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. 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:
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 3,112,580
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 can be run either on a standard desktop/laptop or, for much faster results, on a computing cluster using the distributed computing framework Apache Spark; a cloud framework and accompanying website will appear in the future. See SpecterStandaloneUserGuide.pdf for instructions on how to set up and use Specter without a computing cluster, and SpecterSparkUserGuide.pdf for instructions on how to set up and use Specter on a computing cluster with Spark.