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UltiMate 3000 RSLCnano Standard Applications Guide Page 3
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Page 4 UltiMate 3000 RSLCnano Standard Applications Guide
Contents
1 Using this Manual ............................................................................ 9
UltiMate 3000 RSLCnano Standard Applications Guide Page 7
Contents
Page 8 UltiMate 3000 RSLCnano Standard Applications Guide
1 Using this Manual
1 Using this Manual
This chapter provides information about this manual, the conventions used
throughout the manual, and the reference documentation that is available
in addition to this manual.
UltiMate 3000 RSLCnano Standard Applications Guide Page 9
1 Using this Manual
1.1 About this Manual
This document describes the setups, recommended experimental
conditions and testing procedures required to run standard applications
on the Thermo Scientific Dionex UltiMate 3000 RSLCnano system.
NOTICE This document is intended for Thermo Fisher Scientific (or
authorized) service personnel as well as customers to assist in the
installation and application testing of UltiMate 3000 RSLCnano systems.
It does not replace the IQ or OQ procedures. It is assumed that the
individual using this manual has had sufficient training in the installation
and usage of analytical instrumentation and is aware of the potential
hazards including (but not limited to) electrical hazards, chemical
hazards, exposure to UV radiation and exposure to pressurized solvents.
This manual contains important information about the correct care and
use of the UltiMate 3000 RSLCnano. Please read this manual carefully
before installing or running any of the applications described. Keep this
manual close to the UltiMate 3000 RSLCnano for future reference and
pass it on to any subsequent user.
Page 10 UltiMate 3000 RSLCnano Standard Applications Guide
1.2 Conventions
This section describes the conventions used throughout this manual
1.2.1 Special Notices and Informational Notes
Special notices and informational notes in this manual appear different
from the main flow of text. They appear in boxes and a note label
identifies them. The label text appears in uppercase letters and in bold
type.
NOTICE Highlights information necessary to prevent damage to the
instrumentor invalid test results.
1 Using this Manual
TIP Highlights information of general interest or helpful information that
can make a task easier or optimize the performance of the instrument
UltiMate 3000 RSLCnano Standard Applications Guide Page 11
1 Using this Manual
1.2.2 Typographical Conventions
These typographical conventions apply to the descriptions in this
manual:
References and Messages
References to figures and tables appear italicized.
Viewpoint
If not otherwise stated, the expressions left and right in this manual
always refer to the viewpoint of a person that is facing the instrument
from the front.
Particularly Important Words
Particularly important words in the main flow of text appear in bold.
Electronic Manual Version (PDF)
The electronic version (PDF) of the manual contains numerous links that
you can click to go to other locations within the manual. These include:
Table of contents entries
Index entries
Cross-references (in blue text), for example, to sections, figures or
online reference materials
Page 12 UltiMate 3000 RSLCnano Standard Applications Guide
1.3 Reference Documentation
Further information relating to the UltiMate 3000 RSLCnano systems
and associated applications is available as follows:
VWD-3100 and VWD-3400RS variable wavelength detectors
WPS-3000TPL RS and WPS-3000FC autosamplers
Additionally, you can also find these operating instructions in the
following installation folder (Chromeleon 7/ SII):
“C:\Program Files (x86)\Thermo\Chromeleon\bin\Troubleshooting
Guides”(or “C:\Chromel\Bin\Troubleshooting Guides” when using
Chromeleon 6.80)
1 Using this Manual
Upgrading the UltiMate 3000 RSLCnano System with ProFlow
Technology – Quick Installation Guide
ViperTM and nanoViperTM EASY-SprayTM Column tips and tricks
document
Details on Viper and nanoViper capillaries and application kits
Thermo Scientific Viper and nanoViper Fingertight Fitting System -
brochure
Viper and nanoViper Fingertight Fitting Systems - specifications
The complete and easy guide to configuring your Thermo Scientific
nano LC
Nano, Capillary and Micro LC Columns detailed in the
Chromatography Columns and Consumables catalogue
UltiMate 3000 RSLCnano Standard Applications Guide Page 13
2 Application Setup
2 Application Setup
This chapter provides details on each of the application kits available for
the UltiMate 3000 RSLCnano system.
