X!TandemPipeline Crack Full Version Free Download (2022)

The Open Source X!TandemPipeline is a small tool that can help you filter and group your peptide / protein identifications from MS / MS mass spectra.
X!Tandem Pipeline is a Java-based software that can perform database searching and matching on a list of MS / MS runs in one shot, using a list of easily user selected paramaters and databases.
Moreover, the app also filters data according to statistical values at peptide and protein levels.







X!TandemPipeline 3.1.4 Crack+ Activation [Mac/Win]

* Analyzes a list of mass spectra and returns the peptides with the best scores and the corresponding parameters (e.g. peptide mass, peptide score, peptide delta mass, precursor charge, etc.).
* Converts the list of peptides to a list of proteins and returns the list of proteins with their identification parameters.
* Converts the list of proteins to a list of peptides and returns the list of peptides with their best score.
* Based on some user selected parameters, the results are filtered at peptide and protein levels:
o Peptide score > 50: Lists the best peptides (list of peptides)
o Peptide delta mass > 0.4: Lists the peptides with the highest delta mass
o Protein score > 100: Lists the proteins
o Protein delta mass > 0.4: Lists the proteins with the highest delta mass
* Note: Peptides that are hits by less than three proteins are not listed.
* Keywords: Peptide/protein identification, peptide, protein, ID, list, analysis, database, search, search and identification, filtering

A cluster-based image analyzer software to assist and facilitate the selection of the most representative areas of a group of images for pattern-matching in mass spectrometry.
Features include:
– Location and extraction of clusters, from an initial set of regions of interest
– Extraction of the main clusters of the image for the analysis of the spectral quality
– Filtering of the main clusters by removing noisy clusters based on the distribution of the spectra for the different clusters
– Filtering of the main clusters by removing those with a noise level higher than a predefined threshold
– Topology based extraction of local patterns for the pattern matching of the main clusters
– Creation of pseudo patterns for the extraction of the best match between the main clusters and the pseudo patterns (local neighborhood extraction)
– Creation of pseudo patterns with a tolerance value (the distance between the main cluster and the pseudo patterns to be matched)
– Pattern matching of the pseudo patterns with the main clusters
– Local optimization of the best match between the main clusters and the pseudo patterns
– For each local optimization, the pseudo patterns to be matched are filtered by removing those with a similarity lower than a predefined threshold
– The resulting pattern is matched to the main clusters (global optimization)
– Matching of the best pseudo pattern for each main cluster
– Creation of a

X!TandemPipeline 3.1.4 Crack Activation [Win/Mac]

Filter MS / MS runs according to a defined MS / MS pattern.
You can either use all the MS / MS runs at once or you can pick them individually.
Allows you to filter by MS / MS identification name, search engine, retention time, scan number, spectral count, p.p.m. error, peptide count, charge and Xcorr p.p.m.
Allows you to filter by score, ppm, chromatogram and mass accuracy.
Allows you to group MS / MS runs according to statistical values ( p.p.m. error, peptide count and spectral count).
This tool uses our own scoring algorithm for peptide and protein identifications.
KEYMACRO Tested with:
MS / MS runs which were searchable using X!Tandem against NCBInr, UniProtKB, TrEMBL, Ensembl, RefSeq, RefSeqProtein, PeptideAtlas, MSDB, SwissProt, EBI, UniProtKB, BatchDB, IPI and RefSeq, as well as a list of custom peptide mass lists.
All other databases are not supported.
It uses an own unique scoring algorithm to match peptide sequences against databases.
Moreover, it uses other statistical values ( p.p.m. error, peptide count and spectral count) to group runs which are similar to each other.
Download and Use:
Download the software and run the executable. A usage guide is included.
More Information:
Visit our site at
More help:
X!Tandem Pipeline User Guide
X!Tandem Pipeline User Guide
Contact us:
We appreciate comments and questions at:
Boudewijn Rob
Ph. D
Institute for Genomic Research
University of California
Santa Cruz, CA 95064

A x!tandem pipeline is an easy to use Java-based software which you can use to search your MS / MS runs for identification of peptides against a list of custom peptide mass lists.
X!Tandem Pipeline can perform database searching and matching on a list of MS / MS runs in one shot, using a list of easily user selected paramaters and databases.

