Proteolysis API

This interface provides a means to calculate the insilico predicted proteolytic peptides from known proteins.

Why have a peptide homology engine?

This creates a nice abstraction to the complicated method of calculating insilico predicted proteolytic peptides. In addition, it provides a method for error checking the core foundation to the TANDEM IO API.

USAGE

URL

./Proteolysis/?key=<str_access_key>&p=<str_protein_name>

Methods

GET or POST
Both methods are compatible with either http or https. It is recommended to use https as this encrypts your data and access token.

Request Parameters :: Summary
parameter type usage default accepted note
p STRING required * *
ul INTEGER 53 6:72
ll INTEGER 6 0:ul-1
um INTEGER 6000 600-10000
lm INTEGER 400 0:um-1
mc INTEGER 3 0,1,2,3
rx STRING .*?[KR\#] any regex # signifies the C-term
Request Parameters :: Detail
Responses:
code type content
200 success see example 1
400 bad request { error : "precursor mass (pm) parameter undefined" }
401 unauthorized { error : "key not found" }
429 too many requests { error : "too many requests" }

Note: unknown protein names will fail silently


EXAMPLES

Example 01

A simple example.

API Call
  http://pub.jvln.io/Homology/?key=a1b-2c3-e4f-5&p=EF2_YEAST
JSON Return Object
 {
  "protein": {
    "source": "uniprot_sprot",
    "protein_name": "EF2_YEAST",
    "protein_id": "P32324",
    "protein_desc": "Elongation factor 2",
    "organism": "Saccharomyces cerevisiae strain ATCC 204508 - S288c",
    "sequence": "MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL"
  },
  "length_limit_upper": 53,
  "length_limit_lower": 6,
  "mass_limit_upper": 6000,
  "mass_limit_lower": 400,
  "misclevages": 3,
  "proteoltyic_regex": ".*?[KR\#]",
  "result_n": 330,
  "result_time": "065ms",
  "result_data": [
    {
      "n": 1,
      "peptide": "MVAFTVDQMR",
      "mass": 1196.5681994879,
      "length": 10,
      "mc": 0
    },
    {
      "n": 2,
      "peptide": "MVAFTVDQMRSLMDK",
      "mass": 1770.8466825377,
      "length": 15,
      "mc": 1
    },
    {
      "n": 3,
      "peptide": "MVAFTVDQMRSLMDKVTNVR",
      "mass": 2340.1752273221,
      "length": 20,
      "mc": 2
    },
    {
      "n": 4,
      "peptide": "MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGK",
      "mass": 3628.8098668907,
      "length": 32,
      "mc": 3
    },
    {
      "n": 5,
      "peptide": "SLMDKVTNVR",
      "mass": 1161.6175925206,
      "length": 10,
      "mc": 1
    },
    ...
    {
      "n": 330,
      "peptide": "VAFTVDQMRSLMDKVTNVRNMSVIAHVDHGK",
      "mass": 3497.7693822828,
      "length": 31,
      "mc": 3
    }
  ]
}
Example 02

Limiting to zero miscleavages and maximum neutral mass of 1000 amu.

API Call
  http://pub.jvln.io/Homology/?key=a1b-2c3-e4f-5&p=EF2_YEAST&mc=0&um=1000
JSON Return Object
 {
  "protein": {
    "source": "uniprot_sprot",
    "protein_name": "EF2_YEAST",
    "protein_id": "P32324",
    "protein_desc": "Elongation factor 2",
    "organism": "Saccharomyces cerevisiae strain ATCC 204508 - S288c",
    "sequence": "MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL"
  },
  "length_limit_upper": 53,
  "length_limit_lower": 6,
  "mass_limit_upper": 1000,
  "mass_limit_lower": 400,
  "misclevages": 0,
  "proteoltyic_regex": ".*?[KR\#]",
  "result_n": 15,
  "result_time": "046ms",
  "result_data": [
    {
      "n": 1,
      "peptide": "AGIISAAK",
      "mass": 729.43848916502,
      "length": 8,
      "mc": 0
    },
    {
      "n": 2,
      "peptide": "QALGER",
      "mass": 672.35548781677,
      "length": 6,
      "mc": 0
    },
    {
      "n": 3,
      "peptide": "PVVVINK",
      "mass": 767.49052473575,
      "length": 7,
      "mc": 0
    },
    {
      "n": 4,
      "peptide": "ALLELQVSK",
      "mass": 999.59644637114,
      "length": 9,
      "mc": 0
    },
    {
      "n": 5,
      "peptide": "DTDAEGK",
      "mass": 734.30826285249,
      "length": 7,
      "mc": 0
    },
    ...
    {
      "n": 15,
      "peptide": "AGEIVLAAR",
      "mass": 898.52361577866,
      "length": 9,
      "mc": 0
    }
  ]
}
Example 03

Changing the proteolytic regex to Chymotrypsin.