Page 14 UltiMate 3000 RSLCnano Standard Applications Guide
2 Application Setup
2.1 General Recommendations for Applications
The experimental conditions for each application are described together
with schematics, installation tips, examples and results.
2.1.1 nanoViper Connections
NanoViper (Figure 1) is a fingertight high-pressure fitting that is virtually
dead volume free by design and rated for backpressures up to 1200 bar.
All high-pressure fittings used in the applications on the UltiMate 3000
RSLCnano system use nanoViper. The fittings are factory assembled to
ensure quality and prevent experimental failure due to bad connections.
Figure 1: Internal and external view of a nanoViper fitting
1. Install nanoViper using the removable knurled black nut.
2. Do not overtighten connections (the general guideline is fingertight
plus an additional one eighth of a turn).
3. Remove the knurled black nut once the fitting is tight.
UltiMate 3000 RSLCnano Standard Applications Guide Page 15
2 Application Setup
Nano connector sleeve (1.1 cm)
PTFE sleeve (1.8 cm)
Figure 3: Nano connector (top) and PTFE (bottom) sleeve comparison
2.1.2 Making Connections using the Nano Connector
The outlet of the linear nano columns are fitted with a nano connector.
This zero dead volume connection is designed to interface the linear
column outlet with 280 µm fused silica capillaries and is pressure stabile
up to 300 bars. The nano connector uses a special sleeve to ensure
pressure tightness. The assembly of a nano connector is described step
by step in Figure 2 below.
Figure 2: The components of the nano connector
Use a new nano connector sleeve (P/N 6720.0391) each time the
connection is made.
NOTICE: Do NOT use a PTFE sleeve (P/N 160486; supplied with the
columns). The size does not match the nano connector union (Figure 3)
and the pressure resistance is much lower.
1. Slide the black nut and transparent union onto one of the ends of
the fused silica, and the other black nut onto the other fused silica
end Figure 4a.
2. Slide the nano connector sleeve onto one end of the fused silica
until it reaches the middle of the sleeve. Slide the other end of the
fused silica into the connector sleeve. Make sure that the
connection is dead volume free (i.e. that the ends meet in the
middle Figure 4b).
Page 16 UltiMate 3000 RSLCnano Standard Applications Guide
2 Application Setup
3. Tighten both sides of the black nut equally to ensure that the nano
connector sleeve is in the center of the transparent union Figure
4c.
a
b
c
Figure 4: Nano connector assembly. (a) The two black nuts and
transparent union are mounted on the two outlets to be connected.
(b) A dead volume free connection with the nano connector. (c) The
complete fitting with the black nuts and union housing the nano
connector.
2.1.3 Installing and Configuring the Application Fluidics
Each capillary must be installed sequentially starting from the pump
outlet. Please flush each capillary using the respective pump and ensure
that a droplet is visible at the capillary outlet in question before making
the next connection. This will ensure that all air is removed from the
capillaries and connections and that no air is passed through the
column.
2.1.4 Interfacing the UltiMate 3000 RSLCnano with the Nanospray Flex™ Ion
Source
LC−MS based applications using linear columns commonly use the
Nanospray Flex Ion source (see Figure 41) to interface with Thermo
Scientific Mass Spectrometers. As of January 2019, 1.5 m of fused silica
(20 µm and 50 µm) and a tile for cutting fused silica capillaries have
been included in the pump (NCS-3500RS and NCP-3200RS) accessory
kits. This capillary should be used to connect the outlet of the column or
UV flow cell, if included in the setup, with the emitter installed in the ion
source. The connection between the capillary outlet and the emitter is
realized using a 1/32” micro tight® union assembly included with the
Nanospray Flex Ion Source. For capillaries and columns with 280 µm O.D.
a black sleeve (P/N SC903) should be used with the microtight fitting.
