Jun 25, 2026
Protocol for filtering water samples using a peristaltic pump 2026
- Katrina Lohan1,
- Emma Palmer1,
- Calli Wise1,
- Ruth DiMaria1,
- Tara Sill1,
- Lael Collins1,
- Emma Palmer1
- 1Smithsonian Environmental Research Center, Coastal Disease Ecology Lab
- Coastal Disease Ecology Lab - SERC
Protocol Citation: Katrina Lohan, Emma Palmer, Calli Wise, Ruth DiMaria, Tara Sill, Lael Collins, Emma Palmer 2026. Protocol for filtering water samples using a peristaltic pump 2026. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ldobz7g5b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: May 27, 2026
Last Modified: June 25, 2026
Protocol Integer ID: 318059
Keywords: water filtering, peristaltic pump, water sample, water through sterivex filter, peristaltic pump 2026 this protocol, sterivex filter, peristaltic pump, filtering water sample, water sample, masterflex, dehart
Abstract
This protocol describes how to filter water through Sterivex filters using either a MasterFlex or DeHart pump set-up.
Image Attribution
Figure 1. Photos of a MasterFlex pump including the (A) front side, (B) close-up of the bottom right buttons on the front side, and (C) two ¼” silicone tubes inserted into the retainer notches inside the open pump head.
Figure 2. Final filtration set-up for a single sample using a MasterFlex pump.
Figure 3. Plastic connector between the ¼” and 1/8” silicone tubing.
Figure 4. Photo of Sterivex package. Arrow shows the best side to open the packaging.
Guidelines
This protocol was developed with the assumption that the end-user possesses baseline knowledge of appropriate aseptic/clean techniques and a comprehensive understanding of the potential risks of contamination inherent to the workflow.
Notes on standard CDE clean techniques:
- Clean gloves must be worn while performing tasks sensitive to contamination. More details are provided further in the protocol. At a minimum, the gloves need to be changed between samples, when transitioning from “dirty” to “clean” tasks, or IMMEDIATELY after the gloves come in direct contact with a sample. Take care to minimize touching the tubing and Sterivex filters throughout this process.
Materials
Quantities are for 2 replicate filters per sample, each consisting of 500mL (if filtering a total of 1L for a single sample, double the number of sterivex filters and Whirl-Paks). Multiply quantities by the number of sites and samples and include one field control per sampling day. Materials cannot be reused between samples or field controls without sterilization.
- Peristaltic pump:
- For MasterFlex pump (each MasterFlex pump can process 2 samples simultaneously):
- 1 length of ½” (outside diameter) silicone tubing
- For DeHart pump (number of samples that each pump can process varies):
- 2 sets of quick-disconnect receptacles and associated tubing
- 1 length of sterile 1/8” (inside diameter) silicone tubing
- 1 1/8”-1/4” barbed plastic coupler (see below for example)
- 1 binder clip large enough for the 1/8”silicone tubing to fit through the metal loop
- 2 new Sterivex filters (more if filters clog)
- 2 new Whirl-Pak baggies
- 4 (minimum) adhesive labels printed on weatherproof paper
- 2 Sterivex labels (one for each filter; more if they clog)
- 2 Whirl-Pak labels (one for each)
- 2 1-gallon Ziplock bags (one per site and replicate filter)
- Parafilm
- Nitrile gloves (1 recommended box per 5 samples)
- Ground-fault interrupter (GFI) extension cord (in case no GFI outlet is available in the working space)
- 1 large beaker or container (at least 500 mL capacity) for output filtered water
Safety warnings
- Chlorine bleach is routinely used to sterilize surfaces and equipment. Bleach is an oxidizer and corrosive. The active ingredient, sodium hypochlorite, is incompatible with several reagents and chemicals used in the laboratory. For more detailed information, refer to the Sodium Hypochlorite (Bleach) Safety Fact Sheet.
- Diluted bleach solutions must be made fresh each day they are needed to ensure the proper concentration is applied for sterilization purposes. Diluted chlorine bleach breaks down into water and salt within 24hrs.
Pre-Sampling Preparation
Bleach the 1/8” silicone tubing following the DNA Sterilization Techniques Protocol 2026. This is best done before shipping to the field site, especially if the tubes do not need to be reused across sites. If the sampling schedule is set, the tubing can be grouped together based on the required number of tubes per day.
Pre-fill out as much as possible of the Whirl-Pak and Sterivex filter labels.
