User:Derrick.gough/sandbox

Article Evaluation
Choose at least 1 question relevant to the article you're evaluating and leave your evaluation on the article's Talk page. Copy/paste this text in your sandbox in a section titled "Text I posed to the article's talk page." Be sure to sign your feedback with four tildes — ~.

Digital microfluidics: Digital microfluidics
 * The written article appears to be neutral and presenting information in an unbiased way from the references. The first seven references with links all worked, to include the duplicate links that go to another website/journal that published the same paper. The lack of an introduction to the subject matter (the initial paragraph is only two sentences that don't really explain the topic) distracts me the most about the article. On the talk page, one user asked for the "Basic" header to be removed and the rest of that section just be added to the introduction to the material.  This makes more sense, and will help a user quickly skimming the article for an overview of the topic to understand what is going on, especially with the included pictures. The "Basic" header is a bit unnecessary.


 * Text I posed to the article's talk page:: "The article references optical tweezers (among other separation and extraction methods), but doesn't provide any sort of definition to the average user. What are optical tweezers? What does the referenced material actually tell us about it, other than that its a thing that is there and is used? ~"

Add to an article
Edited sentence: /* Optical Tweezers */  removed the superscript "10" from the subheading Optical Tweezers as the article was not referenced at that sentence. ~

(added final sentence) Edited sentence and citation added: /* Opitcal Tweezers */ "Optical tweezers have also been used to separate cells in droplets. Two droplets are mixed on an electrode array, one containing the cells, and the other with nutrients or drugs. The droplets are mixed and then optical tweezers are used to move the cells to one side of the larger droplet before it is split. For a more detailed explanation on the underlying principles, see Optical tweezers. "

(grammar edits, content remains same) Edited sentence: /* Implementation */ In one of various embodiments of EWOD-based microfluidic biochips, investigated first by Cytonix in 1987 [1 ] and subsequently commercialized by Advanced Liquid Logic, there are two parallel glass plates. The bottom plate contains a patterned array of individually controllable electrodes and the top plate is coated with a continuous grounding electrode. A dielectric insulator coated with a hydrophobic is added to the plates to decrease the wet-ability of the surface and to add capacitance between the droplet and the control electrode. The droplet containing biochemical samples and the filler medium, such as the silicone oil, a fluorinated oil, or air, are sandwiched between the plates and the droplets travel inside the filler medium. In order to move a droplet, a control voltage is applied to an electrode adjacent to the droplet, and at the same time, the electrode just under the droplet is deactivated. By varying the electric potential along a linear array of electrodes, electrowetting can be used to move droplets along this line of electrodes.

Paper topic: Microfluidics detection: Mass spectroscopy; initial article:

Initial planning for my article
What do I want to add? Not much in there yet, so adding in current applications will be beneficial. Need more than broad topic names that do not describe it.

Can honestly use many of the currently cited articles because the only references currently are big themes / names without going into any detail. Ask Ashleigh

I think i can add in an image from the already referenced articles to explain it. There are currently no pictures on the page.

From the "talk" page, there is an edit I'd like to do.

Paragraph to add to:

Mass spectrometry (MS) is an analytical technique in which chemical species are ionized and sorted before detection, and the resulting mass spectrum is used to identify the ions' parent molecules. Spectroscopy is often used in conjunction with many techniques that are seen in microfluidic applications; incubation of cells within single droplets, droplet-based reaction vessels, sorting of small volume samples, etc., to identify experimentally relevant species. This makes scalable spectroscopic techniques relevant in the field of microfluidics to reduce the overall workload and resource utilization necessary in carrying out microscale fluid-based experiments. There are many cases in which other spectroscopic methods, such as nuclear magnetic resonance (NMR), fluorescence, infrared, or Raman, are not viable as standalone methods due to the particular chemical composition of the droplets, which are often sensitive to fluorescent labels, or contain species that are otherwise indeterminately similar, where MS may be employed along with other methods to characterize a specific analyte of interest. Scarcity and difficulty of separation/purification make entirely microfluidic scale systems coupled to mass spectrometry ideal in the fields of proteomics  enzyme kinetics, drug discovery, and newborn disease screening. The two methods of ionization for mass analysis most commonly used in droplet-based microfluidics today are matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), with surface acoustic wave nebulization (SAWN) approaches being developed as well.