UltiMate 3000 RSLCnano Standard Applications Guide Page 17
2 Application Setup
For 360 µm O.D. capillaries and columns (e.g. the Acclaim PepMap RSLC
C18 75 cm PepMap RSLC, P/N 164939) a beige sleeve (P/N SC603)
should be used (both types are included with the ion source). For more
details on connecting the UltiMate 3000 RSLCnano with a Thermo
Scientific mass spectrometer, please refer to “The Complete and Easy
Guide to Configuring Your Thermo Scientific Nano LC for Mass
Spectrometric Analysis”.
2.1.5 Sample Preparation for Reversed Phase LC Separation
The following are recommendations for Cytochrome C standard digest
(P/N 161089) preparation. The glass vial contains 1.6 nmol lyophilized
Cytochrome C digest. The sample preparation procedure depends on the
system configuration and application in question (e.g. nano, capillary or
micro).
NOTICE The sample dilution protocol described here differs from the
product sheet and is designed to offer the user a starting point. The
sample concentration required to run a particular application may
deviate from the sample concentrations given below. Sample dilutions
may also need to be prepared in a different buffer to that given below.
Please check the required sample concentration and dilution conditions
for the application and prepare the sample accordingly!
Reconstitution Solvent – (98% Water / 2% Acetonitrile containing
0.1% FA). Prepare by mixing 980 µL Water + 0.1% FA and 20 µL 100%
Acetonitrile + 0.1% FA in a vial. (See section 2.3.4.4 for information
about the individual solvents on page 32.). The use of 2%
acetonitrile is recommended, to ensure complete dissolution of
hydrophobic peptides.
Reconstituted the sample in 200 µL reconstitution solvent to
prepare a stock solution of 8 pmol / µL for nano / cap applications.
Reconstituted the sample in 100 µL reconstitution solvent to
prepare a stock solution of 16 pmol / µL for micro applications.
Vortex briefly and wait at least 10 minutes to ensure reconstitution
of all peptides prior to use / further dilution.
Page 18 UltiMate 3000 RSLCnano Standard Applications Guide
2 Application Setup
TIP: To limit the risk of peptide or protein adsorption on the walls of the
vials, Thermo Fisher Scientific recommends using vials containing glass
inserts (Polypropylene vials for WPS with glass insert, 250 µL, set of 100,
P/N 6820.0027).
For nano flow applications, dilute the stock solution to 500 fmol /
µL using mobile phase A (direct injection) or loading buffer (pre-
concentration) as follows:
Prepare 150 µL mobile phase A in an autosampler vial (with
insert) and add 10 µL from the 8 pmol / µL Cytochrome C stock
solution.
Mix (on Vortex or with pipette) briefly to homogenate the
solution.
Ensure there are no air bubbles at the bottom of the vial.
UltiMate 3000 RSLCnano Standard Applications Guide Page 19
2 Application Setup
IMPORTANT: When installing fresh mobile phase on the LC system,
replace the mobile phase solvent in the bottle completely. DO NOT “top up” mobile phases to avoid solvent composition changes or unwanted
components building up in the mobile phase bottles.
2.1.6 Mobile Phases
Always use fresh LC-MS grade solvents.
Thermo Fisher Scientific recommends replacing your solvents at
least once every two weeks.
Avoid the use of detergents when cleaning glassware. All glassware
used for LC-MS applications (including graduated cylinders) should
be rinsed with LC-MS grade solvents prior to use and should be
labelled and stored separately.
Page 20 UltiMate 3000 RSLCnano Standard Applications Guide
2.2 Available Trapping Columns
2.2.1 Available Formats
Trap columns are available in two formats, which are a cartridge-based
µ-precolumn (Figure 5) and a nano trap column (Figure 6). Both types of
trapping columns are UHPLC compatible due to the nanoViper fittings
employed. The choice between a µ-precolumn or a nano trap depends
on application needs such as flexibility, sample loading flow rate and
robustness as well as sample quality, desired loading capacity and
personal preference.