X!TandemPipeline 3.1.4

Program’s Scope:
– Identify MS/MS peptide and proteins
– Visualize MS/MS peptides and proteins
– Filter MS/MS peptides and proteins by
– Modify parameters
– Filter data by statistical values (Likelihood and confidence)
– Group MS/MS runs by parameters
– Compare MS/MS runs with each other (from different samples)
– Compare MS/MS runs with a running peak list
– Define a cut-off point for a parameter, any peptide with value below it will be removed
– Import excel file for adding new data
Description of program features:
– A reference MS spectrum can be copied and pasted
– Add MS / MS runs one by one by clicking on “Add run”
– Import mass list by “File” and “Import mass list” from “Help”
– Group MS / MS runs by parameter
– Filter MS / MS runs by statistical parameters
– Identify peptides and proteins
– Link MS / MS runs (and peak lists) to each other
– Import MS / MS results from PEAKS DB
– Export MS / MS results to excel
– Export PEAKS DB records for MS / MS runs
– Setup tools for filtering and modifying parameters
– Import peak list from FASTA (Lines, FASTA) and Peptide Quant (min to max)
– Copy imported peak list to another list
– Add from list (copy MS / MS run), from list (copy peak list)
– Add/delete from list, delete from list
– Sort list by column
– Sort list
– Preview
– Import/Export mass list
– Import/Export/Save FASTA from/to mass list
– Export selected data to pdf, word, excel
– Sort by column
– Export selected data to excel
– Export selected data to pdf, word
– Export selected data to csv
– Export selected data to TSV
– Export selected data to libriX format
– Export selected data to apk format
– Import run numbers from clipboard
– Export selected data to CSV
– Export selected data to Excel (.xls)
– Export selected data to XLS
– Export selected data to TXT
– Export selected data to CSV
– Export selected data to CSV
– Export selected data to CSV
– Export selected data to CSV
– Export selected data to CSV
– Export selected data to

What’s New In X!TandemPipeline?

X!Tandem Pipeline is an easy-to-use software designed to help you filter your data using a list of user selected parameters and then export data to X!Tandem, as well as to any desired file.
X!Tandem Pipeline is useful for users, who wants to filter database searching results or who wants to group MS / MS runs into desired identifications.

The article and the tutorial says I can easily install x!TandemPipeline as follows,

Download the x!Tandem Pipeline package
$ wget
$ unzip xtandemPipeline-
$ cd xtandemPipeline-
$ java -jar./xtandemPipeline-

So I did the same. Unfortunately, the app does not work for me. I follow the steps and was only able to find and extract the contents of the zip file. If I run the app by double clicking on the extracted zip file, then I get the following error:
java.lang.NoClassDefFoundError: org/netbeans/junit/NbTest

I am using Netbeans 6.9.1, JDK 1.7, X!Tandem 2.3.3, OS: Win7.


It seems to me you did not unzip the app correctly, so that the package “xtandemPipeline-” is not the same directory, where the app is run from. So the error comes up, because the class-loader cannot find this package.
Try the following:
cd xtandemPipeline-
java -jar xtandemPipeline-

If the app runs without errors, you can unzip the app (e.g. with 7-zip) and run the same command.

1. Field of the Invention
The present invention relates to a light source control apparatus which is used for controlling light output of an image forming apparatus such as a laser beam printer or a copying machine.
2. Description of the Related Art
Conventionally, an image forming apparatus such as a laser beam printer (LBP) which is used in

System Requirements:

Processor: 1.7 GHz Dual-Core or faster (but Quad-Core will do)
Video Card: OpenGL 2.0 compatible
DirectX 10 compatible
Hard Drive: 13GB free space
Processor: 1.7 GHz Dual-Core or faster (but Quad-Core will do)RAM: 1GBVideo Card: OpenGL 2.0 compatibleDirectX 10 compatibleHard Drive: 13GB free space
NOTE: Please check our DISCLAIMER to make sure you


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