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How does x tandem work?

X! Tandem is an open-source search engine that matches tandem mass spectra with peptide sequences. LabKey Server uses X! Tandem to search an mzXML file against a FASTA database and displays the results in the MS2 viewer for analysis.

What is x tandem?

Tandem is an open source software that can match tandem mass spectra (usually the experiment) with peptide sequences from a database. This process allows identification of proteins in one or more samples.

Is MaxQuant free?

MaxQuant is freely available and can be downloaded from this site. The download includes the search engine andromeda, which is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results.

What does MaxQuant do?

MaxQuant is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets. It supports all main labeling techniques like SILAC, Di-methyl, TMT and iTRAQ as well as label-free quantification.

How long does MaxQuant take to run?

Hi, it depends on your workstation that you are using to do your analysis. It varies for me for a day or two on the basis of computer I have used. My laptop (8 GB RAM) takes around 2 days to give back the output of 7 such raw files, while the another PC at lab (16 GB) takes less than day to process it.

What is a razor peptide?

A razor peptide is a peptide that has been assigned to the Protein Group with the largest number of total peptide identified (IDs). If the razor peptide is also unique it only matches to this single Protein Group. If it is not unique, it will only be a razor peptide for the group with the largest number of peptide IDs.

How does MaxQuant work?

MaxQuant is a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets. High mass accuracy is achieved by weighted averaging and through mass recalibration by subtracting the determined systematic mass error from the measured mass of each MS isotope pattern.

What is PSM in mass spec?

A peptide-spectrum match (PSM) scoring function assigns a numerical value to a peptide-spectrum pair (P,S) expressing the likelihood that the fragmentation of a peptide with sequence P is recorded in the experimental mass spectrum S.

What is iBAQ?

iBAQ is the total intensities divided by the identified peptides for one protein. It is hard to do absolute quantification of proteins. iBAQ works if all peptides were ionized and detected at the same efficency. LFQ is very similar to the “protein intensities” used by iBAQ.

Why are proteins studied collectively?

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins.

What is PEP in proteomics?

This score is calculated on the basis of the posterior error probability (PEP) values of the (peptide spectrum matches) PSMs. The PEP is the probability that the observed PSM is incorrect. Coverage. The percentage of the protein that is covered by the identified peptides.

What is a pep score?

The PEP score is the probability that a peptide (PSM-peptide spectral match) is incorrect. The Sequest score is a calculation that scores and sums each peptide for a given protein. Basically, the higher the score the more confidence you can have that the given peptide identification is correct.

How does X ! Tandem help in protein identification?

X!Tandemis an open source software that can match tandem mass spectra (usually the experiment) with peptide sequences from a database. This process allows identification of proteins in one or more samples. The X!Tandem search engine calculates a statistical confidence (expectation value) for all of the individual spectrum-to-sequence assignments.

What can X Tandem spectrum modeler be used for?

X! TANDEM Spectrum Modeler X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.

How does the X Tandem search engine work?

The X!Tandem search engine calculates a statistical confidence (expectation value) for all of the individual spectrum-to-sequence assignments. Some spectra might map to more than one protein, in this case X!Tandem will pick the best match with the highest confidence score (see Figure 7). The output is a lists all of the high confidence assignments.

What kind of API does X Tandem use?

This software has a very simple, sophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. This version of X! Tandem is a full release and it includes extensive source level documentation.