eamag/protocols-with-steps huggingface dataset:
TITLE: BiomekFXp Robot Minipreps (RoboPreps)
AUTHORS: James Angstman

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RoboPreps are great for high-throughput cloning and subcloning, especially if you’re going to be doing Maxipreps afterward anyway. RoboPreps must be done in 96 well format as of now, though future generations may one day break through this technological barrier.</div></div>

[STEPS]
?. [Cell Prep]
Pick colonies into  into a 96-well assay block and grow at   overnight with shaking.
[LB cultures]
37 °C
?. [Cell Prep]
Pellet the cells by spinning at  for 5-15 minutes .
?. [Cell Prep]
Remove the media by quickly inverting the block over a waste container.
If intended for later use, you can freeze the block in   for several weeks or keep it at   for hours.
?. [Pre Qialyse2]
For a batch lysis, load the pelleted cultures onto the BiomekFXp robot using the qialyse2 program.
?. [Pre Qialyse2]
For the qialyse2 program, you need to assemble a two-component filter consisting of a low-profille 1.2 ml 96-well block and a 96-well filter block. They should be affixed to each other using tape as shown before loading on to the robot deck.
For simplicity, use inverted tip-box covers as reservoirs for the resuspension, lysis, and neutralization buffers.
Qiagen Buffers P1, P2, and P3 can be used as the resuspension, lysis, and neutralization buffers (to be put in the reservoirs on the robot deck), but similar home-made buffers should be fine.
?. [Qialyse2 Steps]
Resuspend cell pellet in  and shake.
[ P1 buffer]
?. [After Qialyse2]
Spin down the lysate through the filter block at  for at least  (longer is fine).
Make sure to balance with a blank filter. Another blank with improper dimensions may cause an imbalance error, even if the weight matches the filter.
?. [After Qialyse2]
Collect the block and remove the filter.
Take care not to jostle the low-profile 96-well block, since the flow-through can easily splash between wells.
?. [After Qialyse2]
Transfer the flow-through to an Axygen 96-well block and load it on to the robot using the RoboPrep program.
?. [RoboPrep Steps]
Mix filtered cell lysate with
[SPRI-Bead binding buffer]
?. [Qialyse2 Steps]
Add  and shake.
[P2]
?. [Qialyse2 Steps]
Pause for .
?. [Qialyse2 Steps]
Add  and shake for  (100 seconds).
[P3 buffer]
?. [Qialyse2 Steps]
Transfer contents to assembled filter apparatus.
?. [RoboPrep Steps]
Wash with 70% EtOH. (2/3)
?. [RoboPrep Steps]
Wash with 70% EtOH. (1/3)
?. [RoboPrep Steps]
Wash with 70% EtOH supplemented with 1% TritonX-114.
?. [RoboPrep Steps]
Remove Supernatant.
?. [RoboPrep Steps]
Place on magnet and allow separation.
?. [RoboPrep Steps]
Incubate  for .
0 Room temperature
?. [RoboPrep Steps]
Wash with 70% EtOH. (3/3)
?. [RoboPrep Steps]
Remove all ethanol and dry  beads for .
?. [RoboPrep Steps]
Resuspend beads in .
[elution buffer]
?. [RoboPrep Steps]
Remove from beads.
TITLE: Human Knee Cartilage Collection Protocol for Single Cell RNAseq
AUTHORS: molmer  , Martin  Lotz

[DESCRIPTION]
Cartilage from the medial femoral condyle is shaved for Single Cell RNAseq processing. The attached image indicates where the cartilage shavings are collected from.

[BEFORE_START]
Knee blocks are shipped on wet ice and received within 48 hours post-mortem from certified tissue banks. The average time from receiving the sample to harvesting cartilage from both knees is about 2 hours. Pictures are taken and macroscopic scoring of the cartilage is completed.

[STEPS]
1. Prepare harvesting area with sterile drapes, tools and gauze. All harvesting is completed within an aseptic environment.

