1236 Hach Hall

515-294-5544
www.cif.iastate.edu

LCMS 2020 Training Manual

Kamel Harrata (November 2014)

Location: 1238 Hach Hall

Contact: Kamel Harrata, 1236 Hach Hall

Safety

All researchers working in 1238 Hach Hall must complete the EH&S courses: “Fire Safety and
Extinguisher Training”, and “Lab Safety: Compressed Gas Cylinders”. When preparing samples in
1238A, please wear all appropriate personal protective equipment. Aprons, safety glasses, and
rubber gloves are available.

Properly dispose of waste solvents and glass pipettes in the containers provided in 1238A. All of the
data processing computers and many of the data acquisition computers in this lab have direct links
from the desktop to MSDS sheets, the EH&S Laboratory Safety Manual and to the CIF Safety Manual.

Photo: Toshia Zessin (Graduate Student)

 Table of Contents

Important Notes 1

ESI (Electrospray Ionization) 2

DUIS (Dual Ion Source) 4

Tuning and Calibration 5

Data Acquisition 7

Data Processing 15

Solvents considerations 18

Important Notes:

This training manual is property of Chemical Instrumentation Facility of Iowa State University. A
proper training, usually one-on-one, is provided along with this manual. For those students who are
not well versed in Chromatography and Mass Spectrometry, a 1 hour course/session is usually
provided by mass spec personnel prior to actual training.

Before starting analysis!!!!!

Samples must be completely dissolved prior to Injection. Please filter and/or centrifuge your sample.
Next to the instrument there is a Vortex, Micro centrifuge, and 1,5 ml Micro centrifuge polypropylene
tubes. For Flow Injection (FI) ESI work, sample concentrations of less than 100 ppm (100ng/ul) are
usually enough.

Vortex Micro Centrifuge Tubes and vials

Take a look at the pressure reading from the Acquisition software (When IG is on).

The pressure value should be close to 6 10-4 Pa.

Files structures:

• Each user has data files folder located in his or her directory:
• C:\LabSolutions\Data\username\filename
• Username is the iastate email id, e.g. kamel
• Filename is always: xyz-month-day-nm e.g. akh-8-20-01
• xyz is your initials
• Method files are located in C:\Labsolutions\Methods
• Tune files are located in C:\LabSolutions\Tune Files

LCMS 2020 Configuration:

LCMS 2020 is a single quadrupole mass spectrometer (mass range up to 2000) that is equipped with
ESI source and ESI/APCI combination source called DUIS. This is the same as ESI with the addition of
corona discharge. It is important to indicate that there is no true APCI source with our system. The
system will always be configured for LCMS using a XDB C18 column from Agilent. The column
dimensions are 4.6*50 mm, 1.8 um. If other column is needed, please consult with lab personnel.
ESI (Electrospray Ionization)

The formation of positive or negative ions (depending on the sign of the applied electrical field) occurs
in high yield. In the positive ion mode protonated and/or alkali adduct analyte molecules are generally
observed in the mass spectra. In the negative ion mode operation peaks corresponding to
deprotonated analyte molecules are observed. ESI is described as a very "soft" ionization technique
where the surrounding bath gas has a moderating effect on the internal and translational energies of
desorbed ions.

Advantages of ESI:

• Soft ionization process so intact molecular ions are observed

• ESI allows production of multiply charged ions. This results in the ability of analyzing very high
molecular weight species using the most available mass analyzers (e.g. quadrupoles).
• ESI is an atmospheric pressure process. This makes it easy to use and easy to interface with
HPLC and CE separation techniques.

DUIS (dual ion source)

A high voltage is applied to the corona discharge needle located just underneath the sprayer.
The DUIS ion source adds a corona discharge needle with a voltage of few kV. This latter induces ion
formation from low polarity compounds that may not ionize with ESI.

Tuning and Calibration:

The mass spectrometer is tuned for sensitivity, resolution, and mass calibration.

The system can be tuned automatically or manually. This step is performed only when deemed
necessary by lab personnel. Autotune is always performed without corona needle voltage, and with
heater block of 400 deg. Tune results copies are stored in the computer and a binder.

