: Low OT temperature readback raises “Temperature too high” failure.

8297

Chromeleon: MS Tuning ePanel: Passed calibration file is named as Failed.

8180

Instrument Status: Electronics does not recognize readbacks being outside possible set range.

8284

Instrument Status: Threshold for warning “UHV gauge not ignited” is too high.

8070

Method Editor: System Templates: SureQuant method is not fully functional.

8031

Method Editor: TopN with multiple outcomes and ddSIM: Method Editor closes after appending a Targeted Mass Filter.

8040

System Calibration: Wrong threshold used in IF Low m/z RF Calibration.

New features

7538

System Calibrations must provide improved user experience.
User Story 4140—Tune: Diagnostics provide single-component sub procedures of system calibration.
User Story 6961—Tune Calibration: System calibrations are resume-able. Intermediate results are saved as checkpoints. This allows for optimizing spray conditions or refilling the syringe.

365

The user must be able to define favorite scan settings for easy access to sets of parameters.
User Story 748—Tune: Favorites pane: System Settings: Favorite settings for ESI source provide default ion source and define scan properties for calibration and diagnostics procedures.

7084

The Dynamic Exclusion filter must support a global list option (exclusion across experiments and outcomes).
User Story 819—Method Editor: Dynamic Exclusion Filter provides global functionality across all experiments in the method time line (new property “Share dynamic exclusion list with other selected dynamic exclusion filters”).

7126

Method Editor: Must have import list functionality from QE exported lists.
User Story 7339—Method Editor: Import of Exactive Series mass lists (CSV files) into Orbitrap Exploris Series 1.1 mass list tables is supported.

• Exactive Series global inclusion lists can be imported into Orbitrap Exploris Series mass list tables of scans (tMS2, Product Ion Scan, SIM Scan) and filters (Targeted Mass Filter).
• Exactive Series global exclusion lists can be imported into Orbitrap Exploris Series Targeted Mass Exclusion Filter.

762

The instruments must be able to interface with Chromeleon Software.
User Story 3174—Chromeleon: Tune and Method Editor are integrated in Chromeleon 7.2.10 (please install Chromeleon 7.2.10 hotfix files from thermo.flexnetoperations.com or from support.thermoinformatics.com).

Improvements

7297

FAIMS: Acquisition sequence will pause if system recognizes a DV drop. This gives the opportunity to run a DV Check or DV Tune procedure before resuming the sequence.

7538

System Calibrations must provide improved user experience.
User Story 6227—Tune Diagnostics: improved bake-out procedure.
User Story 6228—Tune Calibration: System calibrations are improved regarding robustness.
User Story 7167—Tune Diagnostics: improved ICS calibrations (EASY-IC option).
User Story 7295—Tune Calibration: Additional calibration information is displayed in gray box.
User Story 7328—Tune Diagnostics: “FlexMix Solution Evaluation” procedure to check for contaminated FlexMix.

7231

Tune Diagnostics: improved ion optics maintenance check.

7587

Tune Alert Window: improved messages about instrument status, calibration/check and diagnostics.

371

Users must have access to user manuals and online Help.
User Story 2145—UI: Tune shall display tooltips for each UI element.
User Story 2146—UI: Method Editor shall display Tooltips for each UI element.

7098

Updated system templates must be applied.
User Story 7420—Method Editor: Templates tab provides updated system templates for all application modes and for all models of Orbitrap Exploris Series MS systems.

Defect fixes

6490

Tune: APCI Source Optimization: Pos and Neg ion discharge current not supported.

6493

Tune: APPI Lamp of APPI ion source not controlled.

6733

Chromeleon: Data Acquisition via MS Tune panel is not supported.

6736

Chromeleon: Instrument Status ePanel needs to be configured manually.

6760

Chromeleon: Anomaly on first sequence acquisition in a series of sequences.

6790

Chromeleon: User mode selection anomaly.

6799

Instrument needs to be set to standby manually after reboot.

6812

ME and Tune GUI allows isolation low being higher than 2500.

6817

User does not reliably get a message when vacuum is not ready for instrument electronics to be set to “On” or “Standby.”

6819

Tune: Define Scan: Collision Energy Mode: Stepped CE is not supported.

6821

PDF Reports: Diagnostics: Quadrupole Maintenance Check Plot not included.

6850

Tune: Status Pane: Peripheral Devices: “Turbo Pump 1” show Status “Not Connected” although turbo pump is connected.

6877

Data Acquisition via Method: Source type “ESI” not supported.

6929

After boot, Orbitrap Supply throws a warning (Device Limit exceed and Status-Warn), which can be ignored.

6930

Sometimes system calibration can fail due to unstable spray.