Note: The CDE lab typically collects 2 1L replicate bottles per sample in the field (1 for filtering and 1 as a back-up). We then filter 500mL of water through 2 replicate filters. Only one of those replicate filters will be used for extractions later with the other acting as a back-up. If the water is too turbid or other issues arise, the 500mL can be split between multiple filters (1-2 additional filters). Therefore, it is important to label how much water was filtered through each filter.
Overview
Wear nitrile gloves to prevent contamination, changing them in between every sample. Take care to minimize touching the tubing and Sterivex filters throughout this process. While this can be done by only one person, having two is ideal with one having “clean hands” and the other having “dirty hands”. To help reduce the risk of contamination, it can be helpful to distinguish the roles visually and tactically by only having the designated “clean hands” individual wear gloves. For the “dirty hands” individual, the absence of gloves provides a continuous physical reminder of their role to discourage any unconscious transition to clean handling. If the water filtering is being done solo, read through the protocol completely before starting as steps like 6 and 14 in the water filtering protocol can be performed prior to completing the proceeding “clean” steps to avoid changing gloves multiple times.
For all users, ensure that gloves are donned or changed before switching from “dirty” to “clean”
tasks. Gloves do not need to be changed when performing only clean or dirty steps unless the gloves come in direct contact with the sample.
Process the water samples in the order that they were collected, always filtering the field control last.
Option #1. MasterFlex Pump Set-Up
Note: MasterFlex pumps are dual-channel pumps and can run 2 replicate filters simultaneously.
Figure 1. Photos of a MasterFlex pump including the (A) front side, (B) close-up of the bottom right buttons on the front side, and (C) two ¼” silicone tubes inserted into the retainer notches inside the open pump head. The middle dial on the front side controls the speed the pump runs at while the bottom switch controls the direction of the pump. When at the top, the water runs from the left to the right while the water flows from the right to the left when the switch is at the bottom. Move the switch to the center position to turn it off.
First, plug the peristaltic pump into a ground fault interrupter (GFI) outlet to prevent yourself from being shocked or having the equipment short circuit if the plug gets wet.
Note: Ensure that the workstation stays organized and immediately clean up any spills or puddles to reduce any shock risk throughout this protocol.
Ensuring that the pump is off (bottom switch is in the center position), rotate the handle counterclockwise (to the left) to open the pump head (Figure 1A).
Scooch two pieces (Figure 1C; if running more than one sample; otherwise only one is necessary) of ¼” silicone tubing inside of the retainer starting with the rear tube position.
Note: Make sure enough of the tubing is hanging off the outflow side to reach an outflow beaker/area and that the tubing is positioned within the retainer notches.
Rotate the handle clockwise (to the right) to close (Figure 1A). The pump head will be fully closed when the handle is at the horizontal position against the cam stop.
Note: While it may feel like the tubing is being crushed while closing the retainer, the waterflow will be preserved if the tubing sits correctly in the retainer notches.
Decide the direction of water flow (to the right or left) based on your workspace setup and place the outflow portion in the outflow beaker or in a sink/bathtub. If using an outflow beaker, thread the outflow end through the metal loops of a binder clip and secure it to the outside of the beaker. Otherwise, the outflow end may wiggle out of the beaker and start spraying water all over your workspace.
Note: The pump works best -by leveraging gravity- if the outflow beaker is placed lower than the pump.
Go to Step 6.1 of "Water Filtering"
Option #2. DeHart Pump Set-up
Note: DeHart pumps are customizable and may be single to triple-channel pumps, running anywhere from 1-3 samples simultaneously.
First, make sure that the battery for the pump is charged (>4 volts).
Connect the quick-disconnect receptacles and associated tubing to the quick-disconnect couplers.
Note: The bottom couplers are for the outflow, and the top are for the input.
Place the outflow tubbing in an outflow beaker or a sink. If using an outflow beaker, thread the outflow end through the metal loops of a binder clip and secure it to the outside of the beaker. Otherwise, the outflow end may wiggle out of the beaker and start spraying water all over your workspace.
Place the plastic coupler on the intake end of the quick-disconnect receptacle associated tubing.
Note: The plastic coupler does not need to be changed or sterilized between samples.
Go to Step 6.1 of "Water Filtering".
Water Filtering
Figure 2. Final filtration set-up for a single sample using a MasterFlex pump.
Place the plastic coupler on the intake end of the ¼” silicone tubing (Figure 2).
Note: The plastic coupler does not need to be changed or sterilized between samples.
Figure 3. Plastic connector between the ¼” and 1/8” silicone tubing.
