Second Edition, Version 2.03
April 2017
PlasmaDive
™ Mini Manual, © Biognosys AG, Switzerland
Page 19 of 22
Qvalue
Qvalue assigned by SpectroDive
™ (see step 95.1).
User Verified
Specifies whether the user has accepted, rejected or not
checked the protein manually in the respective sample (see
step 96.1).
User Integrated
TRUE or FALSE, states whether the peptide peak has been
manually integrated by the user.
Protein Comment
Comment made while reviewing the peptide in step 96.4.
Troubleshooting Guide
This troubleshooting guide may be helpful in solving issues that may arise.
Issue
Possible Cause
Recommended Solution
LC column is clogged
during sample analysis
Solid particles were not
completely removed
from the samples during
the centrifugation (step
44)
Transfer final samples to
single vials and repeat a cold
centrifugation (4°C) as
described in step 44.
The first iRT peptide
behaves irregularly
LC gradient starts with
> 1% AcN
Ensure you use the LC
settings as recommended in
Section E.
Because of the high peptide
hydrophilicity slight
irregularities of the first iRT
peptide behaviour still can be
observed. This usually does
not influence the quality of
calibration.
iRT calibration is not
linear
Non-linear gradient was
used
Use linear gradient and LC
settings as recommended in
the Section E.
A minor issue in
chromatographic system
if there are only 1 or 2
outliers from linearity
Check manually if respective
iRT peaks are correctly
integrated and if the peak
shapes are satisfactory. If
not, exclude outliers from
calibration by clicking on
“Edit…” in ‘2) Choose LC
calibration’ section.