Initial drafting of my article
Need to add in citations for MALDI.
 * Editing an existing article
 * Identify what's missing from the current form of the article. Think back to the skills you learned while critiquing an article. Make notes for improvement in your sandbox. Keep reading your sources, too, as you prepare to write the body of the article.
 * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4318794/ Good paper to cite - coupling techniques
 * Mass spectrometry (MS) is a near universal detection technique that is recognized throughout the world as the gold standard for identification of most compounds (make this the new first sentence). Additionally, unlike previous discussed techniques, MS is label-free, i.e. there is no need to bind additional ligands or groups to the molecule of interest in order to receive a signal. However, it has only recently (in the past decade) gained popularity with droplet-based microfluidics (and microfluidics as a whole) due to the challenges associated with coupling mass spectrometers with the miniaturized-nature of microfluidics-based devices (make this the sentence after "MS may be employed along with...).
 * Re-order ESI before MALDI.
 * Should I put in sub-sections being advantages vs disadvantages? Is one paragraph enough? Don't need theory behind each technique as they each have their own Wiki page.
 * One complication offered by droplet-based microfluidics is the high-throughput of dispersed samples that is produced at comparatively low flow rates compared to traditional MS-injection techniques. ESI is able to easily accept these low flow rates and is now commonly exploited for on-line microfluidic analysis (cite). ESI offers a high throughput answer to the problem of label-free droplet detection
 * ESI offers a similarly high throughput answer to the problem of label-free droplet detection to MALDI, with less intensive sample preparation and fabrication elements that are scalable to microfluidic device scale. This ionization technique involves the application of a high voltage to a carrier stream of analyte-containing droplets, which aerosolizes the stream, followed by detection at a potential-differentiated analyser region. Droplet size, Taylor cone shape, and flow rate can be controlled by varying the potential differential and the temperature of a drying (to evaporate analyte-surrounding solvent) stream of gas (usually nitrogen). Because ESI allows for online droplet detection, other problems posed by segmented or off-chip detection based systems can be solved, such as the minimizing of sample (droplet) dilution, which is especially critical to microfluidic droplet detection where analyte samples are already diluted to the lowest experimentally relevant concentration.
 * MALDI is typified by the use of an ultraviolet (UV) laser to trigger ablation of analyte species that are mixed with a matrix of crystallized molecules with high optical absorption. The ions within the resulting ablated gasses are then protonated or deprotonated before acceleration into a mass spectrometer. The primary advantages of MALDI detection over ESI in microfluidic devices are that MALDI allows for much easier multiplexing(65), which even further increases the device's overall throughput (63), as well as less reliance on moving parts, and the absence of Taylor cone stability problems posed by microfluidic-scale flow rates(66). The speed of MALDI detection, along with the scale of microfluidic droplets, allow for improvements upon macro-scale techniques in both throughput and time-of-flight (TOF) resolution(60,63). Where typical MS detection setups often utilize separation techniques such as chromatography, MALDI setups require a sufficiently purified sample to be mixed with the organic matrices necessary for MALDI detection(58). While MALDI matrices are preferentially in much higher concentrations than the analyte sample, which allows for microfluidic droplet transportation to be incorporated into online MALDI matrix production, matrix composition must be tuned to produce appropriate fragmentation and ablation of analytes. Due to the low number of known matrices and trial and error nature of finding appropriate new matrix compositions(67), this can be the determining factor in the use of ESI over MALDI.
 * MALDI is typified by the use of an ultraviolet (UV) laser to trigger ablation of analyte species that are mixed with a matrix of crystallized molecules with high optical absorption. The ions within the resulting ablated gasses are then protonated or deprotonated before acceleration into a mass spectrometer. The primary advantages of MALDI detection over ESI in microfluidic devices are that MALDI allows for much easier multiplexing(65), which even further increases the device's overall throughput (63), as well as less reliance on moving parts, and the absence of Taylor cone stability problems posed by microfluidic-scale flow rates(66). The speed of MALDI detection, along with the scale of microfluidic droplets, allow for improvements upon macro-scale techniques in both throughput and time-of-flight (TOF) resolution(60,63). Where typical MS detection setups often utilize separation techniques such as chromatography, MALDI setups require a sufficiently purified sample to be mixed with the organic matrices necessary for MALDI detection(58). While MALDI matrices are preferentially in much higher concentrations than the analyte sample, which allows for microfluidic droplet transportation to be incorporated into online MALDI matrix production, matrix composition must be tuned to produce appropriate fragmentation and ablation of analytes. Due to the low number of known matrices and trial and error nature of finding appropriate new matrix compositions(67), this can be the determining factor in the use of ESI over MALDI.

