[QG] Support for different instrument Vendors and HPLC systems

[cpanse]

The queue generator generates queues for MS control software. These are either comma or tab separated tables specifying the order in which the samples are being acquired.

A minimal queue files would consist of the following columns:

Filename - name of the raw file to be written
path - folder to which the file needs to be written
Plate - plate
Plate-position - position in the sampling plate
Method - mass spectrometric method

Instrument Control Software dependent queue formats.

There are various Instrument vendors each having a different instrument control software, and therefore a different queue file format.

Instrument Control Software currently supported at the FGCZ are :

• Thermo - Xcalibru,
• Evosep,
• Bruker Hystar,
• Waters MassLynx.

The queue generator currently the only support Thermo Xcalibur format
The Thermore Xcalibur queue file format is txt file with a header line:

Bracket Type=4 ?

and a comma separated table with the following columns:

• File Name : "20201023_C23047_001_autoQC01" "20201023_C23047_002_S270071_A_170_Control_Control" ...
• Path: "D:\Data2San\orders\Proteomics\QEXACTIVE_1\analytic_20201023" ....
• Position : "1:F,8" "1:A,1" "1:F,6" "1:A,2" ...
• Inj Vol : 2 2 2 2 2 2 2 2 2 2
• L3 Laboratory: "FGCZ" "FGCZ" "FGCZ" "FGCZ"
• Sample ID: NA 270071 NA 270072 NA 270073
• Sample Name: "autoQC01" "A_170_Control" "clean" "B_95_Control"
• Instrument Method: "C:\Xcalibur\methods\__autoQC\trap\autoQC01" "" "" ""

LC Systems

The Insturment Control Software can support various LC Systems. These LC systems include autosamplers.
The number of plates and the plate formats in the autosamplers differ:

• evosep 4 plates with 96 samples
• Water m-class 2 plates with 48 samples
• easylc and exigent 1 plate with 48 samples

Because of this the format of the queue file will differ:
For instance for Thermo XCalibur the Postion column changes depending on the LC-MS system:

• Waters : 1:F,8 Plate:Row,Column with Plate in 1:2, row-names names ranging from A:F and column-names from 1:8.
• EasyLC: F8 with and row-names names ranging from A:F and column-names from 1:8
• eksigent: 2F08 <?RowColumn> with row-names names ranging from A:F and column-names from 1:8

** QC Samples and blanks **

Some of the LC systems can access the same plate position several times.
In this case, special samples - clean, or QC samples have a fixed position in the plate 1:

• clean : 1:F,6
• autoQC01 : 1:F,7
• autoQC4L : 1:F,8

The Evosep accesses each plate postition only once.

Conclusion.

We need to collect and document the queue file formats we need to support. Hence, we will need examples of queue files but also a brief description of every column (similarly as I did for the Thermo queue file above).
Furhter, important information we need is:

• path of the instrument methods
• path

• Thermo XCalibur (available)
• Bruker Hystar (TK)
• Evosep (JG)
• Waters MassLynx (?)

The QG currently implements only the support for a single instrument control software / queue file format (Thermo Xcalibur), and was not developed more then one queue file format in mind. Therefore adding support for multiple control software is needed.

[cpanse]

M-Class used by the Orbitraps

nanoElute used by the timsTOF

96 well plate (not used at the moment)

EVOSEP used by the timsTOF and the Orbitraps