Commit b558b87d authored by Yan's avatar Yan
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Forked/reworked for ISQ-column

parent d473f093
# ISQ Operation Guide
If you are new to ISQ and need access to it, please read the following guide.
# ISQ-column Operation Guide
If you are new to ISQ LC-MS and need access to it, please read the following guide.
### How to operate the machine
I've made a video. Its not perfect, but most of the things are covered. Bottlenecks of this video-guide are listed below. Once stable operation procedure will be developed, fixed video will be recorded.
There will be a video soon (hopefully). For now, please take the traininig and
follow standard operation procedure (SOP) guide.
#### Video (youtube)
[![IMAGE ALT TEXT](http://img.youtube.com/vi/M8Ol5ormuOg/0.jpg)](http://www.youtube.com/watch?v=M8Ol5ormuOg "ISQ operation guide")
!TODO
#### Notes (FAQ)
* PAY SPECIAL ATTENTION !! DO NOT SET BLANK AS TYPE:BLANK, keep the type as UNKNOWN (as shown in the video).
* Sample tray is dispayed in the video in the photo inset.
* PAY SPECIAL ATTENTION !! DO NOT SET BLANK AS TYPE:BLANK, keep the type as UNKNOWN.
* Sample tray can be moved by hand when not injecting.
* Mass-range is predefined to full operational range
* keep attention to setting proper method - correct solvent and correct mode (positive/negative)
* keep attention to setting proper method
* Stay away of pollutants!!
* [take special measures when working with water](water.md)
### How to gain access
* Contact your MS tutor.
* Watch the video.
* Read this webpage and the SOP
* Measure few times with the MS tutor.
* Request MS tutor to write me (Jan) and I will grant you access for the booking system.
......@@ -36,9 +35,9 @@ I've made a video. Its not perfect, but most of the things are covered. Bottlene
* triphenylphosphine-oxide
### Operation procedure
* Check if the solvent is there (> 200ml). If not, refill with pre-mix. If pre-mix is gone, contact me or Jaya.
* Check if the solvent is there (> 200ml). If not, refill with pre-mix. If pre-mix is gone, contact me (Jan Zelenka, 03.409).
* Insert your samples + blank.
* Copy the standard sample template (or [water template for water experiments](water.md)) to your folder and personalize it.
* Copy the standard sample template to your folder and personalize it.
* Measure the samples.
* Evaluate the samples.
* Print / upload the outcome.
......@@ -46,12 +45,7 @@ I've made a video. Its not perfect, but most of the things are covered. Bottlene
* Write a note into the logbook (its next to the machine, you will see notes from previous users there)
### Network storage
Network storage is working. But uploading for network storage is manual (export either .raw, or .pdf and move it to appropriate network storage folder)
Network storage address:
**\\\\msspectra-srv.science.ru.nl\\msspectra\\**
The network storage serves just as a transfer station and old data will be periodically delted from this storage. It should substitute printing and USB stick. It is not intended as an ultimate research data storage!!
Machine is not connected to the internet at the moment. It will be conected once it will be at its new location.
### When something goes wrong
Contact your MS tutor! If MS tutor is not around contact some other MS tutor.
......@@ -59,18 +53,8 @@ Contact your MS tutor! If MS tutor is not around contact some other MS tutor.
### List of MS Tutors
|Name | Group |
| ----------- | ----------- |
|Morren-Sewing, C. (Claudia)| Eurostars |
|Max Derks | Eurostars |
|Pals, M.J. (Mathijs) | Velema/Huck |
|Crielaard, S. (Stefan) | Velema/Huck |
|Jona Merx | Boltje/Rutjes |
|Meeusen, E. (Evy) | Boltje/Rutjes |
|Yvonne Bartels | Bonger |
|Hamstra, D.F.J. (Daan) | Bonger |
|Venrooij, K.R. (Kevin) | Bonger |
|Bruekers, J.P.J. (Jeroen) | Nolte |
|Gavriel, K. (Katerina) | Wilson |
|Haije, R. (Rianne) | Huck |
|None | Eurostars |
|Sondag, D. (Daan) | Boltje/Rutjes |
Your group not in a list? **Become a MS tutor yourself!** (PhD preferred)
......
# Tips & Tricks - ISQ Maintenance
Ideas and routines which may help you with ISQ maintenance.
### Stucked tubing
* PVG magic: Reverse the flow, mechanical debrits at entrance will simply fall off.
* Rainbow flush: If something was soluble, it can often be dissolved again. You just need to get the right solvent, why not to try them all?
* Prolonged flushing with small flows can do a lot.
### What went wrong??
ISQ has a very nice logging system. Look into it. Usually there is a clue.