Changes/additions to the above:
 * 05Feb: Added in citation #65 to the page. Citation went in at the end of the "Mass Spectrometry" paragraph. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4318794/

Initial Draft / Article I emailed for peer review:
Mass spectrometry[edit]

Mass spectrometry (MS) is a near universal detection technique that is recognized [null throughout the world] as the gold standard for identification of most compounds. MS is an analytical technique in which chemical species are ionized and sorted before detection, and the resulting mass spectrum is used to identify the ions' parent molecules. This makes MS, unlike previously discussed detection techniques, label-free; i.e. there is no need to bind additional ligands or groups to the molecule of interest in order to receive a signal and identify the compound.

There are many cases in which other spectroscopic methods, such as nuclear magnetic resonance (NMR), fluorescence, infrared, or Raman, are not viable as standalone methods due to the particular chemical composition of the droplets, which are often sensitive to fluorescent labels,[55] or contain species that are otherwise indeterminately similar, where MS may be employed along with other methods to characterize a specific analyte of interest.[56][57]However, it has only recently (in the past decade) gained popularity with droplet-based microfluidics (and microfluidics as a whole) due to the challenges associated with coupling mass spectrometers with the miniaturized-nature of microfluidics-based devices (cite: Microfluidics-to-Mass Spectrometry: A review of coupling methods and applications). Scarcity and difficulty of separation/purification make entirely microfluidic scale systems coupled to mass spectrometry ideal in the fields of proteomics [55][58][59] enzyme kinetics,[60] drug discovery,[37] and newborn disease screening.[61] The two primary methods of ionization for mass analysis most commonly used in droplet-based microfluidics today are matrix-assisted laser desorption/ionization (MALDI)[62][63] and electrospray ionization (ESI),[55] with additional methods (such as surface acoustic wave nebulization (SAWN), among others (cite: Microfluidics-to-Mass Spectrometry, now #65)) and approaches being developed as well.[64]

Electrospray ionization[edit]

One complication offered by droplet-based microfluidics is the high-throughput of dispersed samples that is produced at comparatively low flow rates compared to traditional MS-injection techniques. ESI is able to easily accept these low flow rates and is now commonly exploited for on-line microfluidic analysis. ESI offers a high throughput answer to the problem of label-free droplet detection, as does MALDI, but with less intensive sample preparation and fabrication elements that are scalable to microfluidic device scale.[68] This ionization technique involves the application of a high voltage to a carrier stream of analyte-containing droplets, which aerosolizes the stream, followed by detection at a potential-differentiated analyser region. The carrier fluid within a droplet-based microfluidic device, typically an oil, is often an obstacle within ESI. The oil, when part of the flow of droplets going into an ESI-MS instrument, can cause a constant background voltage interfering with the detection of sample droplets (cite #70). This background interference can be rectified by changing the oil used as a carrier fluid and by adjusting the voltage used for the electrospray (cite #70).