The system is tuned either in positive or negative ion modes or both simultaneously. Last tuning file is
usually used in data acquisition unless otherwise specified. The following is a typical autotune results.
Data Acquisition: (Step-by-Step)

The acquisition software uses Realtime browser while data processing uses Postrun analysis.

Real time Analysis browser can be accessed from LabSolution Main program:

Realtime Analysis

1- From Realtime Analysis: File > Open Method File… (Your method will be set and explained
during training.
 2- Make sure there is enough solvent in the solvent reservoir. Bottle A is always aqueous and
bottle B is for organic solvent.
3- Turn on heaters DL and HEAT. They should always be left ON. Turn IG on (should be ON too.
4- Turn on NEBU, MS, and LC pumps.

Wait for IG Vacuum to be about 6 10-4 Pa. This will allow LC and MS to be in ready state.

Start LC pump by clicking on from

If LC column is installed, increase Total Flow from setting slowly so that the back pressure do not go
up abruptly.
5- Check the system for ion formation: Click Plot located in the upper right corner
This allows observation of UV and MS data as it occurs. If background ions are observed, the plot
can be stopped and data acquisition can proceed. Stop the plot.

Instrument or method parameters:

The system can be scanned in positive and negative ion modes simultaneously. This can be
accomplished by setting events. Each event has its own parameters.

In Interface tab, the system can be set for ESI or DUIS.

Data Acquisition Tab allows setting experiment duration in both MS and UV.
Detector Tab allows setting Wavelength value.

Autosampler tab allows setting Rack type and all other parameters.
Pump Tab allows setting type flow, Flow rate, and Pressure limits.

LC Time Prog. allows setting the binary LC gradient.

If any changes are made, click on Download and save method. Make sure that all the starting
conditions are visible in the Detail section of the display.
6- From Main click on Data Acquisition to start data acquisition

7- Click Start Run

Fill in sample name, sample ID, Method file, and set you file name. Filenames can be incremented if
Auto-Increment is checked. Fill in Vial# and Tray number. The Auto sampler Tray id is 12 unless
changed with other tray. Fill in injection volume. This is the only place where injection volume is
selected.

8- Click OK to start acquisition.

Data can be viewed processed and printed from Postrun Analysis browser.
Postrun Analysis: (Data Processing)

From the Main menu of Realtime Analysis software, select Data Analysis.

Open your data folder and select the data file for processing.
Average mass spectrum and background subtraction:

Click on the (+) button (for averaging)

Click and drag on the desired TIC peak

Click the (-) button and drag to select the background or scans to be subtracted
Right clicking on the chromatogram (TIC or UV) will open up Peak table view showing all the areas for
selected peaks.

When You finish all experiment:

Uncheck: MS, NEB, and LC pump Flow

Solvents consideration
1. Solvent Bottles

The LC reservoir bottles are by defaults A (H2O/MeOH/Formic acid 90/10/.1) and B

(MeOH/H2O/Formic acid 90/10/.1). You can use your own solvents in your own bottles, or bottles
that have been assigned to you. You may never use solvents prepared for someone else, or solvent
containers that are not yours. We have a supply of 500 mL and 1000 mL bottles especially designed
for use with the LCMS. These can be loaned to you for the duration of your project. The content and
the owners name must be CLEARLY visible on all containers in our lab. Unlabeled containers will be
discarded without hesitation.

2. Solvent Filtering

Pure organic solvents do not need to be filtered prior to use. If any modifiers have been added to the
organic phase, then the mixture should be filtered. The aqueous phase, regardless of the presence or
absence of modifiers, should be filtered immediately prior to use. Bacterial growth, especially in
aqueous solutions, can lead to clogs in the HPLC mixer, the high-pressure stainless steel tubing, or the
capillary transfer tubing, as well as high background and extraneous mass peaks in the mass spectrum.
As part of your training, Dr. Harrata will show you how to use the filtering apparatus located in our
wet lab.

3. Additives considerations

1- Acids

a- Do not use inorganic acids (may cause source corrosion).

b- Two possible choices are:

• 0.1 % Formic acid

• 0.1 % Acetic acid with 0,02 % TFA

c- Best results arise from acids stored in glass

d- Excellent results have been found with JT Baker acids

2- Surface Active Agents

Detergents and other surface active agents may suppress ionization.