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Update README.md

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......@@ -6,13 +6,20 @@ Specter is an algorithm for the targeted analysis of data-independent acquisitio
2. A spectral library in blib format.
3. A mass accuracy parameter, specified in parts-per-million.
The 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 output file looks like this:
The 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:
```
Scan index Retention time (s) Precursor sequence Precursor charge Total ion intensity
10032 268.3763 ETLDASLPSDYLK 2 1,569,034
10032 268.3763 NPAADAGSNNASKK 2 3,689,112,580
10032 268.3763 NPAADAGSNNASKK 2 3,112,580
10033 268.4273 IVLVDDSIVR 2 722,175
```
with the identifications and quantifications based on these scan-by-scan total ion intensities reported separately:
```
Precursor sequence Precursor charge Quant
ETLDASLPSDYLK 2 148,110,338
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.
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