LUMINOL ONLINE SAMPLE SUBMISSION AND DATA MANAGEMENT · 2019. 2. 7. · 2 Luminol Help v0.4 7 February 2019 ABOUT LUMINOL WELCOME The following document is to support you with the

1

Luminol Help v0.4 7 February 2019

LUMINOL ONLINE SAMPLE SUBMISSION AND DATA MANAGEMENT

................................................................................................................................................................................ About Luminol ................................................................................................................................................... 2

Welcome.........................................................................................................................................................................................................................2 Database and data storage......................................................................................................................................................................................2

Registration and Login ...................................................................................................................................... 3 Register now ..................................................................................................................................................................................................................3

Login Name ..................................................................................................................................................................................... 3 Password.......................................................................................................................................................................................... 3 Salutation ......................................................................................................................................................................................... 3 Email .................................................................................................................................................................................................. 3

Submit New Order / Analysis request............................................................................................................ 4 sample identification ...................................................................................................................................................................................................4 sample Description / Storage...................................................................................................................................................................................4 For your reference to track your analysis .............................................................................................................................................................4

Lab journal reference ................................................................................................................................................................... 4 Project ID ........................................................................................................................................................................................ 4

sample type (important) ............................................................................................................................................................................................5 1. Single Synthetic Molecule ........................................................................................................................................................ 5 2. Polymers...................................................................................................................................................................................... 5 3. Single Peptide/Protein .............................................................................................................................................................. 5 4. Complex Mixture (Peptide/Protein) .................................................................................................................................... 5 5. Other, please specify................................................................................................................................................................ 5

information input .........................................................................................................................................................................................................6 Elemental Composition................................................................................................................................................................ 6 SMILES String (advised) ................................................................................................................................................................ 6 Molecular weight ........................................................................................................................................................................... 6 Exact Mass ....................................................................................................................................................................................... 6 Soluble in ......................................................................................................................................................................................... 6 Melting / Boiling temperature (°C) ........................................................................................................................................... 6 Comment to analysis .................................................................................................................................................................... 6 Files ................................................................................................................................................................................................... 7

proposed structure .................................................................................................................................................................. 7 alternative structure................................................................................................................................................................. 7 analysis relevant files ................................................................................................................................................................ 7 fasta file ........................................................................................................................................................................................ 7 in general ..................................................................................................................................................................................... 7

AA Sequence .................................................................................................................................................................................. 7

Viewing and Downloading results ................................................................................................................... 8 Front End Data Access ...............................................................................................................................................................................................8 Data on the MoBiAS Server .....................................................................................................................................................................................9

feature request................................................................................................................................................. 11 Version info....................................................................................................................................................... 11

2


ABOUT LUMINOL

WELCOME

The following document is to support you with the online sample submission and data management tool, hereafter “Luminol”. Luminol was developed by the MoBiAS team together with Metix GmbH to provide the users of the Mass Spectrometry and Elemental Analysis Service with easy and secure access to their data. Luminol front-end navigation page : https://luminol.ethz.ch/index.php

DATABASE AND DATA STORAGE

Luminol frond-end can be reached (after login) via the main MoBiAS website and is open to the world. All results and analysis data are stored on an ETH server that can only be reached from within the ETH network (physically or via VPN). Results for external customers will be made available elsewhere. See “Data on the MoBiAS Server” section for exact details.

3


REGISTRATION AND LOGIN

REGISTER NOW

Once you have registered with Luminol, your details will be checked by a member of staff, after which your account is activated and ready for use. Your account will be automatically deactivated after 6 months of inactivity. Please contact us to reactivate your account should this happen. As the data is stored on ETH internal servers, only people with an active n-ethz account will be able to access the data. The web front-end is accessible via the www.

LOGIN NAME

Please choose a login name (user account), specific for the MoBiAS online sample submission tool (Luminol). Your login name must be specific in our database. For ETHZ and UZH users we suggest to use your n-ethz login name.

PASSWORD

Due to security and privacy reasons, we cannot use the n-ethz id and password. Hence Luminol needs its own user identification. You can recover your password from the main login page at any time, or via “My Account” in the menu. To check how secure your password is, go here: https://howsecureismypassword.net/ Password rules:

- Minimum 8, maximum 30 characters - Allowed characters (Capitals, Numbers, Special characters): a-z A-Z 0-9

o One special character compulsory # , - . / : = ? @ [ ] ^ { } ~ - Minimum one digit (when password shorter than 12 characters) - No umlauts or white space

SALUTATION

Salutation is used to generate automatic emails.

EMAIL

The following options are available:

• ETH • ETH Domain • UZH • University other than ETH/UZH • Company.

