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# Specter
Specter is an algorithm for the targeted analysis of data-independent acquisition mass spectrometry proteomics experiments. It can analyze data from any instrument type and window acquisition scheme. The required user inputs are a DIA data file in centroided mzML format, a spectral library in blib format, and a mass accuracy parameter, specified in parts-per-million.
Specter is an algorithm for the targeted analysis of data-independent acquisition mass spectrometry proteomics experiments, which is described in detail in our paper in [*Nature Methods*](http://dx.doi.org/10.1038/nmeth.4643). It can analyze data from any instrument type and window acquisition scheme. The required user inputs are a DIA data file in centroided mzML format, a spectral library in blib format, and a mass accuracy parameter, specified in parts-per-million.
The raw output of Specter is a .csv file describing the total ion intensities (= sum of fragment ion intensities) of each precursor in the spectral library at each retention time point of the experiment. A snippet of the typical raw output file looks like this:
```
......@@ -16,6 +16,6 @@ Precursor sequence Precursor charge Quant
NPAADAGSNNASKK 2 32,234,856
IVLVDDSIVR 2 11,768,772
```
Specter currently requires the cluster-computing framework Apache Spark; a cloud framework and accompanying website will appear in the future. See ```SpecterUserGuide.pdf``` for detailed instructions on how to set up and use Specter. To learn more about the algorithm, you can read about Specter in [*Nature Methods*](http://dx.doi.org/10.1038/nmeth.4643).
Specter currently requires the cluster-computing framework Apache Spark; a cloud framework and accompanying website will appear in the future. See ```SpecterUserGuide.pdf``` for detailed instructions on how to set up and use Specter.
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