2 Application Setup
Figure 5: µ-Precolumn (cartridge-based)
TIP P/N 164648 contains two 30 µm ID x 100 mm nanoViper capillaries
and can be used to order replacement capillaries
µ-precolumns are small trap cartridges that are inserted into a cartridge
holder, connected to the switching valve by two 30 µm ID x 100mm
nanoViper capillaries. The stationary phase is retained by a frit at both
ends of the cartridge allowing the mobile phase to flow through it in
both directions without disrupting the column packing. Therefore,
µ-precolumns can be used in both forward- and back-flush operation
(see section 2.2.2 for details). The bed volume is large, but short, giving
it higher absolute loadability compared to nano traps, but the short bed
could result in earlier sample breakthrough for hydrophilic components.
Backpressure is lower compared to nano trap columns and therefore µprecolumns can accommodate higher loading flows and are often
preferred when large sample volumes need to be injected.
UltiMate 3000 RSLCnano Standard Applications Guide Page 21
2 Application Setup
TIP: Note that for Acclaim PepMap RSLCnano columns, the difference
between the pressures on the nano trap column and analytical column is
smaller than with the combination of the µ-precolumn and the analytical
column.
Figure 6: Nano trap
Nano trap columns consist of a single 15-cm-long nanoViper capillary
containing 1 or 2 cm of stationary phase at one end of the capillary.
Nano traps must be operated exclusively in forward-flush mode. The
chromatographic bed volume is lower than that of µ-precolumns, but
the longer bed length minimizes sample breakthrough. Nano traps give a
higher backpressure than µ-precolumns and are thus operated at lower
flow rates.
2.2.2 The Difference between Forward Flush and Back Flush
The terms forward-flush and back-flush are used to indicate whether the
mobile phase from the NC pump during gradient elution flows in the
same or opposite direction compared to the mobile phase flow during
sample loading. Figure 7 shows the different fluidic setups for a forwardand a back-flush fluidic pathway.
Figure 7: The different fluidic configurations for forward-flush (left) and
back-flush (right)
Page 22 UltiMate 3000 RSLCnano Standard Applications Guide
2 Application Setup
For nano trap columns, the packing material is only retained by the frit
at one end of the trap column. In order not to damage nano traps, only
forward-flush can be used.
In the µ-precolumn design, the stationary phase is retained by a frit at
both ends of the column packing. This means that the mobile phase can
flow through the cartridge in either direction without disrupting the
column packing, i.e. forward-flush and back-flush operation.
The choice between forward- and back-flush for the µ-precolumn design
is made on the following criteria.
In forward-flush, the trap column also acts as a guard column to
protect the separation column.
In back-flush, better separation is obtained, but any particulates or
insoluble debris from the sample could end up on the separation
column.
NOTICE For pre-concentration applications, better chromatographic
resolution (narrower chromatographic peaks) are produced when the
µ-precolumn is installed in back-flush mode.
UltiMate 3000 RSLCnano Standard Applications Guide Page 23
2 Application Setup
Figure 8: RSLCnano system overview
SRD-3400, (Optional):
SRD-3200 with degassing
or SR-3000 without degassing.
