Supporting information

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Annice Fleming
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1 Supporting information 1S. DECOMP output for the peptide amino-acid decomposition test with monoisotopic mass = /- 0.2 # imsdecomp 1.3 # Copyright 2007,2008 Informatics for Mass Spectrometry group # at Bielefeld University # # # # precision: # allowed error: 0.2 Da # mass mode: mono # modifiers: none # fixed modifications: none # variable modifications: none # alphabet (character, mass, integer mass): # Wat # Gly # Ala # Ser # Pro # Val # Thr # Cys # Leu # Ile # Asn # Asp # Gln # Lys # Glu # Met # His # Phe # Arg # Tyr # Trp # constraints (character, min, max): # Wat 1 1 # Gly none 20 # Ala none 20 # Ser none 20 # Pro none 20 # Val none 20 # Thr none 20 # Cys none 20 # Leu none 20 # Ile none 20 # Asn none 20 # Asp none 20 # Gln none 20 # Lys none 20 # Glu none 20 # Met none 20 # His none 20 # Phe none 20 # Arg none 20 # Tyr none 20 # Trp none 20 # chemical plausibility check: off # # Shown in parentheses after each decomposition: # - actual mass # - deviation from actual mass 1

2 # # mass 1000 has 5 decompositions: Wat1 Gly1 Thr1 Cys8 ( ; ) Wat1 Ala1 Ser1 Cys8 ( ; ) Wat1 Ser3 Cys7 ( ; ) Wat1 Gly2 Cys7 Phe1 ( ; ) Wat1 Cys7 Asn1 Phe1 ( ; ) # done 2

3 2S. R Example: Retrieving information for a molecular formula library(rjson) mf="c10h20cl2" query <- paste(" resjson <- fromjson(paste(readlines(query), collapse="")) resjson$em resjson$mw 3

4 R Example: Find possible molecular formula for a specific monoisotopic mass library(rjson) target=300 mfrange="c0-100h0-100n0-10o0-10" query <- paste(" "&mfrange=", mfrange,"&action=em2mf",sep="") resjson <- fromjson(paste(readlines(query), collapse="")) for (mf.index in 1:length(resJSON$results)) { results <- data.frame( "mf"=resjson$results[[mf.index]]$mf, "em"=resjson$results[[mf.index]]$em, "error"=resjson$results[[mf.index]]$error ) ifelse(!exists('report'),report <- results, report <- rbind(report,results)) } report[] 4

5 Javascript Example: Retrieving information for a molecular formula <html> <head> <script type="text/javascript" src=" </script> </head> <body> <script language="javascript"> var parameters={ mf: "C10H20Cl2", resolution: 0.001, isotopomers: "xy, jcamp" }; $.getjson(' function(result) { parameters, document.write(json.stringify(result)); }); </script> </body> </html> 5

6 Javascript Example: Find possible molecular formula for a specific monoisotopic mass <html> <head> <script type="text/javascript" src=" </script> </head> <body> <script language="javascript"> var parameters={ monoisotopicmass: 300, mfrange: "C0-100H0-100O0-10N0-10", action: "em2mf" }; $.getjson(' function(result) { parameters, document.write(json.stringify(result)); }); </script> </body> </html> 6

7 Python 2.6/2.7 example: Retrieving information for a molecular formula #!/usr/bin/python # Requires Python 2.6 or higher # for 2.5 and lower, install and use simplejson instead of json import urllib, urllib2 import json ccurl = ' # Define a molecular formula string mf = 'C10H20Cl2' # Define the parameters and send them to Chemcalc params = {'mf': mf,'isotopomers':'jcamp,xy'} response = urllib2.urlopen(ccurl, urllib.urlencode(params)) # Read the output and convert it from JSON into a Python dictionary jsondata = response.read() data = json.loads(jsondata) 7

8 Python 2.6/2.7 example: Find possible molecular formula for a specific monoisotopic mass #!/usr/bin/python import urllib, urllib2 import json chemcalcurl = ' # Define a molecular formula string mf = 'C0-100H0-100N0-10O0-10' # target mass mass = 300 # Define the parameters and send them to Chemcalc # other options (mass tolerance, unsaturation, etc. params = {'mf': mf,'monoisotopicmass': mass, 'action': 'em2mf'} response = urllib2.urlopen(chemcalcurl, urllib.urlencode(params)) # Read the output and convert it from JSON into a Python dictionary jsondata = response.read() data = json.loads(jsondata) print data 8

9 Python 3 example: Retrieving information for a molecular formula (Python 3 version) #!/usr/bin/python # Requires Python 3.x import urllib.request, urllib.parse import json ccurl = ' # Define a molecular formula string mf = 'C100H100' # Define the parameters and send them to Chemcalc params = {'mf': mf,'isotopomers':'jcamp,xy'} response = urllib.request.urlopen(ccurl, urllib.parse.urlencode(params).encode('utf-8')) # Read the output and convert it from JSON into a Python dictionary jsondata = response.read() data = json.loads(jsondata.decode('utf-8')) 9

10 3S. Isotopic distribution of C100H100 calculated and displayed using the ChemCalc web application 10

Giri Narasimhan & Kip Irvine

COP 4516: Competitive Programming and Problem Solving! Giri Narasimhan & Kip Irvine Phone: x3748 & x1528 {giri,irvinek}@cs.fiu.edu Problems to think about!! What is the least number of comparisons you