Droplet size, Taylor cone shape, and flow rate can be controlled by varying the potential differential and the temperature of a drying (to evaporate analyte-surrounding solvent) stream of gas (usually nitrogen).[69] Because ESI allows for online droplet detection, other problems posed by segmented or off-chip detection based systems can be solved, such as the minimizing of sample (droplet) dilution, which is especially critical to microfluidic droplet detection where analyte samples are already diluted to the lowest experimentally relevant concentration.[70]

Matrix-assisted laser desorption/ionization[edit] (No changes yet)

MALDI is typified by the use of an ultraviolet (UV) laser to trigger ablation of analyte species that are mixed with a matrix of crystallized molecules with high optical absorption. The ions within the resulting ablated gasses are then protonated or deprotonated before acceleration into a mass spectrometer. The primary advantages of MALDI detection over ESI in microfluidic devices are that MALDI allows for much easier multiplexing,[65] which even further increases the device's overall throughput,[63] as well as less reliance on moving parts, and the absence of Taylor cone stability problems posed by microfluidic-scale flow rates.[66] The speed of MALDI detection, along with the scale of microfluidic droplets, allow for improvements upon macro-scale techniques in both throughput and time-of-flight (TOF) resolution.[60][63] Where typical MS detection setups often utilize separation techniques such as chromatography, MALDI setups require a sufficiently purified sample to be mixed with pre-determined organic matrices, suited for the specific sample, necessary for MALDI detection.[58] MALDI matrix composition must be tuned to produce appropriate fragmentation and ablation of analytes.

One method to obtain a purified sample from droplet-based microfluidics is to end the microfluidic channel onto a MALDI plate, with aqueous droplets forming on hydrophilic regions on the plate. Solvent and carrier fluid is then allowed to evaporate, leaving behind only the dried droplets of the sample of interest, after which the MALDI matrix is applied to the dried droplets. (cite microfluidics-to-mass spec review; new #65, and #62) This sample preparation has notable limitations and complications, which are not currently overcome for all types of samples. Additionally, MALDI matrices are preferentially in much higher concentrations than the analyte sample, which allows for microfluidic droplet transportation to be incorporated into online MALDI matrix production. Due to the low number of known matrices and trial and error nature of finding appropriate new matrix compositions,[67] this can be the determining factor in the use of other forms of spectroscopy over MALDI.

Can add in a tag / link: "which are often sensitive to fluorescent labels" can be linked to "Fluorescent Tag"

Changes/additions to the above:
 * 07Feb: Added in citation #70 to the page. Citation went in at the end of the "Electrospray Ionization" paragraph. https://www.ncbi.nlm.nih.gov/pubmed/20491430/

Revised Article after peer review
Mass spectrometry[edit]

Mass spectrometry (MS) is a near universal detection technique that is recognized throughout the world as the gold standard for identification of manycompounds. MS is an analytical technique in which chemical species are ionized and sorted before detection, and the resulting mass spectrum is used to identify the ions' parent molecules. This makes MS, unlike other detection techniques (such as fluorescence), label-free; i.e. there is no need to bind additional ligands or groups to the molecule of interest in order to receive a signal and identify the compound.

There are many cases in which other spectroscopic methods, such as nuclear magnetic resonance (NMR), fluorescence, infrared, or Raman, are not viable as standalone methods due to the particular chemical composition of the droplets. Often, these droplets are sensitive to fluorescent labels,[55] or contain species that are otherwise indeterminately similar, where MS may be employed along with other methods to characterize a specific analyte of interest.[56][57]However, MS has only recently (in the past decade) gained popularity as a detection method for droplet-based microfluidics (and microfluidics as a whole) due to challenges associated with coupling mass spectrometers with these miniaturized devices. Difficulty of separation/purification make entirely microfluidic scale systems coupled to mass spectrometry ideal in the fields of proteomics, [55][58][59] enzyme kinetics,[60] drug discovery,[37] and newborn disease screening.[61] The two primary methods of ionization for mass analysis used in droplet-based microfluidics today are matrix-assisted laser desorption/ionization (MALDI)[62][63] and electrospray ionization (ESI).[55]  Additional methods for coupling, such as (but not limited to) surface acoustic wave nebulization (SAWN), and paper-spray ionization onto miniaturized MS, are being developed as well. [64]