If you are a customer from ETH, from an ETH Domain (EMPA, PSI, EAWAG, EPFL, WSL), you must provide your work email address with the respective domain (i.e. ethz.ch / empa.ch etc), likewise for the University of Zurich (uzh.ch). This information is used for billing and data storage purposes.

4


SUBMIT NEW ORDER / ANALYSIS REQUEST

In general one order per sample is generated (99% of our current daily business is the verification of elemental composition). Unless the order is submitted, it will be removed from the DB, also the MoBiAS team members do not see your information in the system. Batch submission of samples currently is not possible, but this is a feature we would like to include in the future.

Clearly, until you physically bring in the sample, the status of your order will be “Order Submitted” in the “My Order” list. Your order can have one the following statuses:

Depending on the analysis, you will receive email notifications from the system indicating the status of the analysis, if the data is on the server, or if we need further input from you. Billed and Paid are for non D-CHAB customers only. See our website for pricing: http://www.mobias.ethz.ch/de/service/MS-Labor/Preise.html

SAMPLE IDENTIFICATION

Personal sample identification. With this ID you can identify your sample. Please keep as short as possible. Maximum of 21 characters in clean format:

• no umlaut, no brackets --> a-Z, 0-9, - , _ (a to Z, zero to nine, dash, underscore) • white spaces will be replaced with underscore "_"

Special characters cannot be used in the sample ID, because the ID will be used to general a folder on the data storage server. This way you can easily identify your sample/analysis. See page 1

SAMPLE DESCRIPTION / STORAGE

Please provide storage information in this field. We assume that samples can be stored between 4 and 25°C. Also you can use this field to fully describe your sample should that be necessary i.e. the 21 characters of the sample ID are not sufficient (e.g. 5th fraction from C18 clean up). Analysis comments please in the “Comment to Analysis” field (see below).

FOR YOUR REFERENCE TO TRACK YOUR ANALYSIS

LAB JOURNAL REFERENCE

Use this field to (voluntarily) organise your data. You will be able to sort and search your various analysis according to this. Also this field can be used to automatically link to your ENL

PROJECT ID

Like with the previous Lab Journal Reference, you will be able to sort your analysis according to your different projects you may have.

5


SAMPLE TYPE (IMPORTANT)

This field will determine what information has to be provided, it is therefore important to choose the correct sample type. Currently following options are available (see below for descriptions):

1. Single Synthetic Molecule 2. Polymers 3. Single Peptide/Protein

4. Complex Mixture (Peptide/Protein) 5. Other, please provide

We tried to cover all eventualities, if you are uncertain the first time, please come and talk us first.

1. SINGLE SYNTHETIC MOLECULE • Elemental composition is known • NO peptides/proteins • Examples

o Small organic (liquid, oil, solid) o Metal organic o Organic salts o Lipids o Dendrimers o Fullerene

2. POLYMERS • Unknown exact elemental composition • Poly- Heterodisperse • Examples

o Everything with a constant repetitive unit

3. SINGLE PEPTIDE/PROTEIN • Elemental composition is known • Molecule derived from amino acids • Example

o Small peptides o Custom proteins o Modified peptides/proteins

4. COMPLEX MIXTURE (PEPTIDE/PROTEIN) • Mixture of 100-10’000s of peptides for proteins • Example

o Lysate derived peptide mix

5. OTHER, PLEASE SPECIFY

• Everything that doesn’t fit category 1-4

6


INFORMATION INPUT

ELEMENTAL COMPOSITION

Provide Elemental composition, separate elements with white space: C14 H11 Cl2 N1 O2 when you use specific isotopes use the following convention: C14 H11 Cl2 ^15N1 O2 (one 15N atom) C14 H11 Cl2 N1 ^18O2 (two 18O atoms) C14 H11 Cl2 N1 ^18O1 O1 (one 18O atom) Polymers C1 H3 (C2 H4 O)n C1 H3

SMILES STRING (ADVISED)

We might use this feature in the future to automatically draw structures

MOLECULAR WEIGHT

Provide rough molecular weight. We use this information to select the proper MS method. In the future we hope to automatically calculate this from the provided elemental composition.

EXACT MASS

Provide either YES/NO, i.e. do you need high resolution.

SOLUBLE IN

Provide the solvent system that is best for your molecule. Please choose one of the following options.

