Documents & Support

1-15 of 854 Results

Brochure: Pierce Products for Mass Spectrometry Sample Preparation Product Literature

Thermo Scientific Pierce Products for Mass Spectrometry Sample Preparation Handbook Product Literature

Can I use protease inhibitors for mass spectrometry (MS) sample prep? Product FAQ

Answer

We don't recommend adding protease inhibitors as they can affect trypsin and trypsin/Lys-C activity. If protease inhibitors are present in the protein sample or cells, they should be removed by dialysis, diafiltration, desalting, or protein precipitation prior to enzymatic digestion. For phosphopeptide enrichment workflows, we recommend adding phosphatase inhibitors to the lysis solution prior to cell lysis.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18854

Was this answer helpful?

Yes No

Thank you for your response

How can I improve the digestion efficiency of my protein mass spec sample? Product FAQ

Answer

Digestion efficiency can be improved by adding more enzyme, incubating for longer digestion times, and ensuring the correct pH for digestion. Avoiding protease inhibitors and strong denaturants is recommended for maximum digestion efficiency for most proteases.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18859

Was this answer helpful?

Yes No

Thank you for your response

How can I determine peptide yield in my mass spectrometry samples after sample clean-up? Product FAQ

Answer

Peptide yield can be measured using the Pierce Quantitative Colorimetric Peptide Assay (Cat. No. 23275) or the Pierce Quantitative Fluorometric Peptide Assay (Cat. No. 23290). The choice of peptide assay depends on the sample type and composition of the sample buffer. The fluorometric peptide assay cannot be used to measure peptides with chemically modified amines such as acetylated peptides or TMT-labeled protein digests. The colorimetric assay can measure a wider range of samples but is not as sensitive as the fluorometric assay, requiring more sample for accurate detection. Finally, both assays are susceptible to interfering compounds in the sample or buffer which should be avoided or removed for best results.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18855

Was this answer helpful?

Yes No

Thank you for your response

What type of negative selection kits do you offer for affinity purification of proteins? Product FAQ

Answer

1. For purification of antibodies, we offer Melon Gel, which binds other proteins from serum, ascites, or culture supernatant, allowing the IgG to be collected in the flow-through. As low pH is typically used to elute IgG from Protein A, G, A/G or L, the use of Melon Gel can spare the IgG from exposure to such harsh conditions, which can be particularly important for monoclonal antibodies.

2. For clean-up of samples prior to mass spectrometry analysis, we offer:
- Kits that remove highly expressed serum proteins such as the top 2 most abundant proteins (IgG and albumin) or top 12 abundant proteins. More details here (http://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-mass-spectrometry-analysis/sample-prep-mass-spectrometry.html%2523relatedprod) .

- Pierce Detergent Removal Spin Columns and Plates, and HiPPR Detergent Removal Spin Columns and Plates for removal of detergent

3. Finally, our endotoxin removal resins (Pierce High Capacity Endotoxin Removal (Cat# 88270) and Detoxi-Gel Endotoxin Removing Gel (Cat# 20339) allow clean-up of samples, which can be particularly important for proteins expressed in certain bacterial cell lines.

Find additional tips, troubleshooting help, and resources within our Protein Purification and Isolation Support Center.

Answer Id: E12903

Was this answer helpful?

Yes No

Thank you for your response

What is the best enzyme to use for protein digestion for mass spectrometry samples? Product FAQ

Answer

Trypsin (Cat. Nos. 90057, 90058) or Trypsin/LysC mix (Cat. Nos. A40007, A40009, A41007) are most commonly used for proteomic applications in order to ensure reproducibility and complete digestion. Other commonly used enzymes for purified protein characterization and unique applications include Chymotrypsin Protease, MS Grade (Cat. No. 90056), Immobilized Pepsin (Cat. No. 20343), LysN Protease, MS Grade (Cat. No. 90300), Asp-N Protease, MS Grade (Cat. No. 90053), and Glu-C Protease, MS Grade (Cat. No. 90054).

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18869

Was this answer helpful?