Dirty gloves: Starting with the water sample that was collected first, invert the sample bottle three times to homogenize the sample. Set the bottle on the counter near the inflow end of the ¼” silicone tubing and unscrew the lid while keeping it on the bottle.
Dirty gloves: slightly open the bag of the 1/8” tubing so that a single tube can be grabbed.
Figure 4. Photo of Sterivex package.
Clean gloves: open a new Sterivex filter – keeping it inside the packaging. It is best to open the Sterivex filter package towards the narrow end of the Sterivex filter.
Clean gloves: grab a single 1/8” silicone tube and attach one end to the narrow end of the Sterivex filter while it is still inside of the packaging.
Dirty gloves: remove the lid from the sample bottle.
Clean gloves: place the Sterivex filter inside of the sample bottle with the output end hanging outside of the bottle.
Note: make sure that the filter stays submerged throughout filtering. Otherwise, the pump will begin to run dry which will greatly slow down the filtering process.
Dirty gloves: place the sample bottle lid either back on top of the bottle
or on the counter next to it face up.
Dirty gloves: connect the output end of the 1/8” tubing with the plastic
connector attached to the ¼” tubing.
Repeat steps 6.1-6.9 for the other samples to be filtered simultaneously
based on your pump and the number of samples that can be run at once.
Dirty gloves: turn on the pump.
a. For Masterflex pump (Figure 1B):
i. Ensure that the dial is set at the lowest water pump speed before turning on the pump.
ii. To turn on the pump, move the control switch either in the up position – this will operate the pump clockwise, moving the water from left to right – or in the down position – this will operate the pump counterclockwise, moving the water from right to left. When turned on, the POWER indicator will light up.
iii. When ready, turn the filter speed up by turning the dial to the right (clockwise).
b. For DeHart pump:
i. To turn on the pump, push the button next to the handle of the yellow case.
Let the pump run until 500 mL of water has passed through the filter or the filter becomes too clogged to push water through.
Note: Keep the number of filters per sample to a minimum. Each filter needs to be processed separately for most of the extraction protocol which increases costs and processing time.
Clean gloves: Before turning off the filter, lift the tubing so that the Sterivex filter is out of the water. Let the pump run to remove as much water from the filter as possible.
Dirty gloves: If the sample lid is on top of the bottle, remove it and place it face-up on the counter.
Dirty gloves: turn off the pump.
For Masterflex pump (Figure 1B): To turn off the filter, slide the switch into the center position.
For DeHart pump: To turn off the pump, push the button next to the handle of the yellow case.
Clean gloves: to start the second replicate filter, open a new Sterivex package towards the narrow end – keeping the filter inside the packaging.
Clean gloves: Remove the 1/8” tubing from inside the sample bottle being careful not to touch anything with it.
Clean gloves: Place the first Sterivex filter inside of the packaging of the second and connect the 1/8” tubing to the second Sterivex filter. The second filter can now be placed inside of the original sample bottle.
Clean gloves: Remove the first Sterivex filter from inside the packaging and affix a filter label to the side ensuring that it is properly labeled with the project name, date, site, sample number, replicate filter number, filter number (if necessary), and volume (mL) of water passed through the filter.
Clean gloves: Place the first Sterivex filter into a new Whirl-Pak. If the complete water volume was passed through a single filter, close the bag. If not, temporarily close the bag and place the other filters inside when they are done filtering.
Note: If Whirl-Paks are unavailable, Ziplocs are an acceptable alternative.
Repeat steps 6.2-6.20 until all samples and replicate filters are completed. Filter the field control last. Place all the Whirl-Paks from a single site and sample replicate into a labeled gallon bag. This makes it easy to find the sample later.
Place the filters in a -20°C manual defrost freezer. Follow standard dry ice transport rules when transporting the frozen samples.
Note: It is important to keep eDNA samples frozen. If a sample begins to thaw, the DNA inside will begin to degrade and the sample will not be comparable to others collected at this time.
Clean-Up
If possible, wash down all workstation surfaces with 10% bleach solution taking care not to get bleach spray on the pumps.
Re-bleach clean the 1/8” inch tubing and 1L sample bottles following the methods in DNA Sterilization Techniques Protocol 2026 before reusing them to collect or process samples. The inside of the tubing does not need to be bleach-cleaned as the water which moves through it has already been filtered.
Shipping/Transport
Before shipping or transporting the samples, ensure that all samples are present and accounted for. Use a packing inventory sheet. Ensure that samples remain frozen during shipping and transport (using dry ice or ice packs).