2. Wipe down the knee blocks with 95% ethanol prior to opening the joint capsule.
3. Once the joint capsule is opened, the femur and tibia are disarticulated. Wet a sterile gauze with DPBS+1% Anti-Anti and use it to wipe down the cartilage and place it on the cartilage surface to keep moist.     

4. Full-thickness medial femoral condyle cartilage is shaved from the bone using a #21 scalpel; pieces typically measure maximum 10mmX25mm. 1.5g of shaved cartilage tissue is collected into a 50mL tube that is filled with 40mLs of DMEM + 1% Anti-Anti, then placed in wet ice until the cell isolation protocol for scRNAseq begins.      
 

SECTION: Tissue Collection for MERFISH
9. Procurement of Medial Femoral Cartilage With Subchondral Bone for MERFISH: Using an autoclaved 12” hacksaw with 24TPI blade, cut a 3-5mm slab from the middle region of the medial condyle. 
SECTION: Tissue Collection for MERFISH
0.9. Three pieces of tissue are placed in 12mLs, per region, of   for 24hrs on a 4oC rocker. 

SECTION: Tissue Collection for MERFISH
0.9. Pour off fixation solution and replace with    and store at 4oC until shipment on wet ice or MERFISH protocol begins.
TITLE: Study Population (Part 4 of &#34;Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain&#34;)
AUTHORS: Yiting Lin

[DESCRIPTION]
This is a Part 4 of "Effects of Online Exercise Intervention on Physical and Mental Conditions in Young Adults with Chronic Neck Pain".
The target participants were adults with self-reported non-specific neck pain for more than three months.

[GUIDELINES]
The target participants were adults with self-reported non-specific neck pain for more than three months. They were recruited through posters and social media in the campus of the Beijing Sport University.

[STEPS]
SECTION: Inclusion Criteria
1. Adults between 18 and 50 years of age with neck pain (from occiput to 7thcervical vertebra) for at least 3 months.
SECTION: Inclusion Criteria
2. A score of >= 4/50 on the NDI.
SECTION: Exclusion Criteria
3. Adults with a history of previous neck surgery, cervical radiculopathy, acute neck injury or fracture.
SECTION: Exclusion Criteria
4. Persons who had more than two hours of moderate intensity exercise or more than four hours of low intensity exercise in a week.
SECTION: Exclusion Criteria
5. Persons who had received any form of physiotherapy treatment in the last 6 months.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<div class="bibliography-item-copy-text content col-md-12" data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">Van Etten, J. (n.d.). Formulation of Modified Bold's Basal Medium (MBBM). Retrieved from http://ncv.unl.edu/vanettenlab/</div>
<div class="bibliography-item-copy-text content col-md-12" data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">
<div>
<div>
<div data-clipboard-target="copy-target-228943496" data-redirect-target="/items/228943496/copy">Contact Dr. Steven Wilhelm (wilhelm@utk.edu) or Samantha Coy (srose16@vols.utk.edu) for additional information regarding this protocol.</div>
</div>
</div>
<div> </div>
</div>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse  Huang

[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)

[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1&#x27; PCR head-primers
2. Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)
 
PCR mixture for head-primers for each reaction
 

 

SECTION: For 1&#x27; PCR head-primers
3. Mix the 1' PCR master mixture gently by pippeting. Quick spin the tube.
SECTION: For 1&#x27; PCR head-primers
4. Transfer  15 µL 1' PCR master mixutre in 8-strip PCR tubes.

SECTION: For 1&#x27; PCR head-primers
5. Add 0.6 µLDNA template in 8-strip PCR tubes, resulting in a 15.6 µL reaction mixture for 1' PCR.

Negative control contains only 15 µL master mixture but not DNA template

SECTION: For 1&#x27; PCR head-primers
6. Mix the reaction mixture gently by tapping the tubes. Quick spin the tubes.
SECTION: For 1&#x27; PCR head-primers
7. Carry out PCR using the following condition:  

1' PCR condition for head-primers
 

SECTION: For 1&#x27; PCR head-primers
7.1. 1' hear-primers used in Huang lab
 

SECTION: For 1&#x27; PCR head-primers
8. Carry out electrophoresis for inspection of DNA products

   

SECTION: For 1&#x27; PCR head-primers
9. Markdown wells and upload the pictures to the Lab Google drive

  

SECTION: For 2&#x27; PCR barcoded-head primers
10. Prepare 2' PCR master mixutre for barcoded-primers (prepare 1.2X of solutions for pipetting error if needed)
 
PCR mixture for barcoded-primers for each reaction (NO PRIMERs at this point!!)
 

