Specter

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.