Electrospray ionization[edit]

One complication offered by the coupling of MS to droplet-based microfluidics is that the dispersed samples are produced at comparatively low flow rates compared to traditional MS-injection techniques. ESI is able to easily accept these low flow rates and is now commonly exploited for on-line microfluidic analysis. ESI and MALDI offer a high throughput answer to the problem of label-free droplet detection, but ESI requires less intensive sample preparation and fabrication elements that are scalable to microfluidic device scale. [68] ESI involves the application of a high voltage to a carrier stream of analyte-containing droplets, which aerosolizes the stream, followed by detection at a potential-differentiated analyser region. The carrier fluid within a droplet-based microfluidic device, typically an oil, is often an obstacle within ESI. The oil, when part of the flow of droplets going into an ESI-MS instrument, can cause a constant background voltage interfering with the detection of sample droplets. This background interference can be rectified by changing the oil used as a carrier fluid and by adjusting the voltage used for the electrospray.

Droplet size, Taylor cone shape, and flow rate can be controlled by varying the potential differential and the temperature of a drying (to evaporate analyte-surrounding solvent) stream of gas (usually nitrogen).[69] Because ESI allows for online droplet detection, other problems posed by segmented or off-chip detection based systems can be solved, such as the minimizing of sample (droplet) dilution, which is especially critical to microfluidic droplet detection where analyte samples are already diluted to the lowest experimentally relevant concentration.[70]

Matrix-assisted laser desorption/ionization[edit]

MALDI is typified by the use of an ultraviolet (UV) laser to trigger ablation of analyte species that are mixed with a matrix of crystallized molecules with high optical absorption. The ions within the resulting ablated gasses are then protonated or deprotonated before acceleration into a mass spectrometer. The primary advantages of MALDI detection over ESI in microfluidic devices are that MALDI allows for much easier multiplexing,[65] which even further increases the device's overall throughput,[63] as well as less reliance on moving parts, and the absence of Taylor cone stability problems posed by microfluidic-scale flow rates. [66] The speed of MALDI detection, along with the scale of microfluidic droplets, allows for improvements upon macro-scale techniques in both throughput and time-of-flight (TOF) resolution.[60][63] Where typical MS detection setups often utilize separation techniques such as chromatography, MALDI setups require a sufficiently purified sample to be mixed with pre-determined organic matrices, suited for the specific sample, prior to detection.[58] MALDI matrix composition must be tuned to produce appropriate fragmentation and ablation of analytes.

One method to obtain a purified sample from droplet-based microfluidics is to end the microfluidic channel onto a MALDI plate, with aqueous droplets forming on hydrophilic regions on the plate. Solvent and carrier fluid are then allowed to evaporate, leaving behind only the dried droplets of the sample of interest, after which the MALDI matrix is applied to the dried droplets. This sample preparation has notable limitations and complications, which are not currently overcome for all types of samples. Additionally, MALDI matrices are preferentially in much higher concentrations than the analyte sample, which allows for microfluidic droplet transportation to be incorporated into online MALDI matrix production. Due to the low number of known matrices and trial and error nature of finding appropriate new matrix compositions,[67] this can be the determining factor in the use of other forms of spectroscopy over MALDI.

Reflective Essay
Derrick Gough

26 February 2018

1. What article did you work on? Was this a new article or an existing article?

I worked on an existing article, overall entitled "Droplet-based Microfluidics." Specifically, I updated the sub-section covering "mass spectrometry."

2. Summarize your main contributions in 3-4 sentences or bullet points.

a)   The primary contribution was to provide a better understanding of why MS is desirable and used as a detection method with microfluidic devices, despite the many coupling challenges that face researchers. I did not go in-depth into the coupling challenges as it does not seem like a pertinent topic for this specific Wiki article that is focused on microfluidic devices and their uses.

b)   I doubled the length of the topic to a more appropriate overview length (from 3 paragraphs to 6) that gives enough baseline knowledge for a casual observer and added in more links to already created Wiki articles for more in-depth discussion on specific topics.

c)   I restructured the three paragraphs to fix grammatical errors, add in better structure and details to improve sentence flow, and re-ordered the sub-sections underneath MS.

d)   The addition of sources, as well as properly citing stand-alone sentences that were not backed up with any citation, improves the strength and viability of the article.