NCS-3500RS module featuring
- NC pump, up to 900 bar
- Loading pump, micro Titanium up to 620 bar
- Column compartment with up to two 860
bar switching valves
Optional:- NCP-3200RS, - PAEK valve
VWD-3400RS with flow cells for
- nano (3nL)
- capillary and micro (45 nL) LC
WPS-3000TPL RS
- Temperature controlled autosampler
equipped with a
860 bar switching valve
- Optional:
8-port valve (350 bar) for microfractionation applications
2.3 Installing the UltiMate 3000 RSLCnano System
2.3.1 UltiMate 3000 RSLCnano System Components
Page 24 UltiMate 3000 RSLCnano Standard Applications Guide
2.3.2 NC Pump Configurations
Flow Selector Type
Total Flow Rate (Sum of Channels A and B)
Nominal
Minimum
Maximum
Nano (Nan)
500 nL/min
50 nL/min
1000 nL/min
Capillary (Cap)
5 µL/min
500 nL/min
10 µL/min
Micro (Mic)
25 µL/min
2.5 µL/min
50 µL/min
2.3.2.1 ProFlow™ and Classic Flow Meters
Flow meters are used to actively regulate NC pump flow on the
instrument in order to deliver very precise low-flow gradients. There are
two types of flow meter available:
ProFlow flow meter
The ProFlow flow meter controls pump flow using thermal flow
sensors built into the flow meter. It is a unit dedicated to nano and
low capillary flow rates (50 nL / min – 1500 nL / min) and allows a
pump pressure rating of 900 bar at the full flow rate range for all
common solvents used for reversed phased LC applications.
Classic flow meter
2 Application Setup
The classic flow meter determines the flow rate indirectly by
measuring the pressure drop across a restriction capillary contained
within the flow meter itself. The pressure rating of the pump using
the classic flow meter is 800 bar for flow rates ≤ the nominal flow
rate (see Table 1).
2.3.2.2 Flow Selectors for the Classic Flow Meter
Each classic flow meter contains a flow selector that defines the flow
rate range of the flow meter. These flow selectors are interchangeable.
The flow rate ranges of the respective flow selectors and the nominal
flow rates are given in Table 1 below.
Table 1: Properties of the different flow selectors
UltiMate 3000 RSLCnano Standard Applications Guide Page 25
2 Application Setup
High pressure gradient NC_Pump
Low pressure gradient Micro pump
Rear seal
wash system
Flow meter
Purge
screws
Solvent
shutoff
valves
Inline filter
Purge
screw
Tubing guides
Snap-in valves
Column compartment
2.3.2.3 NCS-3500RS with the ProFlow Flow Meter
Page 26 UltiMate 3000 RSLCnano Standard Applications Guide
Figure 9: NCS-3500RS with ProFlow flow meter
NOTICE The maximum pump pressure available for the column is 900
bar if a ProFlow flow meter is installed.
2.3.2.4 NCS-3500RS with Classic Flow Meter
Low pressure gradient Micro pump
Rear seal wash
system
Flow meter
Purge screws
Inline filter
Purge screw
Column compartment
2 Application Setup
UltiMate 3000 RSLCnano Standard Applications Guide Page 27
Figure 10: NCS-3500RS with classic flow meter
NOTICE The maximum pump pressure available for the column is 800
bar with a classic flow meter installed.
2 Application Setup
Figure 11: NCP 3200RS pump
NCP-3200RS module featuring
- NC pump
2.3.2.5 NCP-3200RS
Figure 12: NCP 3200RS pump with ProFlow flow meter installed
Page 28 UltiMate 3000 RSLCnano Standard Applications Guide
2 Application Setup
Figure 13: NCP-3200RS with a classic flow meter installed
TIP The NCS-3500RS and NCP-3200RS are both compatible with the
ProFlow and classic flow meters.
TIP An upgrade kit from classic nano to ProFlow is available for both
NCS-3500RS and NCP-3200RS. Please order P/N 6041.7850 (ProFlow
flow meter) and P/N 6041.3003 (Upgrade Kit for ProFlow flow meter).
Please see the ProFlow quick installation guide for more details.
2.3.3 Software Compatibility for NCx-3x00RS Operation with ProFlow and
Classic Flow Meters
ProFlow technology is fully compatible with all previous NCx-3x00RS
modules (mandatory firmware upgrade to version ≥ 1.40 required).
For LC control via Xcalibur, ProFlow technology requires SII for