 

SECTION: For 2&#x27; PCR barcoded-head primers
11. Mix the 2' PCR master mixture gently by pippeting. Quick spin the tube.
SECTION: For 2&#x27; PCR barcoded-head primers
12. Transfer 21.5 µL of the 2' PCR master mixture to PCR tubes.

SECTION: For 2&#x27; PCR barcoded-head primers
13. Add 2.5 µL pre-mixed barcoded-head primers (Forward + Reverse) to each PCR tube

SECTION: For 2&#x27; PCR barcoded-head primers
14. Add 1 µL of 1' PCR product as template, resulting in 25 µL reaction mixture for 2' PCR.

Negative control contains only 24 µL master mixture and premixed barcoded-head primers but not DNA template
SECTION: For 2&#x27; PCR barcoded-head primers
15. Mix gently by tapping the tubes. Quick spin the tubes.
SECTION: For 2&#x27; PCR barcoded-head primers
16. Carry out 2' PCR using the following condition:  

2' PCR condition for barcoded-head primers
 

SECTION: For 2&#x27; PCR barcoded-head primers
16.1. 2' barcoded-head primers used in Huang lab
 

SECTION: For 2&#x27; PCR barcoded-head primers
17. Carry out electrophoresis for inspection of DNA products

  

SECTION: For 2&#x27; PCR barcoded-head primers
18. Markdown wells and upload the pictures to the Lab Google drive
TITLE: PBMC isolation 
AUTHORS: Michael   Morgan

[DESCRIPTION]
Isolation of PBMCs from fresh whole human blood in Lithium Heparin blood tubes.