Yes No

Thank you for your response

I want to minimize the number of missed cleaved peptides for maximal digestion of my protein mass spec sample. Which enzyme should I choose: trypsin only, LysC followed by trypsin or a trypsin-LysC mixture? Product FAQ

Answer

Trypsin cleaves at both lysine and arginine but has difficulty in fully digesting peptide sequences if these amino acids are followed by a proline. LysC only cleaves at lysine and can cleave sequences with lysines followed by prolines. Therefore, LysC is often used in conjunction with trypsin to decrease the number of missed cleavages. Sequential digestion with LysC followed by trypsin is the best method to minimize the number of missed cleaved peptides as each enzyme can be used under their optimal conditions. However, trypsin-LysC mixtures can also be used to concurrently digest samples with shorter incubation times (<3 hrs).

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18860

Was this answer helpful?

Yes No

Thank you for your response

After using the Magnetic RNA-Protein Pull-Down Kit, I would like to analyze my elution fraction by mass spectrometry (MS). How can I do this? Product FAQ

Answer

The elution fraction is compatible with preparation of peptides. Samples may be processed using the Mass Spec Sample Prep Kit for Cultured Cells (Cat. No. 89840). Alternatively, the elution fraction may be separated by denaturing PAGE. Bands of interest can be excised, and digested using the In-Gel Tryptic Digestion Kit (Cat. No. 89871).

Answer Id: E15525

Was this answer helpful?

Yes No

Thank you for your response

I'm struggling with mass spectrometry sample clean-up and feel that I'm losing peptides. Can you help me verify? Product FAQ

Answer

We recommend using the Pierce HeLa Protein Digest Standard (Cat. Nos. 88328, 88329) to test your sample clean-up method. Use it directly and also as a control, co-treated with the sample to check for any loss of peptides.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18799

Was this answer helpful?

Yes No

Thank you for your response

Do you offer a mass spec sample prep method for low abundant proteins in samples? Product FAQ

Answer

High Select Top14 Abundant Protein Depletion Mini Spin columns (Cat. Nos. A36369, A36370) can be used to deplete top 14 abundant plasma/serum proteins. The depletion of highly abundant proteins from the sample enables the detection and identification of low abundant proteins. The depleted samples can be processed with EasyPep MS sample prep kit to generate digested plasma/serum samples. The clean digested samples can be processed by nanoLC-MS/MS analysis for discovery experiments or nanoLC-PRM/MS analysis for targeted experiments.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18862

Was this answer helpful?

Yes No

Thank you for your response

How do I proceed to downstream mass spec sample preparation after abundant plasma protein depletion? Product FAQ

Answer

After the depletion, samples are significantly diluted in buffer. Depleted samples should be concentrated by speed vac drying, solvent precipitation, or diafiltration. Samples dried using a speedvac are directly compatible with the EasyPep kit chemistry after resuspension using the Lysis Solution.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18884

Was this answer helpful?

Yes No

Thank you for your response

Should I use protein A/G or streptavidin beads for affinity purification of my mass spec samples? Product FAQ

Answer

Both methods provide robust results for immunoprecipitation. Biotin-tagged antibodies with streptavidin beads provide lower background but require more upfront sample prep. Protein A/G beads are robust and straightforward in use but result in higher background than streptavidin beads.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18856

Was this answer helpful?

Yes No

Thank you for your response

I want to fractionate a complex mass spectrometry sample, but my sample is different from the one described in the manual for the Pierce High pH Reversed-Phase Peptide Fractionation Kit. Should I use a customized fractionation gradient? Product FAQ

Answer

Recommended gradients are available for typtic protein digest samples with or without TMT labeling. Use of other chemical labels, performing selective peptide enrichment, or using a different digestion enzyme other than trypsin may affect the elution profile of the peptides during fractionation. For the best sample peptide coverage, an ideal elution profile would result in relatively equal amounts of peptides in each fraction.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E18874

Was this answer helpful?

Yes No

Thank you for your response

What is the digestion efficiency when using the EasyPep Mini MS Sample Prep Kit? Product FAQ

Answer

The digestion efficiency with the EasyPep Mini MS Sample Prep Kit is >90% with a high efficiency in alkylation/reduction.

Find additional tips, troubleshooting help, and resources within our Mass Spectrometry Support Center.

Answer Id: E17293

Was this answer helpful?

Yes No

Thank you for your response

Results per page