• Acetone • ACN - Acetonitrille • ACN/H2O - Acetonitrille/water • CHCL3 - Chloroform • DCM - Dichloromethane • EtAc - Ethylacetate

• MeOH - Methanol • MeOH/H2O - Methanol/water • THF - Tetrahydrofuran • Not soluble • Other, please specify

MELTING / BOILING TEMPERATURE (°C)

Please provide the melting or boiling temperature in case you have a non-polar molecule that you think will have to be measured by Electron Impact ionisations (EI)

COMMENT TO ANALYSIS

Provide any comment / request regarding the analysis

7


FILES

Depending on the compound class you have selected (Sample type) we ask here for different files, some are compulsory. For the fast majority of analysis we currently perform (read: 95%) we are tasked to verify the mass of the proposed elemental composition. We have to categorise the analysis files. You have the following options:

PROPOSED STRUCTURE

This is your primary structure. You can only upload one.

ALTERNATIVE STRUCTURE

The name speaks for itself. Upload structures here that could or should also be considered.

ANALYSIS RELEVANT FILES

Here you can upload (AND WE RECOMMEND) your ChemDraw file, or any other files that you think might aid the analysis.

FASTA FILE

For Single Peptide/Protein please provide the single letter amino acid sequence. In fasta format: >Identifier Description (separated by a white space) ACDEFGHIKL

IN GENERAL

For the moment we can only except PNG files of your structure. You can save your structure in ChemDraw as PNG my choosing “Save As”. - Max. filesize for upload = 100 kB - Allowed chars in filename: 0-9a-zA-Z_-.)( and space (No Umlauts!) - Allowed filetypes: - Synthetic molecule --> provide structure (png) - Polymer --> provide structure (png) - Single Peptide/Protein --> provide sequence (FASTA) (txt) - Complex mixture (peptide) (no file upload required) - Complex mixture (proteins) (no file upload required) - Other please provide (no file upload required) - Analysis relevant files: png, cds, cdx, cdxml, chm, d, txt, pdf - max 10 files may be uploaded per order

AA SEQUENCE

Paste your AA sequence here in single AA-letter code.

8


VIEWING AND DOWNLOADING RESULTS

FRONT END DATA ACCESS

Your primary access point is the Luminol front end webpage in which you also submitted the analysis order. You can access this via https://luminol.ethz.ch/index.php?act=myorders. The screen should look something like this:

Click on “My Orders” and expand the order by clicking on the Order ID (see arrow). From the moment you have submitted the analysis order to order completion. Once we have accepted and measured your sample(s) we will enter the most relevant information here. You will find a summary of the information you have provided. Should you notice a discrepancy, please contact a member of staff and we can set your order again to “edit”. Under “Workflow” you can track the status here and who is working on your analysis.

The next part of the expanded window deals with the immediate results (where applicable) and the location and number of files in the repository. In the example below you see the typical status of a “small molecule” analysis. You will find information such as the operator, calculated and measured mass as well as any comments we may have to the analysis.

9


Under “Repository Location:” the location of your results file is listed as well as which files we have created. Should you have a special request how you would like your data represented, simply talk to a member of staff and where ever can we will upload those to the location of the analysis.

DATA ON THE MOBIAS SERVER

The data is stored on the MoBiAS server nas22.ethz.ch. It can be accessed via the file-paths below. Standard users will only be able to see their own “username” folder. We suggest you mount this as a drive. Group leaders can see the whole file structure under their respective group.

macOS: smb://nas22.ethz.ethz.ch/chab_loc_mobias_luminoldata/MSservice/Prod/ETH/department/institute/group/username windows: \\nas22.ethz.ethz.ch\chab_loc_mobias_luminoldata\MSservice\Prod\ETH\department\institute\group\username IMPORTANT: make sure that you map the entire path including your username. You will find this link to each individual analysis/order on the front-end under “Repository location” (see screenshot above).

Logon with your n-ethz ID (username including the “d\”) like this:

.

10


11


FEATURE REQUEST

1. Allow batch sample submission 2. Notify user when analysis complete – done 181002 3. Email pdf result 4. Automatically calculate molecular weight from elemental composition. 5. BE - simplified analysis view 6. Increase file size for upload ? 7. Introduce naming convention for NN-AA 8. Implement copy/paste from ChemDraw

VERSION INFO

Version Date Change(s) / Comment

v0.4 2019/02/07

• Page 2: removed the server path links from the general description and moved them to the section “Data on the MoBiAS Server” page 10

• Page 8: corrected wrong URL • Page 10: clarified / improved the text how to mount the MoBiAS data storage

server TO BE COMPLETED 07/02/2019

Documents

LUMINOL ONLINE SAMPLE SUBMISSION AND DATA MANAGEMENT · 2019. 2. 7. · 2 Luminol Help v0.4 7 February 2019 ABOUT LUMINOL WELCOME The following document is to support you with the