API Call
  http://pub.jvln.io/Homology/?key=a1b-2c3-e4f-5&p=EF2_YEAST&rx=.*?[^PFYWL\%23]

Note: in the case of URL encoding the hash needed to signify the C-term is represented by a % number (# == %23). Also, the hash needs to be escaped (i.e. \) in the regex.

JSON Return Object
 {
  "protein": {
    "source": "uniprot_sprot",
    "protein_name": "EF2_YEAST",
    "protein_id": "P32324",
    "protein_desc": "Elongation factor 2",
    "organism": "Saccharomyces cerevisiae strain ATCC 204508 - S288c",
    "sequence": "MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKSTLTDSLVQRAGIISAAKAGEARFTDTRKDEQERGITIKSTAISLYSEMSDEDVKEIKQKTDGNSFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDTIEGVCVQTETVLRQALGERIKPVVVINKVDRALLELQVSKEDLYQTFARTVESVNVIVSTYADEVLGDVQVYPARGTVAFGSGLHGWAFTIRQFATRYAKKFGVDKAKMMDRLWGDSFFNPKTKKWTNKDTDAEGKPLERAFNMFILDPIFRLFTAIMNFKKDEIPVLLEKLEIVLKGDEKDLEGKALLKVVMRKFLPAADALLEMIVLHLPSPVTAQAYRAEQLYEGPADDANCIAIKNCDPKADLMLYVSKMVPTSDKGRFYAFGRVFAGTVKSGQKVRIQGPNYVPGKKDDLFIKAIQRVVLMMGRFVEPIDDCPAGNIIGLVGIDQFLLKTGTLTTSETAHNMKVMKFSVSPVVQVAVEVKNANDLPKLVEGLKRLSKSDPCVLTYMSESGEHIVAGTGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSKSPNKHNRIYLKAEPIDEEVSLAIENGIINPRDDFKARARIMADDYGWDVTDARKIWCFGPDGNGPNLVIDQTKAVQYLHEIKDSVVAAFQWATKEGPIFGEEMRSVRVNILDVTLHADAIHRGGGQIIPTMRRATYAGFLLADPKIQEPVFLVEIQCPEQAVGGIYSVLNKKRGQVVSEEQRPGTPLFTVKAYLPVNESFGFTGELRQATGGQAFPQMVFDHWSTLGSDPLDPTSKAGEIVLAARKRHGMKEEVPGWQEYYDKL"
  },
  "length_limit_upper": 53,
  "length_limit_lower": 6,
  "mass_limit_upper": 6000,
  "mass_limit_lower": 400,
  "misclevages": 3,
  "proteoltyic_regex": ".*?[^PFYWL\#]",
  "result_n": 233,
  "result_time": "067ms",
  "result_data": [
    {
      "n": 1,
      "peptide": "LTDSLV",
      "mass": 646.353756482,
      "length": 6,
      "mc": 3
    },
    {
      "n": 2,
      "peptide": "AISLYS",
      "mass": 652.34319179561,
      "length": 6,
      "mc": 3
    },
    {
      "n": 3,
      "peptide": "ISLYSE",
      "mass": 710.34867110412,
      "length": 6,
      "mc": 3
    },
    {
      "n": 4,
      "peptide": "SLYSEM",
      "mass": 728.30509173104,
      "length": 6,
      "mc": 3
    },
    {
      "n": 5,
      "peptide": "LYSEMS",
      "mass": 728.30509173104,
      "length": 6,
      "mc": 3
    },
    ...
    {
      "n": 233,
      "peptide": "WQEYYDK",
      "mass": 1030.4396113773,
      "length": 7,
      "mc": 3
    }
  ]
}