What is peptide mass tolerance?

Peptide mass tolerance indicates the fit of theoretical peptide mass with the experimental measurements, and choice of this parameter sufficiently influences the protein identification. The role of peptide mass tolerance was estimated by counting the number of identified proteins for the reference set of mass-spectra.

What is mass tolerance in mass spectrometry?

The fragment mass tolerance is based on the mass accuracy of the analyzer used to measure the fragment ions in the MS/MS scans. This parameter can be referred to as MS/MS tolerance, fragment mass error, or product ion tolerance.

What is ppm in mass spectrometry?

Mass Tolerance / Error. ppm (parts per million) Formula: Δ Theoretical value.

What is Mr value of protein?

Mr= average mass of the protein.

What is a base peak chromatogram?

Definition: A plot of ion current vs. retention time obtained from a chromatography experiment with mass detection. The base peak intensity chromatogram represents the intensity of the most intense peak at any one time.

How do you calculate ppm from mass?

Parts Per Million (ppm) Concentration Calculations

1. Write an equation representing the ppm concentration: ppm = mass solute (mg) ÷ volume solution (L)
2. Extract the data from the question: mass solute (NaCl) = 0.0045 g.
3. Convert the mass in grams to a mass in milligrams: mass NaCl = 0.0045 g = 0.0045 g × 1000 mg/g = 4.5 mg.

What is high resolution mass spectrometry?

High-resolution mass spectrometry (HRMS) uses mass spectrometers capable of high resolution, as well as high mass accuracy measurements. These instruments can be used to distinguish between compounds with the same nominal mass, determine elemental compositions, and identify unknowns.

How do you calculate protein mass?

How to calculate protein molecular weight from the sequence? It’s just as simple as it seems – add together all the molecular weights of the amino acids present in your sequence. You also need to subtract the molecular weight of water for every bond created.

How is protein size determined?

An important part of characterizing any protein molecule is to determine its size and shape. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte.

What is the base peak in a mass spectrum?

The most intensive peak in a spectrum is called the “Base Peak”, whose intensity is taken as 100 percent. This ion exists most abundantly in the ion source and represents the most stable ion, which is useful for identifying the compound.

How does MS / MS fragment ion tolerance affect peptide?

False Positive Rate Decreases With Improving Precursor Mass Accuracy Fragment mass tolerance = 40 ppm 0 200 400 600 800 1000 1200 4 4.5 5 5.5 6 6.5 5 ppm 10 ppm 20 ppm 50 ppm 100 ppm 200 ppm 500 ppm 1000 ppm Spectrum Mill Reverse Database Search Score # of false positive matches 7 Accurate Mass MS/MS Agilent eseminar Page 16 February 28, 2008

Can a peptidemass return the mass of a peptide?

If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants. Instructionsare available.

How can peptidemass be used to check for post translational modifications?

The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants. Instructions are available.

What is the mass tolerance of a fragment?

Fragment mass tolerance = 40 ppm 0 200 400 600 800 1000 1200 4 4.5 5 5.5 6 6.5 5 ppm 10 ppm 20 ppm 50 ppm 100 ppm 200 ppm 500 ppm 1000 ppm Spectrum Mill Reverse Database Search Score # of false positive matches 7 Accurate Mass MS/MS Agilent eseminar Page 16 February 28, 2008