[STEPS]
SECTION: Lymphocyte separation
1. -       Start with everything at room temperature:
SECTION: Lymphocyte separation
2. -       Add 15 mL Ficoll-Paque Plus to each SepMate tube by pipetting directly into centre of plastic separator (try not to introduce a lot of air beneath the separator)
SECTION: Lymphocyte separation
3. -       Pool anti-coagulated blood tubes (3 x 9 mL Li Hep tubes) – should come to 27ml
SECTION: Lymphocyte separation
4. -       Dilute 1:1 in PBS + 2% FBS (now have ~54 mL diluted blood)
SECTION: Lymphocyte separation
5. -       Layer blood on top of Ficoll-Paque Plus by gently pipetting down the side of the SepMate tube (avoid pipetting directly above the small notches as this lets blood through to below the separator)
SECTION: Lymphocyte separation
6. -       Cap tightly and spin at 1200 x g, 10m, RT, accelerator and break on full 
SECTION: Washing
7. -       Cool PBS + 2% FBS in refrigerator and set centrifuge to cool (4C, though 10C should be sufficient)
SECTION: Washing
8. -       Pour interface off SepMate tube into new 50 mL falcon (2 SepMate tubes per falcon – if odd number of tubes, even out the volumes between falcons)
SECTION: Washing
9. -       Top cells up to 45 mL with chilled PBS + 2% FBS, mix well
SECTION: Washing
10. -       Centrifuge 900 x g, 10m in cooled centrifuge
SECTION: Washing
11. -       Meanwhile, centrifuge 5 mL serum tube in the same spin
SECTION: Washing
12. -       Discard supernatant and flick to dislodge pellet
SECTION: Washing
13. -       Resuspend cells in chilled PBS + 2% FBS and pool cells from each individual into 1 tube with 40 mL buffer
SECTION: Washing
14. -       Centrifuge 300 x g, 10m in cooled centrifuge
SECTION: Washing
15. -       Meanwhile, aliquot serum (avoid any red) and store aliquots in freezer (these do not contain any human cells)
SECTION: Washing
16. -       Discard supernatant and flick to dislodge pellet
SECTION: Washing
17. -       Resuspend cells in 25 mL chilled PBS + 2% FBS
SECTION: Washing
18. -       Take 10 uL aliquot and count on haemocytometer
SECTION: Washing
19. -       Centrifuge 300 x g, 10m in cooled centrifuge
SECTION: Washing
20. -       Discard supernatant and pipet off final drips, flick to dislodge pellet  
SECTION: Freezing
21. -       Resuspend cells in chilled 1-1.5 mL FBS + 10% DMSO (if more than 15 million cells, make multiple aliquots) – Freeze in ~5million cell aliquots
SECTION: Freezing
22. -       Rapidly move cryovials to Mr Frosty and put in -80C Freezer
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol describes methods for a mouse xenograft study designed to measure in vivo BiTE® efficacy against antigen-expressing human tumor cells. In a modified version, the protocol is used to measure BiTE®-mediated bystander killing. Mixtures of human EGFR-positive (unlabeled) and EGFR-negative (luciferase-labeled) cells are implanted in nude mice along with human T cells. Mice are treated daily with BiTE®, beginning one day after tumor implant for 20 days. Growth of EGFR-negative cells is measured by imaging (luminescence) and by calipers (tumor volume).</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This plasmid is designed to integrate within the small subunit ribosomal RNA gene region of <em>B. saltans</em>. It carries 1 kb of the <em>B. saltans</em> small subunit ribosomal RNA gene. To construct this cassette, we first sequenced the complete ribosomal operon of <em>B. saltans</em>, which has a total length of   ̴9 kb. The structure of the ribosomal operon of <em>B. saltans</em> is similar in the closely related kinetoplastida <em>Leishmania</em>, where the ribosomal RNA genes are arranged in head- to-tail repeats (Figure 4b and Yan et al., <em>Molecular and biochemical parasitology</em> 103, no. 2 (1999): 197-210). For the cassette construction, we used only a 1 kb region of the 18S ribosomal RNA gene, which is represented in the schematic as Homologous Recombination Region 1 (HR1) and Homologous Recombination Region 2 (HR2) each, of which is 500 bp . The GFP and Neo genes are located in the middle of the construct and their expression is controlled by the presence of the <em>B. saltans</em> tubulin intergenic region (Bs TUB IGR) at the 3’ and 5’ ends of each gene. As the transcription in <em>B. saltans</em> is polycistronic, the presence of the tubulin intergenic region is necessary for trans-splicing and polyadenylation.  </p>
<p> </p>
<p> </p>

[STEPS]
TITLE: Plasmid construction
AUTHORS: Chunmei  Chang

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">plasmid construction</div></div>

[STEPS]
?. Purify the DNA from gel using a Gel extraction kit (Bio Basic).
?. Linearize the backbone with restriction enzymes (NEB).
?. Amplify the insert gene fragment by PCR with primers including 21 nt of overlapping sequence with the target gene.
?. Run  PCR products and linearized backbone in an agarose gel to confirm the size.
?. Ligate the linearized backbone and the insert with the T4 ligase (NEB).
?. Treat linearized backbone with quick CIP (NEB).
?. Transform the ligation products into home made competent cells.
?. Perform colony PCR to screen for colons that with inserted gene.
?. Sequence to verify that the inserted gene is correct.
TITLE: Quantitative real-time PCR
AUTHORS: Tatiana Tkatch

[DESCRIPTION]
Quantitative real-time PCR protocol used for Day et al. 

[STEPS]
SECTION: gDNA digestion
1. -For each sample prepare 10ul gDNA digestion reaction mix according to SuperScript IV VILO Master Mix protocol (see pdf attached or substeps below). 
SECTION: gDNA digestion
1.1. Digest gDNA for 2 min min at 37 °C . 

SECTION: gDNA digestion
1.2. Place the tubes on ice. 
SECTION: gDNA digestion
1.3. Add SuperScript IV VILO Master Mix and Nuclease-free water. 
SECTION: gDNA digestion
1.4. Gently mix and incubate at 25 °C for 10 min . 

