BookitLab - Mass Spectrometry Laboratory

Instructions for submitting a request for analysis using BookitLab

Sample submission with BookitLab is available to BSc, MSc and PhD students; researchers; and other personnel at the Department of Chemistry (KI) and Department of Pharmacy (FAI) at UiO. Other clients are kindly asked to contact the MS laboratory directly.

Register to use BookitLab

Before you can send in a request for analysis, you need to register in BookitLab and be assigned to the proper project.

First, go to bookitlab.uio.no and log in using Feide to register you user.

Secondly, register your affiliation, position and funding type using this form. Based on you answers, you will be assigned to one of the following "dummy" projects in BookitLab (each project exists in two versions, one for KI and one for FAI):

MS BSc dummy

If you are a bachelor student.

MS MSc dummy

If you are a master student.

MS Bidragsprojekt dummy

This project should be used for all PhD students, researchers, etc. who are submitting samples from a research project that pays overhead to either KI or FAI.

MS KD-Stipendiat dummy

This project is for PhD students that are financed directly by either KI or FAI using funding from the Ministry of Education and Research (Kunnskapsdepartementet).

 

If none of the above dummy projects fit your circumstances, please contact us directly.

Once you have been assigned to one of the projects, you can start submitting requests for analysis.

Important: if your status changes with regards to the above mentioned categories, e.g., when you change from being a BSc to an MSc, please resubmit the form so we can make sure you are in the correct project.

Creating a request

In BookitLab, on the pane on the left hand side, select "request services" and then "requests".

Make sure that you have the correct selection for core; the core is indicated in the top right of the screen, immediately to the left of your name. You have the option to view all cores or a specific core; however, if you view a single core you can only make requests of services from that specific core. Hence, you need to select either "All Cores" or "KI-Mass Spectrometry Laboratory".

At the top of the screen, select the "+" sign (new order). Select the appropriate lab service (MS analysis ...) and then select the appropriate project, e.g., "FAI-MS MSc dummy" or "KI-MS bidragsprosjekt dummy"; then press "select".

Regarding the projects, you will be able to choose from any projects that you are a part of in BookItLab; please make sure that you pick an MS dummy project. If you are a part of more than one MS dummy project, please make sure to choose the dummy project that corresponds to the project within which the sample was produced.

Filling out a request

The request has a few different parts:

Submission details

Unless you need to change anything, this can be ignored.

Milestones

This can also be ignored.

Request form

Fill out as appropriate.

Request lines

This is the part that contains information about your sample(s) (a single request can be used for the submission of multiple samples). For each sample, create a row by pressing the "+" sign underneath the columns and fill out the details.

Please note that depending upon which type of request you have selected, not all of the fields or options below will be present.

Sample identifier

The sample identifier should be a short, unique, code identifying your sample, for example your initials and a number. Some people use the labeling scheme for their compounds also for their samples; this is fine as long as each sample has a unique identifier (append the label with, e.g., -1, -2, 3-; -a, -b, -c; etc.).

Naturally, the sample itself has to be physically labeled with this identifier.

Chemical structure

To ensure that the chosen analysis is appropriate for the sample, we need to know the structure.

Draw the molecule in a chemical structure drawing program like ChemDraw and save the structure as an image file. If you do not have ChemDraw, you can also use the free, open-source, online software Ketcher 2.3 Standalone.

To upload the structure to BookitLab, click the -button all the way to the right of the current line (you might have to scroll horizontally); you can then drag-and-drop the image file into BookitLab.

Formula

Please specify the molecular formula of the main analyte(s), e.g., C17H13Br2NO.

If you have your analyte(s) drawn in ChemDraw, you can find the molecular formula by selecting the structure, right-clicking and selecting Analysis > Chemical Formula. In Ketcher, click ""  and copy the formula.

Monoisotopic mass

Please specify the monoisotopic molecular mass to four decimals.

The monoisotopic mass of a compound is the exact mass of the compound where only the most abundant isotope of each atom is considered and can be very different from the molar mass. For instance, C17H13Br2NO has the monoisotopic molecular mass 404.9364 u and a molar mass of 407.10 g/mol.

In ChemDraw, the monoisotopic mass can be found by selecting the structure, right-clicking and selecting Analysis > Exact Mass. To change the number of decimals shown, click View > Show Analysis Window and change Decimals. Or you can write the chemical formula into ChemCalc and copy the monoisotopic mass.

