2014-10-15

LWG Geochemistry/MBIO meeting minutes,

Oct 15, 2014

Attendees: Bogus, Peng, Peters, Julson, Zarikian, Houpt, Morgan, Cannon, Brandt, Moortgat (call in), and Petronotis

1. Review cruise evaluations from EXP350, EXP351, and EXP352

· EXP350

o Scientist requested the software Aabel to plot and edit data

- LWG decision: it’s a personal preference, we cannot support every scientist’s preference. We have commonly used software available (e.g., Kaleidagraph, Excel)

ACTION: NONE

o Scientist felt the ICP analysis turnaround times were too slow.

- LWG decision: This was not mentioned during the expedition, and it’s only an issue can be addressed during the cruise.

ACTION: NONE

· EXP351

o IC: problem with integration of K peak.

- Problem was solved during the cruise. It was not an issue on the subsequent cruise.

ACTION: NONE

o TOC: we were not able to get the instrument running properly. After some diagnosis, it was determined the detector died. The instrument was sent back from EXP352, and is in the process of been sent to the vendor for repair.

ACTION: Send to vendor and keep track of progress; earliest estimate for shipboard use is EXP355 (Houpt)

o ICP IW analysis: Typo and inconsistency between Quick Start Guide (QSG) and User Guide (UG) in standard preparation method

- LWG: The issue is fixed (Peters)

ACTION: NONE

o ICP IW analysis: Standard preparation method was modified to justify the acid strength differences between standards. However, by doing so, the dilution method needed to be changed resulting in using different volumes of matrix solution between standards and samples. After some testing done during EXP351, we showed that the acid strength difference is negligible after the final dilution.

- LWG decision: It is more important to keep the dilution volume of the matrix solution the same between standards and samples. Therefore, it is agreed we use the standards formula created during EXP344.

ACTION: Provide correct method to Peters for editing in both QSG and UG (PENG)

o ICP: the torch was installed improperly resulting in random bad data.

- LWG: Discussion focused on if the vendor manual shows the proper position of the torch and during on-site training received by the chemistry technician (Brandt). The new hire needs to attend this training.

ACTION: NONE

o ICP: scientist suggested running calibration standards interspersed between samples as opposed to the beginning of a run.

- LWG: This is not as commonly done as a standard calibration before a run. We do run QC standards as unknowns within a run already, and this is sufficient.

ACTION: NONE

· EXP 352

o X-Ray lab: scientist didn’t realize we still have the heat treatment and glycolation capability onboard.

- LWG: Result of new technicians on both crews. Our training needs to be more complete.

ACTION: We will show both new X-ray technicians the capabilities and provide training (BARNES)

o ICP, scientist complaints about the in-house data reduction software, ICP Analyzer. The software doesn’t allow the use of internal standards, it doesn’t force calibration curve through zero, and it is not flexible in identifying and removal of standards in calibration. Currently the data processing for ICP is as follow

i. Optimize the signal with alignment standard solution prior to sample analysis, determine best lines to use, exclude “bad” lines if possible

ii. Produce a .csv file with raw data using instrument software Salsa

iii. Load the csv file into in-house software ICP Analyzer, and generate calibration curve. Go through calibration curve to further eliminate bad standard lines.

iv. Continue using ICP Analyzer to produce drift correction and final data in Excel file

v. Share the Excel file with scientists to review the data

vi. Once the reviewing process is complete to satisfaction, chemistry technician(s) then upload the final Excel spreadsheet into LIMS.

vii. Scientists can further manipulate the data in Excel spreadsheet for personal purpose, this will not affect the data which has already been loaded into LIMS

ACTION: LWG would like to propose a programming project to have another program developed/installed for ICP data analysis. It needs to include internal standards addition, to simplify standards editing both in the standard table and of multiple lines. Details need to be further discussed. (HOUPT)

o The hand held XRF was used extensively during EXP352, so a large quantity of data was produced. We do not have any protocols or a User Guide currently in place. The pXRF was also used on EXP350, but we have yet to receive any reports or documentation.

ACTION: A User Guide for the pXRF is needed. It should be based on methods created from EXP350 and EXP352 scientists. We also need a protocol for data management, including raw data and final data in LIMS, and a Curation protocol on creating tests (TextID). We would like to see these protocols put in place prior to EXP360. (HOUPT)

2. Instrument computer data backup scheme

· David Houpt would like to see an automatic backup system put in place to back up each instrument computer, due to missing raw data in data1 coming back from the ship.

· Mike Cannon (MCS) explained that shipboard instrument computers are being backed up on a daily basis; these daily backups are stored for up to 2 weeks. There is also an automatic weekly full backup, and this information is stored up for to 4 months. The only files not being backed up automatically are the SHIL image files (due to size).

ACTION: We request that the full backup storage period be extended up to 6 months, or until Rakesh can verify all raw data from each expedition are present and stored in data1 (MCS)

3. Biomarker requests for future expeditions: How much of this work should we support on the ship? Or what is the basic service/support for this work we could reasonably provide?

o Currently, we have a 15 year old GC-MS, which is problematic and cumbersome to use, and very likely less sensitive/accurate. We also do not have an automatic solvent extractor and polyvap on board so scientist(s) would have perform manual extraction, which is very time consuming.

ACTION:

· LWG decided that sample collection onboard for both shipboard and shore request is the basic service we will provide for biomarker work, pending SAC approval. Scientist(s) will provide detailed sample collection and shipping procedure.

· When a scientist requests more than sample collection, such as sample processing (extraction) onboard, it will be a case-by-case decision made by the EPM and TAS supervisors.

· We will not, at this point, support a full lipid extraction workup during an expedition

4. Creating chemistry standard table to be managed in LIME, instead of using Sample Master.

ACTION: Discussion needed among chemistry technicians, and a detailed project plan needs to be drafted and presented (HOUPT)