SECTION: gDNA digestion
1.5. Then at 50 °Cfor 10 min . 

SECTION: gDNA digestion
1.6. Inactivate enzyme by incubation at 85 °C for 5 min.

SECTION: Pre-amplification
2. Perform Pre-amplification according to TaqMan PreAmp Master Mix protocol (see pdf attached or substeps below). 
SECTION: Pre-amplification
2.1. -TaqMan PreAmp Master Mix 25ul, pooled assay mix (0.2X) 12.5ul, cDNA 2ul, nuclease free water, total 50ul. 
 
SECTION: Pre-amplification
2.2. Run reaction settings: 95 °C for 10 min then 95 °C for 15 s, 60 °Cfor 4 min (10 cycles), inactivate enzyme 99 °C for 10 min, hold at 4 °C

SECTION: Pre-amplification
3. -Dilute each reaction 10 times. 
SECTION: Amplification
4. -PCR reaction mix: Gene Expression Assay (20X) 1ul, Preamplified cDNA product 5ul, TaqMan Fast Advanced Master Mix (2X) 10ul, nuclease free water 4ul, total 20ul. 
SECTION: Amplification
5. -Run the reactions: Using incubation 50 °C for 2 min then enzyme activation-95 °C for 20 s, Denature 95 °C for 1 s, Anneal/Extend 60 °C for 20 s 40 cycles.

SECTION: Analysis
6. Experimental Ct values were normalized to hprt values using the following
formula: ΔCt = Ct (gene of interest) − Ct (hprt). The final expression levels were shown as ΔCt
values.
TITLE: No Title
AUTHORS: 

[BEFORE_START]
<p>Prepare primary stock solutions (in dH<sub>2</sub>O) of the following:</p>
<ul>
<li>NaNO<sub>3</sub>: 75.00 g/L</li>
<li>NaH<sub>2</sub>PO<sub>4</sub>·H<sub>2</sub>O: 5.00 g/L</li>
<li>Na<sub>2</sub>SiO<sub>3</sub>·9HO: 30.00 g/L (Note: this will only be used if phytoplankton require silicates)</li>
</ul>
<p>Filter sterilize through a 0.2 micron PES membrane and store frozen in 1 mL aliquots.</p>

[GUIDELINES]
<p>First, prepare primary stock solutions. Glassware should be acid-washed and rinsed well with dH<sub>2</sub>O before use. If unable to measure small quantities accurately, either scale up the recipe or prepare additional stock solutions of the individual compounds.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE:          ELISA for measurement of serum macrophage migration inhibitory factor (MIF). 
AUTHORS: Angel  Justiz-Vaillant, Belkis Ferrer-Cosme

[DESCRIPTION]
<div class = "text-blocks"></div>

[STEPS]
?. An anti-human MIF coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?. Add 50 µl of human serum or plasma. Human MIF present in the serum or plasma binds to antibodies adsorbed into the microwells.
?. The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.
?. Fifty (50) µl of biotin-conjugated anti-MIF antibody is added. The optimal dilution must be investigated.
?. The microplate is rewashed with PBS-Tween 20 buffer, pH 7.4.
?. One hundred µl of streptavidin-HRP conjugate is added and it binds to the biotin-conjugated anti-MIF antibody. The optimal dilution of this conjugate must be investigated.
?. The plate is washed following incubation to remove the unbound Streptavidin-HRP.
?. Add 100 µl of 3',3',5',5'- tetramethylbenzidine (TMB; Sigma-Aldrich) into each well.
?. Incubate the microwells in the dark for 20 min.
?. A colored product is formed in proportion to the quantity of MIF present in the sample or standard.
?. The reaction is terminated by addition of 100 µl 3M H2SO4  and the absorbance is measured at 450 nm.
?. A standard curve is made from 7 human MIF standard dilutions and the human MIF sample concentration is determined.
?. For better results place the microplate on a microplate shaker in every incubation.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Protocol to prep plasmid DNA from yeast cells. Preps both plasmid and genomic DNA. Protocol for prepping an entire plate; for selection of correctly assembled plasmids, the prepped DNA is transformed into <em>E. coli</em>, and transformation can be followed by colony PCR to select for the correct plasmids.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>e</p>
<p>qe</p>
<p> </p>
<p>wqeewq</p>
<p> </p>
<p>we</p>
<p>wq</p>
<p> </p>
<p> </p>
<p>e</p>
<p>wq</p>
<p>ew</p>
<p> </p>
<p>wqwq</p>
<p> </p>
<p>wqe</p>
<p>wqeqeqe</p>
<p>wq</p>
<p>e</p>
<p>wqe</p>
<p>wqe</p>
<p>q</p>
<p>ewqe</p>
<p>wqe</p>