# Measuring samples in water with ISQ
Water is a bit problematic solvent for ISQ but measurements in it can be done! It only takes a bit longer and you will need to use different procedure!
### How to measure water samples?
* Do not forget to book some extra time
* Instead of the normal procedure you will use the procedure for water.
<img src="https://gitlab.science.ru.nl/jzelenka/isq/-/raw/master/waterpics/templates_comparison.png" width="1000" >
First and last line of the water template flushes the system to the water and then from the water to generally more accepted solvent - methanol.
### Why is water special?
Water mixes exothermically with other solvents like methanol or acetonitrile. To prove my point this is how it looks when you are going from methanol to water and back:
<img src="https://gitlab.science.ru.nl/jzelenka/isq/-/raw/master/waterpics/mixing_chart.png" width="700" >
Flow was set to **0.5 ml/min**, water was pumped from 5th minute. You see that the pressure raises sharply around 6th minute (0.5 ml dead volume) and then it slowly drops in course of approximately 5 minutes (2.5 ml volume before flushing MeOH). The same applies for the change back from water to methanol. The pressures are lower for the normal operating flow of 0.2 ml/min.
Whereas compounds soluble in methanol are also soluble in acetonitrile and vice-versa, analytes dissolved in water can precipitate when they are introduced to other solvent. From the abovementioned graph it is apparent that it takes approximately 2.5 ml of solvent to flush the system.
#!/usr/bin/env python3
from matplotlib.backends.backend_qt5agg import\
FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.patches import Rectangle as rect
from PyQt5 import QtGui
from PyQt5 import QtWidgets
from PyQt5 import QtCore
import numpy as np
import pandas as pd
import sys
def load_file(fn):
a = np.asarray(pd.read_table(
fn, delim_whitespace=True, skiprows=43, header=None,
names=("Time (min)", "step (ignore)", "Pressure (bar)"))
[['Time (min)','Pressure (bar)']]).T
return a[0], a[1]
def populate(datas, plot, style):
#plot.plot(datas[0], datas[1], color=(0,0.9,0,1))
plot.plot(datas[0], datas[1], linewidth=0.8, **style)
return 0
def main(pathprefix, files, styles, outname, index):
app = QtWidgets.QApplication(sys.argv)
graph = Figure(figsize=(5,2), dpi=100, facecolor="None",
constrained_layout=True)
spectra = graph.subplots(1,1, subplot_kw={"facecolor": (1, 1, 1, 0)})
canvas = FigureCanvas(graph)
canvas.setStyleSheet("background-color:transparent;")
canvas.setAutoFillBackground(False)
spectra.set_xlabel("Time (min)", )
spectra.set_ylabel("Pressure (bar)")
#spectra.set_xticks(np.linspace(100,200,6))
#spectra.set_xlim(0,40)
spectra.set_ylim(-1,50)
#spectra[0].set_yticks(np.linspace(1,8,8))
#spectrum.set_ylim(0.9,100000)
spectra.minorticks_on()
spectra.grid(True)
spectra.grid(True, 'minor', linewidth='0.2')
main_window = QtWidgets.QMainWindow(windowTitle="VSWR view")
for name, style in zip(files, styles):
datas = load_file(pathprefix+name)
populate(datas, spectra, style)
spectra.legend(loc=2)
spectra.axvline(5, color="#FF000088", linestyle=":")
spectra.axvline(10, color="#FF000088", linestyle=":")
spectra.add_patch(rect((-10,-10),15,80,fc="#FFCC0022"))
spectra.add_patch(rect((5,-10),5,80,fc="#0000FF10"))
spectra.add_patch(rect((10,-10),12,80,fc="#FFCC0022"))
spectra.annotate('$100\%\ MeOH$', (0,5), color="#884400FF")
spectra.annotate('$100\%\ H_2O$', (6.25,5), color="#0000AAFF")
spectra.annotate('$100\%\ MeOH$', (11.25,5), color="#884400FF")
graph.savefig(outname+".jpg", dpi=300)
graph.savefig(outname+".png", dpi=300)
pixmap=QtGui.QPixmap(outname+".png")
label = QtWidgets.QLabel(alignment=QtCore.Qt.AlignCenter)
main_window.setCentralWidget(label)
main_window.resizeEvent = lambda x: label.setPixmap(
pixmap.scaled(x.size(), QtCore.Qt.KeepAspectRatio,
QtCore.Qt.SmoothTransformation))
main_window.show()
sys.exit(app.exec_())
return
if __name__ == "__main__":
index = "b)"
pathprefix = ''
files = ['watertest.txt']
styles = [{'color': (0.3, 0, 0.5, 1), 'ls': '-', 'label': "mixing pressure"}]
outname = 'mixing_chart'
main(pathprefix, files, styles, outname, index)
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