Sample amount

Please indicate the amount of your sample, with units. Write the mass for solids and neat liquids and the concentration for solutions. Typically, samples are 0–5 mg or 0–5 mg/mL. Very small samples are more difficult to handle and bigger samples require more dilutions. Note that this is not the same as the amount of analyte, i.e., the comound of interest, if there are many other compounds present in the sample.

If the amount written is wrong, the instrument can be damaged so please take extra care to make sure what you write is correct!

Sample soluble/dissolved in

If the sample is a solution, write the solvent used.

Not all solvents are suitable for MS analysis. If the solvent is ionizable and in excess of the analyte, you will generally only see the solvent in MS; this can be the case for DMSO and DMF. Take care that the solvent is sufficiently pure for MS analysis. Some solvents contain trace compounds or contaminants that give high signals in MS analysis.

If the sample is neat (no solvent), we need to know which solvent it can be dissolved in before dilution. Usually, we will use MeCN for the initial dissolution as most samples have a decent solubility in it.

Depending upon the analysis, the sample will be further diluted using MeOH, MeCN or possibly H2O. If you have a preference, or know or suspect that your compound will react with either of these, please let us know in the comments.

Sample boiling point

Please provide boiling point, or at least an approximate value, in centrigrades. Chromatographic conditions can also be given in the comments and is of great help.

Ion source

For the maXiS II instrument, the most commonly used ionization technique is electrospray ionization (ESI) and this should be considered the default choice as it works for most samples. However, should the need arise, the maXis can be fitted with an atmospheric pressure chemical ionization (APCI) or atmospheric pressure photo ionization (APPI) source.

The SCION instrument is generally only used with its electron ionization (EI) source.

Sample introduction

For the maXis II instrument, there is the option of high-pressure liquid chromatography (HPLC) in combination with ESI, APCI and APPI. There is also the option of gas chromatography (GC) to be used with APCI. For analyzing partially volatile liquid or solid samples, a direct insertion probe (DIP) is available with APCI and APPI ionization. Please note that chromatography is generally not needed for the majority of samples.

The SCION instrument comes standard with GC and also has the option of sample introduction using DIP.

Extras

For the maXis II, there is the option of high resolution mass spectrometry (HRMS) with suggested molecular formula. There is also the option of collision induced dissociation (CID). Note that it is possible to select more than one of these.

Return sample

Do you want the sample back or can it be disposed of after analysis? Returned samples can be picked up at the same place samples are turned in.

Comment

To add comments about the sample or analysis, click the -button all the way to the right (you might have to scroll horizontally), and write a comment in the comment field.

Examples of relevant information you could include are:

  • Safety! In case you sample is particularly toxic or otherwise dangerous, make sure to indicate this.
  • Sensitivity to air, light or certain temperatures of your sample.
  • Solvents unsuitable for dilution due to them reacting with the compound.
  • Requested polarity. Generally, we will record mass spectra in positive mode (the spectrum will show the positive ions of the analyte). For particular samples we might opt to use negative mode instead. If you specifically need to have a spectrum in either positive or negative mode, you can ask for this in a comment.
Additional fields in your BookitLab request that appear after analysis

Each line in your request has some additional fields that are hidden at the time of submission; these fields will be filled in by us during the analysis.

Dilution

Here the approximate dilution of the sample is written. This information is mostly for our internal use, but can provide some insights for the interested.

ID number

This is the consecutive number of the analysis. It also serves as the internal journal number and is the basis for the name of the data files. If you need any extra data processing or similar, please refer to this number when contacting us.

Request comments/Files

In this part of the request you can add additional files and comments; however, we recommend that comments pertaining to a specific sample is added in the request line as described above. This is also where we will upload your spectra and add any comments on our part.

Delivering your sample

Deliver your sample, clearly marked with the sample identifier (and possibly your name) in the bookshelf outside of room V252 in the Chemistry building.

Samples that needs to be kept in the fridge or the freezer are best handed directly to the laboratory staff. If no one is in the lab, check office V248.

For time sensitive samples, please contact us beforehand to set up an appointment.

Additional information sample preparation and delivery is available on the Services page.

Additional information

If you are uncertain about which analysis methods to request, a more in depth description of the available options can be found on the Services page.

The university has a webpage regarding BookItLab (in Norwegian only); it can be found here.

By Mauritz Ryding, Sverre Løyland
Published Feb. 8, 2022 4:04 PM - Last modified Sep. 9, 2022 10:28 AM