[BEFORE_START]
<p>qwd</p>
<p>qdw</p>
<p>qd</p>
<p>q</p>
<p>d</p>
<p>q</p>

[GUIDELINES]
<p>iuwqdhwqkqd</p>
<p>wqd</p>
<p>wq</p>
<p>d</p>
<p>wqdqd</p>
<p> </p>

[STEPS]
?. 
?. 
?. 
?. 
?.
TITLE: Mass Spectrometry analysis and Molecular MS/MS network
AUTHORS: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones

[STEPS]
?. [UHPLC ]
Resuspend the dry extract in 1 mL of methanol (HPLC grade) and dilute 100 µL in 900 µL of methanol (HPLC grade).
?. [UHPLC ]
Filter the final solution using a syringe-filter into vials
?. [UHPLC ]
Perform Ultra-high pressure liquid chromatography-mass spectrometry (UHPLC-MS) analyses in a Thermo Scientific QExactive® Hybrid Quadrupole-Orbitrap Mass Spectrometer. Stationary phase: Thermo Scientific Accucore C-18 2.6 µm (2.1 mm x 100 mm)
?. [UHPLC ]
Set the following parameters in the spectrometer: positive mode, capillary voltage at +3.5 kV; capillary temperature at 250 °C; S-lens of 50 V and m/z range of 133.40-2000.00
?. [UHPLC ]
Perform tandem mass spectrometry (MS/MS) using normalized collision energy (NCE) of 30 eV and 5 precursors per cycle
?. [UHPLC ]
Set the following conditions in the column mobile phase: 0.1% formic acid (A) and acetonitrile (B). Eluent profile (A: B) 0-10 min, gradient from 95:5 up to 2:98; held for 5 min; 15-16.2 min gradient up to 95:5; held for 8.8 min. Flow rate: 0.2 mL min-1
?. [UHPLC ]
Inject 3 µL of each sample , then conduct operation and spectra analyses using Xcalibur software (version 3.0.63) developed by Thermo Fisher Scientific
?. [GNPS Analysis]
Create a molecular network for Streptomyces sp.  using the online workflow at GNPS (https://gnps.ucsd.edu/) for molecular networking analysis.
?. [GNPS Analysis]
Filter the data by removing all MS/MS peaks within ± 17 Da of the precursor m/z
?. [GNPS Analysis]
Window filter the MS/MS spectra by choosing only the top 6 peaks in the ± 50 Da window throughout the spectrum
?. [GNPS Analysis]
Cluster the data with MS-Cluster with a parent mass tolerance of 0.02 Da and an MS/MS fragment ion tolerance of 0.02 Da to create consensus spectra
?. [GNPS Analysis]
Create a network where edges were filtered to have a cosine score above 0.5 and more than 5 matched peaks
?. [GNPS Analysis]
Keep further edges between two nodes in the network only if each of the nodes appeared in each other's respective top 10 most similar nodes
?. [GNPS Analysis]
Search the spectra comparining with those in the network GNPS’ spectral libraries
?. [GNPS Analysis]
Filter the library spectra  in the same manner as the input data.
?. [GNPS Analysis]
Keep all matches of network and library spectra that have a score above 0.5 and at least 5 matched peaks