3. How did you respond to suggestions from peer reviewers? Please list specific changes in 3-5 sentences or bullet points. Also indicate if you used the Wikipedia content expert or received feedback from other Wikipedians outside the course.

I did not receive or use any feedback from Wikipedia content experts or other Wikipedians outside the course.

a)   I corrected nearly all of the edits/suggested reviews from my two peer reviewers. They found nuanced language or grammar flows that I use (without realizing) that are not the best for professional language. For example, word choices to remove passive language and removing word count to enable the article to be clearer and more concise, such as on the last sentence of paragraph 5.

b)   Additionally, I added in some subject specifications that I left out (such as specifying ESI as an ionization technique after referencing both ESI and MALDI) for ease of reading by a casual reader.

c)   There were three items that were suggested to be linked to fellow Wiki pages in addition to ones I already had, so I added these into my Sandbox for easy copy and paste. This helps future viewers a lot as they can dive into more specific details that I felt didn’t need to be expounded upon in this article, especially since the other detection methods/techniques are missing a similar topic.

d)   Advice/corrections I didn’t follow-up on. There were specific points within my article where my reviewers were confused by a thought, redundant sentence structure, or reference. The majority of these (~75%) I left as is, or with very minimal changes, as they were from the current article and I did not know completely what the original author was attempting to say. I didn’t want to completely change someone else’s words without knowing their intent, but I plan to put it on the talk page to see if anyone comes back to edit it or clarify it. I feel that I should give the original author (or fellow authors) a chance to see me changing their sentence structure completely before I simply do so.

e)   Advice/corrections I didn’t follow-up on. I was asked to clarify what problems are associated with coupling MS to a microfluidic device. This can lead down a rabbit hole and is better answered scientifically through published work (that is referenced) than by a more generalized article about MS as a detection method. Additionally, I was told that more detail about what MS techniques don’t allow for on-line detection (in order to expand upon a thought in the ESI paragraph) was not followed up on by me as my main focus was the why we use MS with microfluidics rather than its complications/challenges in connecting it to a device.

4. Reflect on the following questions in a short paragraph: Was this assignment valuable to your learning (of course material, research/literature review skills, ability to critically evaluate peers, etc.) - why or why not? Do you think your article will be valuable to Wikipedia readers? How could this assignment be improved in the future? [You will not lose points for negative comments; please be honest in your critiques of this assignment to improve the course for future years.]

Yes, this assignment was valuable due to the volume of literature I had to read through in order to properly summarize this topic. Reading and skimming through a few dozen published papers and then summarizing it in a fashion for a casual reader to view and understand is always a benefit to one’s own understanding. Additionally, putting a very heavily researched area that isn’t well-publicized for the general public and trying to summarize and communicate it using more common lingo is a skill that is valuable to learn and practice. I don’t believe that this assignment improved my ability to critically evaluate my peers – nothing that was taught in the Wiki educational videos/instructions was novel or presented in a better way than in my past. Overall, I think the general public will benefit from the article, but I also know that not many Wiki readers will find the microfluidic devices page to read it.

The most beneficial part is that I have a greater understanding of how we can couple MS to microfluidic devices – however I didn’t gain much knowledge outside of this one specific segment. This is fine for me, as I’m interested in MS and how it is used, and I was thankfully able to pick a topic that is more suited to me. I think this assignment can be improved by doing the video-chat training for peer reviews and edits together as a class (whether it’s in class or out of class through web-chat). It is definitely useful to have been a part of that training, and I think a second session like that with a completely out-of-scope topic (like the Sims game, or any of those topics chosen) will enable students to understand the overall process better and remember not to focus on scientific details and using very complicated (albeit correct) language, but rather focus on communicating with the public in an understandable way.